1
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Kelley EH, Minasov G, Konczak K, Shuvalova L, Brunzelle JS, Shukla S, Beulke M, Thabthimthong T, Olsen KW, Inniss NL, Satchell KJF, Becker DP. Biochemical and Structural Analysis of the Bacterial Enzyme Succinyl-Diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii. ACS Omega 2024; 9:3905-3915. [PMID: 38284080 PMCID: PMC10809365 DOI: 10.1021/acsomega.3c08231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
There is an urgent need for new antibiotics given the rise of antibiotic resistance, and succinyl-diaminopimelate desuccinylase (DapE, E.C. 3.5.1.18) has emerged as a promising bacterial enzyme target. DapE from Haemophilus influenzae (HiDapE) has been studied and inhibitors identified, but it is essential to explore DapE from different species to assess selective versus broad-spectrum therapeutics. We have determined the structure of DapE from the ESKAPE pathogen Acinetobacter baumannii (AbDapE) and studied inhibition by known inhibitors of HiDapE. AbDapE is inhibited by captopril and sulfate comparable to HiDapE, but AbDapE was not significantly inhibited by a known indoline sulfonamide HiDapE inhibitor. Captopril and sulfate both stabilize HiDapE by increasing the thermal melting temperature (Tm) in thermal shift assays. By contrast, sulfate decreases the stability of the AbDapE enzyme, whereas captopril increases the stability. Further, we report two crystal structures of selenomethionine-substituted AbDapE in the closed conformation, one with AbDapE in complex with succinate derived from enzymatic hydrolysis of N6-methyl-l,l-SDAP substrate and acetate (PDB code 7T1Q, 2.25 Å resolution), and a crystal structure of AbDapE with bound succinate along with l-(S)-lactate, a product of degradation of citric acid from the crystallization buffer during X-ray irradiation (PDB code 8F8O, 2.10 Å resolution).
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Affiliation(s)
- Emma H. Kelley
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - George Minasov
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Katherine Konczak
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Ludmilla Shuvalova
- Department
of Pharmacology, Northwestern University,
Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Joseph S. Brunzelle
- Northwestern
Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - Shantanu Shukla
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Megan Beulke
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Teerana Thabthimthong
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Kenneth W. Olsen
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Nicole L. Inniss
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Karla J. F. Satchell
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Daniel P. Becker
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
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2
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Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Davies OR, Rommelaere S, Rosas‐Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu K, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins 2023; 91:1571-1599. [PMID: 37493353 PMCID: PMC10792529 DOI: 10.1002/prot.26545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.
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Affiliation(s)
- Leila T. Alexander
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | - Janani Durairaj
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | - Luciano A. Abriata
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Yusupha Bayo
- Department of BiosciencesUniversity of MilanoMilanItaly
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
| | - Gira Bhabha
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | | | - James Chen
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | - Damian C. Ekiert
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
- Department of MicrobiologyNew York University School of MedicineNew YorkNew YorkUSA
| | - Benedikte S. Erlandsen
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Peter L. Freddolino
- Department of Biological Chemistry, Computational Medicine and BioinformaticsUniversity of MichiganAnn ArborMichiganUSA
| | - Dominic Gilzer
- Department of ChemistryBielefeld UniversityBielefeldGermany
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Securing Antarctica's Environmental FutureMonash UniversityClaytonVictoriaAustralia
- Centre to Impact AMRMonash UniversityClaytonVictoriaAustralia
- ARC Research Hub for Carbon Utilisation and RecyclingMonash UniversityClaytonVictoriaAustralia
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Centre for Electron Microscopy of Membrane ProteinsMonash Institute of Pharmaceutical SciencesParkvilleVictoriaAustralia
| | - Manickam Gurusaran
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Marcus D. Hartmann
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
| | - Charlie J. Hitchman
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Jeremy R. Keown
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Petri Kursula
- Department of BiomedicineUniversity of BergenBergenNorway
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | | | - Bruno Lemaitre
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Andrea Lia
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
- ISPA‐CNR Unit of LecceInstitute of Sciences of Food ProductionLecceItaly
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Maria Logotheti
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
- Present address:
Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - Shuze Lu
- Lanzhou University School of Life SciencesLanzhouChina
| | | | | | - George Minasov
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | | | - Felipe Opazo
- NanoTag Biotechnologies GmbHGöttingenGermany
- Institute of Neuro‐ and Sensory PhysiologyUniversity of Göttingen Medical CenterGöttingenGermany
- Center for Biostructural Imaging of Neurodegeneration (BIN)University of Göttingen Medical CenterGöttingenGermany
| | - George N. Phillips
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Owen R. Davies
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Samuel Rommelaere
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Monica Rosas‐Lemus
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
- Present address:
Department of Molecular Genetics and MicrobiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Pietro Roversi
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Karla Satchell
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | - Nathan Smith
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Kuan‐Lin Wu
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Xian Xia
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Han Xiao
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BioengineeringRice UniversityHoustonTexasUSA
| | - Wenhua Zhang
- Lanzhou University School of Life SciencesLanzhouChina
| | - Z. Hong Zhou
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | | | - Maya Topf
- University Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- Centre for Structural Systems BiologyLeibniz‐Institut für Virologie (LIV)HamburgGermany
| | - John Moult
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Torsten Schwede
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
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3
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Greenwich JL, Eagan JL, Feirer N, Boswinkle K, Minasov G, Shuvalova L, Inniss NL, Raghavaiah J, Ghosh AK, Satchell KJ, Allen KD, Fuqua C. Control of Biofilm Formation by an Agrobacterium tumefaciens Pterin-Binding Periplasmic Protein Conserved Among Pathogenic Bacteria. bioRxiv 2023:2023.11.18.567607. [PMID: 38014264 PMCID: PMC10680838 DOI: 10.1101/2023.11.18.567607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Biofilm formation and surface attachment in multiple Alphaproteobacteria is driven by unipolar polysaccharide (UPP) adhesins. The pathogen Agrobacterium tumefaciens produces a UPP adhesin, which is regulated by the intracellular second messenger cyclic diguanylate monophosphate (cdGMP). Prior studies revealed that DcpA, a diguanylate cyclase-phosphodiesterase (DGC-PDE), is crucial in control of UPP production and surface attachment. DcpA is regulated by PruR, a protein with distant similarity to enzymatic domains known to coordinate the molybdopterin cofactor (MoCo). Pterins are bicyclic nitrogen-rich compounds, several of which are formed via a non-essential branch of the folate biosynthesis pathway, distinct from MoCo. The pterin-binding protein PruR controls DcpA activity, fostering cdGMP breakdown and dampening its synthesis. Pterins are excreted and we report here that PruR associates with these metabolites in the periplasm, promoting interaction with the DcpA periplasmic domain. The pteridine reductase PruA, which reduces specific dihydro-pterin molecules to their tetrahydro forms, imparts control over DcpA activity through PruR. Tetrahydromonapterin preferentially associates with PruR relative to other related pterins, and the PruR-DcpA interaction is decreased in a pruA mutant. PruR and DcpA are encoded in an operon that is conserved amongst multiple Proteobacteria including mammalian pathogens. Crystal structures reveal that PruR and several orthologs adopt a conserved fold, with a pterin-specific binding cleft that coordinates the bicyclic pterin ring. These findings define a new pterin-responsive regulatory mechanism that controls biofilm formation and related cdGMP-dependent phenotypes in A. tumefaciens and is found in multiple additional bacterial pathogens.
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Affiliation(s)
| | - Justin L. Eagan
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
| | - Nathan Feirer
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
| | - Kaleb Boswinkle
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Ludmilla Shuvalova
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Nicole L. Inniss
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Jakka Raghavaiah
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Arun K. Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Karla J.F. Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Kylie D. Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
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4
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Rosas-Lemus M, Dey S, Minasov G, Tan K, Anderson SM, Brunzelle J, Nocadello S, Shabalin I, Filippova E, Halavaty A, Kim Y, Maltseva N, Osipiuk J, Minor W, Joachimiak A, Savchenko A, Anderson WF, Satchell KJF. A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile. Microbiol Resour Announc 2023; 12:e0050723. [PMID: 37747257 PMCID: PMC10586155 DOI: 10.1128/mra.00507-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/15/2023] [Indexed: 09/26/2023] Open
Abstract
Clostridioides difficile causes life-threatening gastrointestinal infections. It is a high-risk pathogen due to a lack of effective treatments, antimicrobial resistance, and a poorly conserved genomic core. Herein, we report 30 X-ray structures from a structure genomics pipeline spanning 13 years, representing 10.2% of the X-ray structures for this important pathogen.
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Affiliation(s)
- Monica Rosas-Lemus
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Supratim Dey
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Kemin Tan
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Spencer M. Anderson
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Joseph Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Salvatore Nocadello
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Ivan Shabalin
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ekaterina Filippova
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Andrei Halavaty
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Youngchang Kim
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Natalia Maltseva
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Jerzy Osipiuk
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Wladek Minor
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Andrzej Joachimiak
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Alexei Savchenko
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Wayne F. Anderson
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Center for Structural Biology of Infectious Diseases team members
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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5
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Inniss NL, Kozic J, Li F, Rosas-Lemus M, Minasov G, Rybáček J, Zhu Y, Pohl R, Shuvalova L, Rulíšek L, Brunzelle JS, Bednárová L, Štefek M, Kormaník JM, Andris E, Šebestík J, Li ASM, Brown PJ, Schmitz U, Saikatendu K, Chang E, Nencka R, Vedadi M, Satchell KJ. Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors. ACS Infect Dis 2023; 9:1918-1931. [PMID: 37728236 PMCID: PMC10961098 DOI: 10.1021/acsinfecdis.3c00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.
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Affiliation(s)
- Nicole L. Inniss
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Ján Kozic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - George Minasov
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Yingjie Zhu
- WuXi AppTec Co., Ltd, China (Shanghai) Pilot Free Trade Zone, Shanghai, 201308, China
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Ludmilla Shuvalova
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Joseph S. Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL, 60439, United States
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Milan Štefek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Ján Michael Kormaník
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Alice Shi Ming Li
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Uli Schmitz
- Structural Chemistry, Gilead Pharmaceuticals, San Mateo, CA, 94404, United States
| | - Kumar Saikatendu
- Takeda Development Center Americas, Inc., San Diego, CA, 92121, United States
| | - Edcon Chang
- Takeda Development Center Americas, Inc., San Diego, CA, 92121, United States
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Masoud Vedadi
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Karla J.F. Satchell
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
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6
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Vandervaart JP, Inniss NL, Ling-Hu T, Minasov G, Wiersum G, Rosas-Lemus M, Shuvalova L, Achenbach CJ, Hultquist JF, Satchell KJF, Bachta KER. Serodominant SARS-CoV-2 Nucleocapsid Peptides Map to Unstructured Protein Regions. Microbiol Spectr 2023; 11:e0032423. [PMID: 37191546 PMCID: PMC10269789 DOI: 10.1128/spectrum.00324-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is highly immunogenic, and anti-N antibodies are commonly used as markers for prior infection. While several studies have examined or predicted the antigenic regions of N, these have lacked consensus and structural context. Using COVID-19 patient sera to probe an overlapping peptide array, we identified six public and four private epitope regions across N, some of which are unique to this study. We further report the first deposited X-ray structure of the stable dimerization domain at 2.05 Å as similar to all other reported structures. Structural mapping revealed that most epitopes are derived from surface-exposed loops on the stable domains or from the unstructured linker regions. An antibody response to an epitope in the stable RNA binding domain was found more frequently in sera from patients requiring intensive care. Since emerging amino acid variations in N map to immunogenic peptides, N protein variation could impact detection of seroconversion for variants of concern. IMPORTANCE As SARS-CoV-2 continues to evolve, a structural and genetic understanding of key viral epitopes will be essential to the development of next-generation diagnostics and vaccines. This study uses structural biology and epitope mapping to define the antigenic regions of the viral nucleocapsid protein in sera from a cohort of COVID-19 patients with diverse clinical outcomes. These results are interpreted in the context of prior structural and epitope mapping studies as well as in the context of emergent viral variants. This report serves as a resource for synthesizing the current state of the field toward improving strategies for future diagnostic and therapeutic design.
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Affiliation(s)
- Jacob P. Vandervaart
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nicole L. Inniss
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ted Ling-Hu
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Grant Wiersum
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ludmilla Shuvalova
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chad J. Achenbach
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Judd F. Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kelly E. R. Bachta
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
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7
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Herrera A, Packer MM, Rosas-Lemus M, Minasov G, Brummel JH, Satchell KJF. Vibrio MARTX toxin processing and degradation of cellular Rab GTPases by the cytotoxic effector Makes Caterpillars Floppy. bioRxiv 2023:2023.04.19.537381. [PMID: 37131655 PMCID: PMC10153396 DOI: 10.1101/2023.04.19.537381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Vibrio vulnificus causes life threatening infections dependent upon the effectors released from the Multifunctional-Autoprocessing Repeats-In-Toxin (MARTX) toxin. The Makes Caterpillars Floppy-like (MCF) cysteine protease effector is activated by host ADP ribosylation factors (ARFs), although the targets of processing activity were unknown. In this study we show MCF binds Ras-related proteins in brain (Rab) GTPases at the same interface occupied by ARFs and then cleaves and/or degrades 24 distinct members of the Rab GTPases family. The cleavage occurs in the C-terminal tails of Rabs. We determine the crystal structure of MCF as a swapped dimer revealing the open, activated state of MCF and then use structure prediction algorithms to show that structural composition, rather than sequence or localization, determine Rabs selected as MCF proteolytic targets. Once cleaved, Rabs become dispersed in cells to drive organelle damage and cell death to promote pathogenesis of these rapidly fatal infections.
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Affiliation(s)
- Alfa Herrera
- Department of Microbiology-Immunology and Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Megan M. Packer
- Department of Microbiology-Immunology and Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology and Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - George Minasov
- Department of Microbiology-Immunology and Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - John H. Brummel
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- SickKids IBD Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology and Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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8
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Minasov G, Inniss NL, Shuvalova L, Anderson WF, Satchell KJF. Structure of the Monkeypox virus profilin-like protein A42R reveals potential functional differences from cellular profilins. Acta Crystallogr F Struct Biol Commun 2022; 78:371-377. [PMID: 36189721 PMCID: PMC9527652 DOI: 10.1107/s2053230x22009128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
The structure of the Monkeypox virus protein A42R has been determined at a resolution of 1.52 Å. This protein has a backbone structure similar to that of cellular profilin, but structural variation in loop regions and a surface basic patch support biochemical data showing that this protein has distinct binding interactions with actin and phosphatidylinositol lipids and is not likely to bind proline-rich domain proteins or microtubules. The infectious disease human monkeypox is spreading rapidly in 2022, causing a global health crisis. The genomics of Monkeypox virus (MPXV) have been extensively analyzed and reported, although little is known about the virus-encoded proteome. In particular, there are no reported experimental MPXV protein structures other than computational models. Here, a 1.52 Å resolution X-ray structure of the MPXV protein A42R, the first MPXV-encoded protein with a known structure, is reported. A42R shows structural similarity to profilins, which are cellular proteins that are known to function in the regulation of actin cytoskeletal assembly. However, structural comparison of A42R with known members of the profilin family reveals critical differences that support prior biochemical findings that A42R only weakly binds actin and does not bind poly(l-proline). In addition, the analysis suggests that A42R may make distinct interactions with phosphatidylinositol lipids. Overall, the data suggest that the role of A42R in the replication of orthopoxviruses may not be readily determined by comparison to cellular profilins. Furthermore, these findings support the need for increased efforts to determine high-resolution structures of other MPXV proteins to inform physiological studies of the poxvirus infection cycle and to reveal potential new strategies to combat human monkeypox should this emerging infectious disease with pandemic potential become more common in the future.
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9
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Blum TR, Liu H, Packer MS, Xiong X, Lee PG, Zhang S, Richter M, Minasov G, Satchell KJ, Dong M, Liu DR. Phage-Assisted Evolution of Botulinum Neurotoxin Proteases With Reprogrammed Specificity. Toxicon 2022. [DOI: 10.1016/j.toxicon.2021.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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10
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Rosas‐Lemus M, Minasov G, Shuvalova L, Brunzelle J, Satchell K. Structural studies reveal unique features of nsp16 from SARS‐CoV‐2, a protein essential for immune system evasion and a possible drug target. FASEB J 2022. [PMCID: PMC9347677 DOI: 10.1096/fasebj.2022.36.s1.r6257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
RNA viruses have several mechanisms to modify the viral RNA genome to protect from host immune surveillance. SARS‐CoV‐2, the etiological agent of COVID‐19, and other coronaviruses encode capping proteins in its genome that modify the 5’ untranslated region of the viral genome and mRNA. Capping viral RNAs promotes translation, prevents degradation, and reduces the activation of host immune responses. This process is initiated by the viral proteins nsp13 and nsp12, which cleave the 5’ phosphate group and transfer a GMP from GTP to the 5′ end of the nascent (+)ssRNA. The nsp14‐nsp10 complex then catalyzes the transfer of a methyl group from S‐adenosylmethionine (SAM) to the N7 position of the GMP cap, generating Cap‐0. Finally, the nsp16‐nsp10 complex utilizes SAM to catalyze the 2′‐O‐methylation of the first ribonucleotide, generating Cap‐1. Several structures of the nsp16‐nsp10 complex have been solved previously for SARS‐CoV, MERS and SARS‐CoV‐2 with SAM, Cap‐0 and Cap‐0‐RNA bound to the complex as well as the products of the reactions. Recently, we determined the first structure of nsp16‐nsp10 with Cap‐0‐RNA and Cap‐1 RNA, revealing that Mn2+ coordinates the first four nucleotides of the bound RNA to orient the 2’‐OH of the ribose of the first nucleotide toward the methyl group of SAM for catalysis. Herein, we also show the first apo‐crystal structure of nsp16 determined in which neither SAM nor RNA substrates bound. This new structure and comparison to structures with substraces and products bound, will reveal critical movements of the enzyme for binding substates. This study shows an important set of structures of the viral 2’‐O‐methyltransferases revealing unique features of this complex that could be used for molecular dynamics studies and designing coronavirus‐specific inhibitors.
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Affiliation(s)
| | | | | | - Joseph Brunzelle
- Life Sciences Collaborative Access TeamNorthwestern UniversityLemontIL
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11
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Pincus NB, Rosas-Lemus M, Gatesy SW, Shuvalova L, Minasov G, Satchell K, Brunzelle JS, Lebrun-Corbin M, Ozer EA, Hauser AR, R Bachta KE. 1237. Characterization and crystallization of OXA-935, a novel class D OXA-10-like beta-lactamase, found in Pseudomonas aeruginosa. Open Forum Infect Dis 2021. [PMCID: PMC8644311 DOI: 10.1093/ofid/ofab466.1429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Recently, we described a collection of ST298 Pseudomonas aeruginosa (PA) isolates that caused a prolonged epidemic of XDR infections. Many of these contain derivatives of a new plasmid, pPABL048, that harbors an MDR integron, in1697. In1697 contains a series of antimicrobial resistance (AMR) genes, one of which is the class D β-lactamase blaOXA-10. Variants of blaOXA-10 have been described that confer both extended-spectrum β-lactamase (ESBL) and carbapenemase activity. Methods Of all ST298 isolates, three were resistant to ceftazidime (CTZ). Genomic comparison of in1697 in CTZ-resistant and CTZ-sensitive strains revealed that all three strains harbored a blaOXA-10 allele with two single nucleotide variations resulting in amino acid changes at positions 153 (F153S) and 157 (G157D). Using the NCBI database, we identified this allele as unique and defined this β-lactamase as OXA-935. OXA-935 shares the G157D variation with OXA-14 which is known to confer resistance to ceftazidime. We sought to characterize the function of OXA-935 and to determine the crystal structures of OXA-14 and OXA-935. Results Deletion of blaOXA-935 phenotypically converted all three strains to CTZ-susceptible. Expression of blaOXA-14 and blaOXA-935 conferred CTZ-resistance to laboratory PA strains PA01 and PA14. Determination of the crystal structures of OXA-14 (PDB code 7L5R) and OXA-935 (PDB code 7L5V) revealed that the F153S variant resulted in increased flexibility in the enzyme’s Ω loop. Conformational changes in the Ω loop likely contributed to the lack of carbamylation at lysine-70 (K70) observed in OXA-935. Carbamylation of K70 is known to be critical for enzymatic activity of class D β-lactamases. Conclusion OXA-935 is very similar to OXA-14; however, comparison revealed that the F153S variant has unique structural features and is functionally distinct. Despite these differences, both enzymes confer high-level CTZ resistance. As we increasingly rely on β-lactam antimicrobial therapy (e.g. ceftazidime, cefepime) and combination (e.g. ceftazidime-avibactam) therapy to treat MDR PA infections, it is critical that we continue to explore the mechanistic basis of β-lactam AMR in an effort to preserve existing treatments and design novel ones. Disclosures All Authors: No reported disclosures
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Affiliation(s)
| | | | | | | | - George Minasov
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Karla Satchell
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois
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12
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Lemus MR, Minasov G, Shuvalova L, Inniss NL, Brunzelle JS, Daczkowski CM, Hoover P, Mesecar AD, Satchell KJF. Mg 2+ and Mn 2+ coordinate Cap-0-RNA to position substrates for efficient 2′- O-methyl transfer by SARS-CoV-2 nsp16. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321098652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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13
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Minasov G, Rosas-Lemus M, Shuvalova L, Inniss NL, Brunzelle JS, Daczkowski CM, Hoover P, Mesecar AD, Satchell KJF. Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O-methyl transfer by SARS-CoV-2 nsp16. Sci Signal 2021; 14:scisignal.abh2071. [PMID: 34131072 PMCID: PMC8432954 DOI: 10.1126/scisignal.abh2071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Virally encoded 2′-O-methyltransferases catalyze the last step in the capping of viral RNAs, which protects the RNAs from degradation and prevents them from triggering host defenses. Minasov et al. report structures of the SARS-CoV-2 methyltransferase, a heterodimeric complex of the enzyme nsp16 and its coactivator nsp10, in complex with a short, capped RNA (instead of the RNA cap analogs used to generate previous structures), the methyl donor SAM, and divalent metal cations. The metal ions and a four-residue insert of nsp16 were important for precisely aligning the RNA substrate in the active site for efficient catalysis. This insert is present in coronavirus but not in mammalian methyltransferases, suggesting this site as a potential target for the design of coronavirus-specific methyltransferase inhibitors. Capping of viral messenger RNAs is essential for efficient translation, for virus replication, and for preventing detection by the host cell innate response system. The SARS-CoV-2 genome encodes the 2′-O-methyltransferase nsp16, which, when bound to the coactivator nsp10, uses S-adenosylmethionine (SAM) as a donor to transfer a methyl group to the first ribonucleotide of the mRNA in the final step of viral mRNA capping. Here, we provide biochemical and structural evidence that this reaction requires divalent cations, preferably Mn2+, and a coronavirus-specific four-residue insert. We determined the x-ray structures of the SARS-CoV-2 2′-O-methyltransferase (the nsp16-nsp10 heterodimer) in complex with its reaction substrates, products, and divalent metal cations. These structural snapshots revealed that metal ions and the insert stabilize interactions between the capped RNA and nsp16, resulting in the precise alignment of the ribonucleotides in the active site. Comparison of available structures of 2′-O-methyltransferases with capped RNAs from different organisms revealed that the four-residue insert unique to coronavirus nsp16 alters the backbone conformation of the capped RNA in the binding groove, thereby promoting catalysis. This insert is highly conserved across coronaviruses, and its absence in mammalian methyltransferases makes this region a promising site for structure-guided drug design of selective coronavirus inhibitors.
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Affiliation(s)
- George Minasov
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ludmilla Shuvalova
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nicole L Inniss
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL 60439, USA
| | - Courtney M Daczkowski
- Department of Biochemistry and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Paul Hoover
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA
| | - Andrew D Mesecar
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.,Department of Biochemistry and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA. .,Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
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14
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Wilamowski M, Sherrell DA, Minasov G, Kim Y, Shuvalova L, Lavens A, Chard R, Maltseva N, Jedrzejczak R, Rosas-Lemus M, Saint N, Foster IT, Michalska K, Satchell KJF, Joachimiak A. 2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography. Proc Natl Acad Sci U S A 2021; 118:e2100170118. [PMID: 33972410 PMCID: PMC8166198 DOI: 10.1073/pnas.2100170118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus has a capping modification at the 5'-untranslated region (UTR) to prevent its degradation by host nucleases. These modifications are performed by the Nsp10/14 and Nsp10/16 heterodimers using S-adenosylmethionine as the methyl donor. Nsp10/16 heterodimer is responsible for the methylation at the ribose 2'-O position of the first nucleotide. To investigate the conformational changes of the complex during 2'-O methyltransferase activity, we used a fixed-target serial synchrotron crystallography method at room temperature. We determined crystal structures of Nsp10/16 with substrates and products that revealed the states before and after methylation, occurring within the crystals during the experiments. Here we report the crystal structure of Nsp10/16 in complex with Cap-1 analog (m7GpppAm2'-O). Inhibition of Nsp16 activity may reduce viral proliferation, making this protein an attractive drug target.
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Affiliation(s)
- Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology of Jagiellonian University, Krakow 30387, Poland
| | - Darren A Sherrell
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - Ludmilla Shuvalova
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Alex Lavens
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - Ryan Chard
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - Monica Rosas-Lemus
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Nickolaus Saint
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
| | - Ian T Foster
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
| | - Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - Karla J F Satchell
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637;
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439
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15
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Klancher CA, Minasov G, Podicheti R, Rusch DB, Dalia TN, Satchell KJF, Neiditch MB, Dalia AB. The ChiS-Family DNA-Binding Domain Contains a Cryptic Helix-Turn-Helix Variant. mBio 2021; 12:e03287-20. [PMID: 33727356 PMCID: PMC8092284 DOI: 10.1128/mbio.03287-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
Sequence-specific DNA-binding domains (DBDs) are conserved in all domains of life. These proteins carry out a variety of cellular functions, and there are a number of distinct structural domains already described that allow for sequence-specific DNA binding, including the ubiquitous helix-turn-helix (HTH) domain. In the facultative pathogen Vibrio cholerae, the chitin sensor ChiS is a transcriptional regulator that is critical for the survival of this organism in its marine reservoir. We recently showed that ChiS contains a cryptic DBD in its C terminus. This domain is not homologous to any known DBD, but it is a conserved domain present in other bacterial proteins. Here, we present the crystal structure of the ChiS DBD at a resolution of 1.28 Å. We find that the ChiS DBD contains an HTH domain that is structurally similar to those found in other DNA-binding proteins, like the LacI repressor. However, one striking difference observed in the ChiS DBD is that the canonical tight turn of the HTH is replaced with an insertion containing a β-sheet, a variant which we term the helix-sheet-helix. Through systematic mutagenesis of all positively charged residues within the ChiS DBD, we show that residues within and proximal to the ChiS helix-sheet-helix are critical for DNA binding. Finally, through phylogenetic analyses we show that the ChiS DBD is found in diverse proteobacterial proteins that exhibit distinct domain architectures. Together, these results suggest that the structure described here represents the prototypical member of the ChiS-family of DBDs.IMPORTANCE Regulating gene expression is essential in all domains of life. This process is commonly facilitated by the activity of DNA-binding transcription factors. There are diverse structural domains that allow proteins to bind to specific DNA sequences. The structural basis underlying how some proteins bind to DNA, however, remains unclear. Previously, we showed that in the major human pathogen Vibrio cholerae, the transcription factor ChiS directly regulates gene expression through a cryptic DNA-binding domain. This domain lacked homology to any known DNA-binding protein. In the current study, we determined the structure of the ChiS DNA-binding domain (DBD) and found that the ChiS-family DBD is a cryptic variant of the ubiquitous helix-turn-helix (HTH) domain. We further demonstrate that this domain is conserved in diverse proteins that may represent a novel group of transcriptional regulators.
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Affiliation(s)
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
| | - Triana N Dalia
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Karla J F Satchell
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Matthew B Neiditch
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, New Jersey, USA
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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16
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Blum TR, Liu H, Packer MS, Xiong X, Lee PG, Zhang S, Richter M, Minasov G, Satchell KJF, Dong M, Liu DR. Phage-assisted evolution of botulinum neurotoxin proteases with reprogrammed specificity. Science 2021; 371:803-810. [PMID: 33602850 DOI: 10.1126/science.abf5972] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/24/2020] [Indexed: 12/14/2022]
Abstract
Although bespoke, sequence-specific proteases have the potential to advance biotechnology and medicine, generation of proteases with tailor-made cleavage specificities remains a major challenge. We developed a phage-assisted protease evolution system with simultaneous positive and negative selection and applied it to three botulinum neurotoxin (BoNT) light-chain proteases. We evolved BoNT/X protease into separate variants that preferentially cleave vesicle-associated membrane protein 4 (VAMP4) and Ykt6, evolved BoNT/F protease to selectively cleave the non-native substrate VAMP7, and evolved BoNT/E protease to cleave phosphatase and tensin homolog (PTEN) but not any natural BoNT protease substrate in neurons. The evolved proteases display large changes in specificity (218- to >11,000,000-fold) and can retain their ability to form holotoxins that self-deliver into primary neurons. These findings establish a versatile platform for reprogramming proteases to selectively cleave new targets of therapeutic interest.
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Affiliation(s)
- Travis R Blum
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Hao Liu
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Michael S Packer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Xiaozhe Xiong
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Pyung-Gang Lee
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Sicai Zhang
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle Richter
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA. .,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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17
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Rosas-Lemus M, Minasov G, Shuvalova L, Inniss NL, Kiryukhina O, Brunzelle J, Satchell KJF. High-resolution structures of the SARS-CoV-2 2'- O-methyltransferase reveal strategies for structure-based inhibitor design. Sci Signal 2020; 13:eabe1202. [PMID: 32994211 PMCID: PMC8028745 DOI: 10.1126/scisignal.abe1202] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
There are currently no antiviral therapies specific for SARS-CoV-2, the virus responsible for the global pandemic disease COVID-19. To facilitate structure-based drug design, we conducted an x-ray crystallographic study of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase complex, which methylates Cap-0 viral mRNAs to improve viral protein translation and to avoid host immune detection. We determined the structures for nsp16-nsp10 heterodimers bound to the methyl donor S-adenosylmethionine (SAM), the reaction product S-adenosylhomocysteine (SAH), or the SAH analog sinefungin (SFG). We also solved structures for nsp16-nsp10 in complex with the methylated Cap-0 analog m7GpppA and either SAM or SAH. Comparative analyses between these structures and published structures for nsp16 from other betacoronaviruses revealed flexible loops in open and closed conformations at the m7GpppA-binding pocket. Bound sulfates in several of the structures suggested the location of the ribonucleic acid backbone phosphates in the ribonucleotide-binding groove. Additional nucleotide-binding sites were found on the face of the protein opposite the active site. These various sites and the conserved dimer interface could be exploited for the development of antiviral inhibitors.
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Affiliation(s)
- Monica Rosas-Lemus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ludmilla Shuvalova
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nicole L Inniss
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Olga Kiryukhina
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joseph Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL 60439, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
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18
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Roy SM, Minasov G, Arancio O, Chico LW, Van Eldik LJ, Anderson WF, Pelletier JC, Watterson DM. Correction to "A Selective and Brain Penetrant p38αMAPK Inhibitor Candidate for Neurologic and Neuropsychiatric Disorders That Attenuates Neuroinflammation and Cognitive Dysfunction". J Med Chem 2020; 63:8649. [PMID: 32672466 PMCID: PMC8154559 DOI: 10.1021/acs.jmedchem.0c01060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Minasov G, Lam MR, Rosas-Lemus M, Sławek J, Woinska M, Shabalin IG, Shuvalova L, Palsson BØ, Godzik A, Minor W, Satchell KJF. Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis. Protein Sci 2020; 29:1618-1628. [PMID: 32306515 DOI: 10.1002/pro.3876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 11/06/2022]
Abstract
Protein degradation by aminopeptidases is involved in bacterial responses to stress. Escherichia coli produces two metal-dependent M17 family leucine aminopeptidases (LAPs), aminopeptidase A (PepA) and aminopeptidase B (PepB). Several structures have been solved for PepA as well as other bacterial M17 peptidases. Herein, we report the first structures of a PepB M17 peptidase. The E. coli PepB protein structure was determined at a resolution of 2.05 and 2.6 Å. One structure has both Zn2+ and Mn2+ , while the second structure has two Zn2+ ions bound to the active site. A 2.75 Å apo structure is also reported for PepB from Yersinia pestis. Both proteins form homohexamers, similar to the overall arrangement of PepA and other M17 peptidases. However, the divergent N-terminal domain in PepB is much larger resulting in a tertiary structure that is more expanded. Modeling of a dipeptide substrate into the C-terminal LAP domain reveals contacts that account for PepB to uniquely cleave after aspartate.
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Affiliation(s)
- George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA
| | - Matthew R Lam
- Department of Molecular Biosciences, Weinberg School of Arts and Sciences, Northwestern University, Evanston, Illinois, USA
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA
| | - Joanna Sławek
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Magdalena Woinska
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ivan G Shabalin
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ludmilla Shuvalova
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA
| | - Bernhard Ø Palsson
- Department of Bioengineering and Pediatrics, University of California, San Diego, California, USA
| | - Adam Godzik
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA.,Department of Biomedical Sciences, University of California, Riverside School of Medicine, Riverside, California, USA
| | - Wladek Minor
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA
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20
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Rosas-Lemus M, Minasov G, Shuvalova L, Inniss NL, Kiryukhina O, Wiersum G, Kim Y, Jedrzejczak R, Maltseva NI, Endres M, Jaroszewski L, Godzik A, Joachimiak A, Satchell KJF. The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine. bioRxiv 2020:2020.04.17.047498. [PMID: 32511376 PMCID: PMC7263505 DOI: 10.1101/2020.04.17.047498] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 is a member of the coronaviridae family and is the etiological agent of the respiratory Coronavirus Disease 2019. The virus has spread rapidly around the world resulting in over two million cases and nearly 150,000 deaths as of April 17, 2020. Since no treatments or vaccines are available to treat COVID-19 and SARS-CoV-2, respiratory complications derived from the infections have overwhelmed healthcare systems around the world. This virus is related to SARS-CoV-1, the virus that caused the 2002-2004 outbreak of Severe Acute Respiratory Syndrome. In January 2020, the Center for Structural Genomics of Infectious Diseases implemented a structural genomics pipeline to solve the structures of proteins essential for coronavirus replication-transcription. Here we show the first structure of the SARS-CoV-2 nsp10-nsp16 2'-O-methyltransferase complex with S-adenosylmethionine at a resolution of 1.80 Å. This heterodimer complex is essential for capping viral mRNA transcripts for efficient translation and to evade immune surveillance.
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Affiliation(s)
- Monica Rosas-Lemus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Ludmilla Shuvalova
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Nicole L. Inniss
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Olga Kiryukhina
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Grant Wiersum
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Natalia I. Maltseva
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Michael Endres
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Lukasz Jaroszewski
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Biomedical Sciences, University of California, Riverside School of Medicine, Riverside, CA, USA
| | - Adam Godzik
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Biomedical Sciences, University of California, Riverside School of Medicine, Riverside, CA, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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21
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Rosas‐Lemus M, Minasov G, Shuvalova L, Wawrzak Z, Kiryukhina O, Mih N, Jaroszewski L, Palsson B, Godzik A, Satchell KJF. Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment. Protein Sci 2020; 29:711-722. [PMID: 31811683 PMCID: PMC7021002 DOI: 10.1002/pro.3796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/24/2019] [Accepted: 12/04/2019] [Indexed: 11/06/2022]
Abstract
Galactarate dehydratase (GarD) is the first enzyme in the galactarate/glucarate pathway and catalyzes the dehydration of galactarate to 3-keto-5-dehydroxygalactarate. This protein is known to increase colonization fitness of intestinal pathogens in antibiotic-treated mice and to promote bacterial survival during stress. The galactarate/glucarate pathway is widespread in bacteria, but not in humans, and thus could be a target to develop new inhibitors for use in combination therapy to combat antibiotic resistance. The structure of almost all the enzymes of the galactarate/glucarate pathway were solved previously, except for GarD, for which only the structure of the N-terminal domain was determined previously. Herein, we report the first crystal structure of full-length GarD solved using a seleno-methoionine derivative revealing a new protein fold. The protein consists of three domains, each presenting a novel twist as compared to their distant homologs. GarD in the crystal structure forms dimers and each monomer consists of three domains. The N-terminal domain is comprised of a β-clip fold, connected to the second domain by a long unstructured linker. The second domain serves as a dimerization interface between two monomers. The C-terminal domain forms an unusual variant of a Rossmann fold with a crossover and is built around a seven-stranded parallel β-sheet supported by nine α-helices. A metal binding site in the C-terminal domain is occupied by Ca2+ . The activity of GarD was corroborated by the production of 5-keto-4-deoxy-D-glucarate under reducing conditions and in the presence of iron. Thus, GarD is an unusual enolase with a novel protein fold never previously seen in this class of enzymes.
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Affiliation(s)
- Monica Rosas‐Lemus
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - George Minasov
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - Ludmilla Shuvalova
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center–LS‐CATNorthwestern UniversityArgonneIllinois
| | - Olga Kiryukhina
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - Nathan Mih
- Department of BioengineeringUniversity of California San DiegoLa JollaCalifornia
| | - Lukasz Jaroszewski
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Department of Biomedical SciencesUniversity of California at RiversideRiversideCalifornia
| | - Bernhard Palsson
- Department of BioengineeringUniversity of California San DiegoLa JollaCalifornia
- Systems Biology Center for Antibiotic ResistanceUniversity of California San DiegoLa JollaCalifornia
| | - Adam Godzik
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Department of Biomedical SciencesUniversity of California at RiversideRiversideCalifornia
| | - Karla J. F. Satchell
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
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22
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Ritzert JT, Minasov G, Embry R, Schipma MJ, Satchell KJF. The Cyclic AMP Receptor Protein Regulates Quorum Sensing and Global Gene Expression in Yersinia pestis during Planktonic Growth and Growth in Biofilms. mBio 2019; 10:e02613-19. [PMID: 31744922 PMCID: PMC6867900 DOI: 10.1128/mbio.02613-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022] Open
Abstract
Cyclic AMP (cAMP) receptor protein (Crp) is an important transcriptional regulator of Yersinia pestis Expression of crp increases during pneumonic plague as the pathogen depletes glucose and forms large biofilms within lungs. To better understand control of Y. pestis Crp, we determined a 1.8-Å crystal structure of the protein-cAMP complex. We found that compared to Escherichia coli Crp, C helix amino acid substitutions in Y. pestis Crp did not impact the cAMP dependency of Crp to bind DNA promoters. To investigate Y. pestis Crp-regulated genes during plague pneumonia, we performed RNA sequencing on both wild-type and Δcrp mutant bacteria growing in planktonic and biofilm states in minimal media with glucose or glycerol. Y. pestis Crp was found to dramatically alter expression of hundreds of genes in a manner dependent upon carbon source and growth state. Gel shift assays confirmed direct regulation of the malT and ptsG promoters, and Crp was then linked to Y. pestis growth on maltose as a sole carbon source. Iron regulation genes ybtA and fyuA were found to be indirectly regulated by Crp. A new connection between carbon source and quorum sensing was revealed as Crp was found to regulate production of acyl-homoserine lactones (AHLs) through direct and indirect regulation of genes for AHL synthetases and receptors. AHLs were subsequently identified in the lungs of Y. pestis-infected mice when crp expression was highest in Y. pestis biofilms. Thus, in addition to the well-studied pla gene, other Crp-regulated genes likely have important functions during plague infection.IMPORTANCE Bacterial pathogens have evolved extensive signaling pathways to translate environmental signals into changes in gene expression. While Crp has long been appreciated for its role in regulating metabolism of carbon sources in many bacterial species, transcriptional profiling has revealed that this protein regulates many other aspects of bacterial physiology. The plague pathogen Y. pestis requires this global regulator to survive in blood, skin, and lungs. During disease progression, this organism adapts to changes within these niches. In addition to regulating genes for metabolism of nonglucose sugars, we found that Crp regulates genes for virulence, metal acquisition, and quorum sensing by direct or indirect mechanisms. Thus, this single transcriptional regulator, which responds to changes in available carbon sources, can regulate multiple critical behaviors for causing disease.
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Affiliation(s)
- Jeremy T Ritzert
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ryan Embry
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois, USA
| | - Matthew J Schipma
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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23
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Lazar JT, Shuvalova L, Rosas-Lemus M, Kiryukhina O, Satchell KJF, Minasov G. Structural comparison of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida with PobA from other Pseudomonas spp. and other monooxygenases. Acta Crystallogr F Struct Biol Commun 2019; 75:507-514. [PMID: 31282871 PMCID: PMC6613441 DOI: 10.1107/s2053230x19008653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/17/2019] [Indexed: 11/10/2022] Open
Abstract
The crystal structure is reported of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida, a possible drug target to combat tetracycline resistance, in complex with flavin adenine dinucleotide (FAD). The structure was refined at 2.2 Å resolution with four polypeptide chains in the asymmetric unit. Based on the results of pairwise structure alignments, PobA from P. putida is structurally very similar to PobA from P. fluorescens and from P. aeruginosa. Key residues in the FAD-binding and substrate-binding sites of PobA are highly conserved spatially across the proteins from all three species. Additionally, the structure was compared with two enzymes from the broader class of oxygenases: 2-hydroxybiphenyl 3-monooxygenase (HbpA) from P. nitroreducens and 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO) from Mesorhizobium japonicum. Despite having only 14% similarity in their primary sequences, pairwise structure alignments of PobA from P. putida with HbpA from P. nitroreducens and MHPCO from M. japonicum revealed local similarities between these structures. Key secondary-structure elements important for catalysis, such as the βαβ fold, β-sheet wall and α12 helix, are conserved across this expanded class of oxygenases.
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Affiliation(s)
- John T. Lazar
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60201, USA
| | - Ludmilla Shuvalova
- Department of Microbiology–Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Monica Rosas-Lemus
- Department of Microbiology–Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Olga Kiryukhina
- Department of Microbiology–Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Karla J. F. Satchell
- Department of Microbiology–Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - George Minasov
- Department of Microbiology–Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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24
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Roy SM, Minasov G, Arancio O, Chico LW, Van Eldik LJ, Anderson WF, Pelletier JC, Watterson DM. A Selective and Brain Penetrant p38αMAPK Inhibitor Candidate for Neurologic and Neuropsychiatric Disorders That Attenuates Neuroinflammation and Cognitive Dysfunction. J Med Chem 2019; 62:5298-5311. [PMID: 30978288 PMCID: PMC6580366 DOI: 10.1021/acs.jmedchem.9b00058] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The p38αMAPK
is a serine/threonine protein kinase and a key
node in the intracellular signaling networks that transduce and amplify
stress signals into physiological changes. A preponderance of preclinical
data and clinical observations established p38αMAPK as a brain
drug discovery target involved in neuroinflammatory responses and
synaptic dysfunction in multiple degenerative and neuropsychiatric
brain disorders. We summarize the discovery of highly selective, brain-penetrant,
small molecule p38αMAPK inhibitors that are efficacious in diverse
animal models of neurologic disorders. A crystallography and pharmacoinformatic
approach to fragment expansion enabled the discovery of an efficacious
hit. The addition of secondary pharmacology screens to refinement
delivered lead compounds with improved selectivity, appropriate pharmacodynamics,
and efficacy. Safety considerations and additional secondary pharmacology
screens drove optimization that delivered the drug candidate MW01-18-150SRM
(MW150), currently in early stage clinical trials.
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Affiliation(s)
- Saktimayee M Roy
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - George Minasov
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - Ottavio Arancio
- Columbia University , New York , New York 10032 , United States
| | - Laura W Chico
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | | | - Wayne F Anderson
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - Jeffrey C Pelletier
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - D Martin Watterson
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
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25
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Lykins JD, Filippova EV, Halavaty AS, Minasov G, Zhou Y, Dubrovska I, Flores KJ, Shuvalova LA, Ruan J, El Bissati K, Dovgin S, Roberts CW, Woods S, Moulton JD, Moulton H, McPhillie MJ, Muench SP, Fishwick CWG, Sabini E, Shanmugam D, Roos DS, McLeod R, Anderson WF, Ngô HM. CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii. Front Cell Infect Microbiol 2018; 8:352. [PMID: 30345257 PMCID: PMC6182094 DOI: 10.3389/fcimb.2018.00352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/14/2018] [Indexed: 12/23/2022] Open
Abstract
Toxoplasma gondii, an Apicomplexan parasite, causes significant morbidity and mortality, including severe disease in immunocompromised hosts and devastating congenital disease, with no effective treatment for the bradyzoite stage. To address this, we used the Tropical Disease Research database, crystallography, molecular modeling, and antisense to identify and characterize a range of potential therapeutic targets for toxoplasmosis. Phosphoglycerate mutase II (PGMII), nucleoside diphosphate kinase (NDK), ribulose phosphate 3-epimerase (RPE), ribose-5-phosphate isomerase (RPI), and ornithine aminotransferase (OAT) were structurally characterized. Crystallography revealed insights into the overall structure, protein oligomeric states and molecular details of active sites important for ligand recognition. Literature and molecular modeling suggested potential inhibitors and druggability. The targets were further studied with vivoPMO to interrupt enzyme synthesis, identifying the targets as potentially important to parasitic replication and, therefore, of therapeutic interest. Targeted vivoPMO resulted in statistically significant perturbation of parasite replication without concomitant host cell toxicity, consistent with a previous CRISPR/Cas9 screen showing PGM, RPE, and RPI contribute to parasite fitness. PGM, RPE, and RPI have the greatest promise for affecting replication in tachyzoites. These targets are shared between other medically important parasites and may have wider therapeutic potential.
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Affiliation(s)
- Joseph D. Lykins
- Pritzker School of Medicine, University of Chicago, Chicago, IL, United States
| | - Ekaterina V. Filippova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Andrei S. Halavaty
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ying Zhou
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
| | - Ievgeniia Dubrovska
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kristin J. Flores
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ludmilla A. Shuvalova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jiapeng Ruan
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kamal El Bissati
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
| | - Sarah Dovgin
- Illinois Math and Science Academy, Aurora, IL, United States
| | - Craig W. Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Stuart Woods
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | | | - Hong Moulton
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Martin J. McPhillie
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Colin W. G. Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Elisabetta Sabini
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | | | - David S. Roos
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Rima McLeod
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
- Department of Pediatrics (Infectious Diseases), Institute of Genomics, Genetics, and Systems Biology, Global Health Center, Toxoplasmosis Center, CHeSS, The College, University of Chicago, Chicago, IL, United States
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Huân M. Ngô
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- BrainMicro LLC, New Haven, CT, United States
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26
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Biancucci M, Minasov G, Banerjee A, Herrera A, Woida PJ, Kieffer MB, Bindu L, Abreu-Blanco M, Anderson WF, Gaponenko V, Stephen AG, Holderfield M, Satchell KJF. The bacterial Ras/Rap1 site-specific endopeptidase RRSP cleaves Ras through an atypical mechanism to disrupt Ras-ERK signaling. Sci Signal 2018; 11:11/550/eaat8335. [PMID: 30279169 DOI: 10.1126/scisignal.aat8335] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Ras-extracellular signal-regulated kinase pathway is critical for controlling cell proliferation, and its aberrant activation drives the growth of various cancers. Because many pathogens produce toxins that inhibit Ras activity, efforts to develop effective Ras inhibitors to treat cancer could be informed by studies of Ras inhibition by pathogens. Vibrio vulnificus causes fatal infections in a manner that depends on multifunctional autoprocessing repeats-in-toxin, a toxin that releases bacterial effector domains into host cells. One such domain is the Ras/Rap1-specific endopeptidase (RRSP), which site-specifically cleaves the Switch I domain of the small GTPases Ras and Rap1. We solved the crystal structure of RRSP and found that its backbone shares a structural fold with the EreA/ChaN-like superfamily of enzymes. Unlike other proteases in this family, RRSP is not a metalloprotease. Through nuclear magnetic resonance analysis and nucleotide exchange assays, we determined that the processing of KRAS by RRSP did not release any fragments or cause KRAS to dissociate from its bound nucleotide but instead only locally affected its structure. However, this structural alteration of KRAS was sufficient to disable guanine nucleotide exchange factor-mediated nucleotide exchange and prevent KRAS from binding to RAF. Thus, RRSP is a bacterial effector that represents a previously unrecognized class of protease that disconnects Ras from its signaling network while inducing limited structural disturbance in its target.
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Affiliation(s)
- Marco Biancucci
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.,Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Avik Banerjee
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alfa Herrera
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Patrick J Woida
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Matthew B Kieffer
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lakshman Bindu
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Maria Abreu-Blanco
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Andrew G Stephen
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Matthew Holderfield
- National Cancer Institute-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. .,Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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27
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Gokey T, Halavaty AS, Minasov G, Anderson WF, Kuhn ML. Structure of the Bacillus anthracis dTDP-l-rhamnose biosynthetic pathway enzyme: dTDP-α-d-glucose 4,6-dehydratase, RfbB. J Struct Biol 2018; 202:175-181. [PMID: 29331609 DOI: 10.1016/j.jsb.2018.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/08/2018] [Accepted: 01/09/2018] [Indexed: 11/27/2022]
Abstract
Many bacteria require l-rhamnose as a key cell wall component. This sugar is transferred to the cell wall using an activated donor dTDP-l-rhamnose, which is produced by the dTDP-l-rhamnose biosynthetic pathway. We determined the crystal structure of the second enzyme of this pathway dTDP-α-d-glucose 4,6-dehydratase (RfbB) from Bacillus anthracis. Interestingly, RfbB only crystallized in the presence of the third enzyme of the pathway RfbC; however, RfbC was not present in the crystal. Our work represents the first complete structural characterization of the four proteins of this pathway in a single Gram-positive bacterium.
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Affiliation(s)
- Trevor Gokey
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Andrei S Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA; Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA; Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA; Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, USA.
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28
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Shornikov A, Tran H, Macias J, Halavaty AS, Minasov G, Anderson WF, Kuhn ML. Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC). Acta Crystallogr F Struct Biol Commun 2017; 73:664-671. [PMID: 29199987 DOI: 10.1107/s2053230x17015849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/31/2017] [Indexed: 11/10/2022]
Abstract
The exosporium layer of Bacillus anthracis spores is rich in L-rhamnose, a common bacterial cell-wall component, which often contributes to the virulence of pathogens by increasing their adherence and immune evasion. The biosynthetic pathway used to form the activated L-rhamnose donor dTDP-L-rhamnose consists of four enzymes (RfbA, RfbB, RfbC and RfbD) and is an attractive drug target because there are no homologs in mammals. It was found that co-purifying and screening RfbC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) from B. anthracis in the presence of the other three B. anthracis enzymes of the biosynthetic pathway yielded crystals that were suitable for data collection. RfbC crystallized as a dimer and its structure was determined at 1.63 Å resolution. Two different ligands were bound in the protein structure: pyrophosphate in the active site of one monomer and dTDP in the other monomer. A structural comparison with RfbC homologs showed that the key active-site residues are conserved across kingdoms.
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Affiliation(s)
| | - Ha Tran
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Jennifer Macias
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Andrei S Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, USA
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29
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Law A, Stergioulis A, Halavaty AS, Minasov G, Anderson WF, Kuhn ML. Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose reductase (RfbD). Acta Crystallogr F Struct Biol Commun 2017; 73:644-650. [PMID: 29199984 DOI: 10.1107/s2053230x17015746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/30/2017] [Indexed: 01/27/2023]
Abstract
Bacillus anthracis is the causative agent of the deadly disease Anthrax. Its use in bioterrorism and its ability to re-emerge have brought renewed interest in this organism. B. anthracis is a Gram-positive bacterium that adds L-rhamnose to its cell-wall polysaccharides using the activated donor dTDP-β-L-rhamnose. The enzymes involved in the biosynthesis of the activated donor are absent in humans, which make them ideal targets for therapeutic development to combat pathogens. Here, the 2.65 Å resolution crystal structure of the fourth enzyme in the dTDP-β-L-rhamnose-biosynthetic pathway from B. anthracis, dTDP-4-dehydro-β-L-rhamnose reductase (RfbD), is presented in complex with NADP+. This enzyme catalyzes the reduction of dTDP-4-dehydro-β-L-rhamnose to dTDP-β-L-rhamnose. Although the protein was co-crystallized in the presence of Mg2+, the protein lacks the conserved residues that coordinate Mg2+.
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Affiliation(s)
- Ashley Law
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | | | - Andrei S Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, USA
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30
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Baumgartner J, Lee J, Halavaty AS, Minasov G, Anderson WF, Kuhn ML. Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme glucose-1-phosphate thymidylyltransferase (RfbA). Acta Crystallogr F Struct Biol Commun 2017; 73:621-628. [PMID: 29095156 DOI: 10.1107/s2053230x17015357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/22/2017] [Indexed: 11/10/2022]
Abstract
L-Rhamnose is a ubiquitous bacterial cell-wall component. The biosynthetic pathway for its precursor dTDP-L-rhamnose is not present in humans, which makes the enzymes of the pathway potential drug targets. In this study, the three-dimensional structure of the first protein of this pathway, glucose-1-phosphate thymidylyltransferase (RfbA), from Bacillus anthracis was determined. In other organisms this enzyme is referred to as RmlA. RfbA was co-crystallized with the products of the enzymatic reaction, dTDP-α-D-glucose and pyrophosphate, and its structure was determined at 2.3 Å resolution. This is the first reported thymidylyltransferase structure from a Gram-positive bacterium. RfbA shares overall structural characteristics with known RmlA homologs. However, RfbA exhibits a shorter sequence at its C-terminus, which results in the absence of three α-helices involved in allosteric site formation. Consequently, RfbA was observed to exhibit a quaternary structure that is unique among currently reported glucose-1-phosphate thymidylyltransferase bacterial homologs. These structural analyses suggest that RfbA may not be allosterically regulated in some organisms and is structurally distinct from other RmlA homologs.
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Affiliation(s)
- Jackson Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Jesi Lee
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Andrei S Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, USA
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31
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Lee H, Ren J, Nocadello S, Rice AJ, Ojeda I, Light S, Minasov G, Vargas J, Nagarathnam D, Anderson WF, Johnson ME. Identification of novel small molecule inhibitors against NS2B/NS3 serine protease from Zika virus. Antiviral Res 2016; 139:49-58. [PMID: 28034741 DOI: 10.1016/j.antiviral.2016.12.016] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 01/11/2023]
Abstract
Zika flavivirus infection during pregnancy appears to produce higher risk of microcephaly, and also causes multiple neurological problems such as Guillain-Barré syndrome. The Zika virus is now widespread in Central and South America, and is anticipated to become an increasing risk in the southern United States. With continuing global travel and the spread of the mosquito vector, the exposure is expected to accelerate, but there are no currently approved treatments against the Zika virus. The Zika NS2B/NS3 protease is an attractive drug target due to its essential role in viral replication. Our studies have identified several compounds with inhibitory activity (IC50) and binding affinity (KD) of ∼5-10 μM against the Zika NS2B-NS3 protease from testing 71 HCV NS3/NS4A inhibitors that were initially discovered by high-throughput screening of 40,967 compounds. Competition surface plasmon resonance studies and mechanism of inhibition analyses by enzyme kinetics subsequently determined the best compound to be a competitive inhibitor with a Ki value of 9.5 μM. We also determined the X-ray structure of the Zika NS2B-NS3 protease in a "pre-open conformation", a conformation never observed before for any flavivirus proteases. This provides the foundation for new structure-based inhibitor design.
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Affiliation(s)
- Hyun Lee
- Novalex Therapeutics, Inc., 2242 W Harrison Suite 201, Chicago, IL 60612, USA
| | - Jinhong Ren
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA
| | - Salvatore Nocadello
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Amy J Rice
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | - Isabel Ojeda
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | - Samuel Light
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Jason Vargas
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | | | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Michael E Johnson
- Novalex Therapeutics, Inc., 2242 W Harrison Suite 201, Chicago, IL 60612, USA.
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32
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Kuhn ML, Alexander E, Minasov G, Page HJ, Warwrzak Z, Shuvalova L, Flores KJ, Wilson DJ, Shi C, Aldrich CC, Anderson WF. Structure of the Essential Mtb FadD32 Enzyme: A Promising Drug Target for Treating Tuberculosis. ACS Infect Dis 2016; 2:579-591. [PMID: 27547819 DOI: 10.1021/acsinfecdis.6b00082] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mycolic acids are indispensible lipids of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), and contribute to the distinctive architecture and impermeability of the mycobacterial cell envelope. FadD32 plays a pivotal role in mycolic acid biosynthesis by functionally linking fatty acid synthase (FAS) and polyketide synthase (PKS) biosynthetic pathways. FadD32, a fatty acyl-AMP ligase (FAAL), represents one of the best genetically and chemically validated new TB drug targets. We have determined the three-dimensional crystal structure of Mtb FadD32 in complex with a ligand specifically designed to stabilize the catalytically active adenylate-conformation, which provides a foundation for structure-based drug design efforts against this essential protein. The structure also captures the unique interactions of a FAAL-specific insertion sequence and provides insight into the specificity and mechanism of fatty acid transfer.
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Affiliation(s)
- Misty L. Kuhn
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | | | - George Minasov
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Holland J. Page
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Zdzislaw Warwrzak
- LS-CAT,
Synchrotron Research Center, Northwestern University, Argonne, Illinois 60439, United States
| | - Ludmilla Shuvalova
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Kristin J. Flores
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | | | | | | | - Wayne F. Anderson
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
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33
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Nocadello S, Minasov G, Shuvalova LS, Dubrovska I, Sabini E, Anderson WF. Crystal Structures of the SpoIID Lytic Transglycosylases Essential for Bacterial Sporulation. J Biol Chem 2016; 291:14915-26. [PMID: 27226615 PMCID: PMC4946911 DOI: 10.1074/jbc.m116.729749] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/11/2016] [Indexed: 01/07/2023] Open
Abstract
Bacterial spores are the most resistant form of life known on Earth and represent a serious problem for (i) bioterrorism attack, (ii) horizontal transmission of microbial pathogens in the community, and (iii) persistence in patients and in a nosocomial environment. Stage II sporulation protein D (SpoIID) is a lytic transglycosylase (LT) essential for sporulation. The LT superfamily is a potential drug target because it is active in essential bacterial processes involving the peptidoglycan, which is unique to bacteria. However, the absence of structural information for the sporulation-specific LT enzymes has hindered mechanistic understanding of SpoIID. Here, we report the first crystal structures with and without ligands of the SpoIID family from two community relevant spore-forming pathogens, Bacillus anthracis and Clostridium difficile. The structures allow us to visualize the overall architecture, characterize the substrate recognition model, identify critical residues, and provide the structural basis for catalysis by this new family of enzymes.
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Affiliation(s)
- Salvatore Nocadello
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - George Minasov
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Ludmilla S Shuvalova
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Ievgeniia Dubrovska
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Elisabetta Sabini
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Wayne F Anderson
- From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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34
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Light SH, Krishna SN, Minasov G, Anderson WF. An Unusual Cation-Binding Site and Distinct Domain-Domain Interactions Distinguish Class II Enolpyruvylshikimate-3-phosphate Synthases. Biochemistry 2016; 55:1239-45. [PMID: 26813771 DOI: 10.1021/acs.biochem.5b00553] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes a critical step in the biosynthesis of a number of aromatic metabolites. An essential prokaryotic enzyme and the molecular target of the herbicide glyphosate, EPSPSs are the subject of both pharmaceutical and commercial interest. Two EPSPS classes that exhibit low sequence homology, differing substrate/glyphosate affinities, and distinct cation activation properties have previously been described. Here, we report structural studies of the monovalent cation-binding class II Coxiella burnetii EPSPS (cbEPSPS). Three cbEPSPS crystal structures reveal that the enzyme undergoes substantial conformational changes that alter the electrostatic potential of the active site. A complex with shikimate-3-phosphate, inorganic phosphate (Pi), and K(+) reveals that ligand induced domain closure produces an unusual cation-binding site bordered on three sides by the N-terminal domain, C-terminal domain, and the product Pi. A crystal structure of the class I Vibrio cholerae EPSPS (vcEPSPS) clarifies the basis of differential class I and class II cation responsiveness, showing that in class I EPSPSs a lysine side chain occupies the would-be cation-binding site. Finally, we identify distinct patterns of sequence conservation at the domain-domain interface and propose that the two EPSPS classes have evolved to differently optimize domain opening-closing dynamics.
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Affiliation(s)
- Samuel H Light
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - Sankar N Krishna
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
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Nocadello S, Minasov G, Shuvalova L, Dubrovska I, Sabini E, Bagnoli F, Grandi G, Anderson WF. Crystal structures of the components of the Staphylococcus aureus leukotoxin ED. Acta Crystallogr D Struct Biol 2016; 72:113-20. [PMID: 26894539 PMCID: PMC4756620 DOI: 10.1107/s2059798315023207] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/02/2015] [Indexed: 12/31/2022] Open
Abstract
Staphylococcal leukotoxins are a family of β-barrel, bicomponent, pore-forming toxins with membrane-damaging functions. These bacterial exotoxins share sequence and structural homology and target several host-cell types. Leukotoxin ED (LukED) is one of these bicomponent pore-forming toxins that Staphylococcus aureus produces in order to suppress the ability of the host to contain the infection. The recent delineation of the important role that LukED plays in S. aureus pathogenesis and the identification of its protein receptors, combined with its presence in S. aureus methicillin-resistant epidemic strains, establish this leukocidin as a possible target for the development of novel therapeutics. Here, the crystal structures of the water-soluble LukE and LukD components of LukED have been determined. The two structures illustrate the tertiary-structural variability with respect to the other leukotoxins while retaining the conservation of the residues involved in the interaction of the protomers in the bipartite leukotoxin in the pore complex.
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Affiliation(s)
- S. Nocadello
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - G. Minasov
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - L. Shuvalova
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - I. Dubrovska
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - E. Sabini
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - F. Bagnoli
- Novartis Vaccines and Diagnostics, Research Centre, Siena, Italy
| | - G. Grandi
- Novartis Vaccines and Diagnostics, Research Centre, Siena, Italy
| | - W. F. Anderson
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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Light SH, Minasov G, Shuvalova L, Duban ME, Caffrey M, Anderson WF, Lavie A. Insights into the mechanism of type I dehydroquinate dehydratases from structures of reaction intermediates. J Biol Chem 2015; 290:19008. [PMID: 26232400 PMCID: PMC4521023 DOI: 10.1074/jbc.a110.192831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023] Open
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Halavaty AS, Rich RL, Chen C, Joo JC, Minasov G, Dubrovska I, Winsor JR, Myszka DG, Duban M, Shuvalova L, Yakunin AF, Anderson WF. Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus. Acta Crystallogr D Biol Crystallogr 2015; 71:1159-75. [PMID: 25945581 PMCID: PMC4427200 DOI: 10.1107/s1399004715004228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/01/2015] [Indexed: 02/02/2023]
Abstract
When exposed to high osmolarity, methicillin-resistant Staphylococcus aureus (MRSA) restores its growth and establishes a new steady state by accumulating the osmoprotectant metabolite betaine. Effective osmoregulation has also been implicated in the acquirement of a profound antibiotic resistance by MRSA. Betaine can be obtained from the bacterial habitat or produced intracellularly from choline via the toxic betaine aldehyde (BA) employing the choline dehydrogenase and betaine aldehyde dehydrogenase (BADH) enzymes. Here, it is shown that the putative betaine aldehyde dehydrogenase SACOL2628 from the early MRSA isolate COL (SaBADH) utilizes betaine aldehyde as the primary substrate and nicotinamide adenine dinucleotide (NAD(+)) as the cofactor. Surface plasmon resonance experiments revealed that the affinity of NAD(+), NADH and BA for SaBADH is affected by temperature, pH and buffer composition. Five crystal structures of the wild type and three structures of the Gly234Ser mutant of SaBADH in the apo and holo forms provide details of the molecular mechanisms of activity and substrate specificity/inhibition of this enzyme.
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Affiliation(s)
- Andrei S. Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | | | - Chao Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Jeong Chan Joo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Ievgeniia Dubrovska
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - James R. Winsor
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | | | - Mark Duban
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Ludmilla Shuvalova
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Wayne F. Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
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Roy SM, Grum-Tokars VL, Schavocky JP, Saeed F, Staniszewski A, Teich AF, Arancio O, Bachstetter AD, Webster SJ, Van Eldik LJ, Minasov G, Anderson WF, Pelletier JC, Watterson DM. Targeting human central nervous system protein kinases: An isoform selective p38αMAPK inhibitor that attenuates disease progression in Alzheimer's disease mouse models. ACS Chem Neurosci 2015; 6:666-80. [PMID: 25676389 PMCID: PMC4404319 DOI: 10.1021/acschemneuro.5b00002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
![]()
The
first kinase inhibitor drug approval in 2001 initiated a remarkable
decade of tyrosine kinase inhibitor drugs for oncology indications,
but a void exists for serine/threonine protein kinase inhibitor drugs
and central nervous system indications. Stress kinases are of special
interest in neurological and neuropsychiatric disorders due to their
involvement in synaptic dysfunction and complex disease susceptibility.
Clinical and preclinical evidence implicates the stress related kinase
p38αMAPK as a potential neurotherapeutic target, but isoform
selective p38αMAPK inhibitor candidates are lacking and the
mixed kinase inhibitor drugs that are promising in peripheral tissue
disease indications have limitations for neurologic indications. Therefore,
pursuit of the neurotherapeutic hypothesis requires kinase isoform
selective inhibitors with appropriate neuropharmacology features.
Synaptic dysfunction disorders offer a potential for enhanced pharmacological
efficacy due to stress-induced activation of p38αMAPK in both
neurons and glia, the interacting cellular components of the synaptic
pathophysiological axis, to be modulated. We report a novel isoform
selective p38αMAPK inhibitor, MW01-18-150SRM (=MW150), that
is efficacious in suppression of hippocampal-dependent associative
and spatial memory deficits in two distinct synaptic dysfunction mouse
models. A synthetic scheme for biocompatible product and positive
outcomes from pharmacological screens are presented. The high-resolution
crystallographic structure of the p38αMAPK/MW150 complex documents
active site binding, reveals a potential low energy conformation of
the bound inhibitor, and suggests a structural explanation for MW150’s
exquisite target selectivity. As far as we are aware, MW150 is without
precedent as an isoform selective p38MAPK inhibitor or as a kinase
inhibitor capable of modulating in vivo stress related behavior.
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Affiliation(s)
| | | | | | - Faisal Saeed
- Columbia University, New York, New York 10032, United States
| | | | - Andrew F. Teich
- Columbia University, New York, New York 10032, United States
| | - Ottavio Arancio
- Columbia University, New York, New York 10032, United States
| | | | - Scott J. Webster
- University of Kentucky, Lexington, Kentucky 40536, United States
| | | | - George Minasov
- Northwestern University, Chicago, Illinois 60611, United States
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Ruan J, Mouveaux T, Light SH, Minasov G, Anderson WF, Tomavo S, Ngô HM. The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions. Acta Crystallogr D Biol Crystallogr 2015; 71:417-26. [PMID: 25760592 PMCID: PMC4356359 DOI: 10.1107/s1399004714026479] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 12/01/2014] [Indexed: 12/15/2022]
Abstract
In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein in Toxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated in vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.
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Affiliation(s)
- Jiapeng Ruan
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - Thomas Mouveaux
- Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM U1019, Institut Pasteur de Lille, Université Lille Nord de France, France
| | - Samuel H. Light
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - Stanislas Tomavo
- Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM U1019, Institut Pasteur de Lille, Université Lille Nord de France, France
| | - Huân M. Ngô
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
- BrainMicro LLC, 21 Pendleton Street, New Haven, CT 06511, USA
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Minasov G, Nocadello S, Filippova E, Halavaty A, Anderson W. Structures of the surface exposed proteins of Gram positive bacteria. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314095679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The Center for Structural Genomics for Infectious Diseases (CSGID) applies structural genomics approaches to biomedically important proteins from human pathogens. It also provides the infectious disease community with a high throughput pipeline for structure determination that carries out all steps of the process, from target selection through structure deposition. Target proteins include drug targets, essential enzymes, virulence factors and vaccine candidates. The CSGID has deposited over 680 structures in the Protein Data Bank. The proteins that are exposed on the surface of Gram positive bacterial pathogens (including Staphylococcus aureus, Bacillus anthracis, Listeria monocytogenes, Streptococcus species and Clostridium species) have been one focus area for the CSGID. So far, the structures of more than 55 of these proteins have been determined. The surface proteins are important in the interactions between the pathogen and its host, but many of them are as yet functionally uncharacterized. Among the examples that will be presented is the Bacillus anthracis SpoIID protein. SpoIID is part of a coordinated cell wall degradation machine that is essential for sporulation and the morphological changes involved. It represents a new family of lytic transglycosylases that degrade the glycan strands of the peptidoglycan cell wall. The two active site clefts in the dimeric enzyme include residues from both subunits, suggesting that the dimer is required for activity. This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contracts No. HHSN272200700058C and HHSN272201200026C.
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Kuhn M, Majorek K, Filippova E, Minasov G, Wolfe A, Minor W, Anderson W. Structural analysis of GNAT acetyltransferases and protein acetylation. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314097009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The Center for Structural Genomics for Infectious Diseases (CSGID) applies structural genomics approaches to biomedically relevant proteins from human pathogens and provides the infectious disease community with a high throughput pipeline for structure determination. Target proteins include drug targets, essential enzymes, virulence factors and vaccine candidates. Bacterial species generally have many acetyl-coenzyme A dependent GCN5-like Acetyl Transferases (GNATs), however, the substrates of most of them are unknown. Proteomic analysis has also revealed extensive post-translational modification of bacterial proteins, especially acetylation of lysine Nε. These observations led the CSGID to develop a high throughput substrate screen and initiate characterization of bacterial GNATs. One of the bacterial GNATs that acetylates lysine residues, is the Pseudomonas aeruginosa protein PA4794, that acetylates both peptides having a C-terminal lysine and the drug, chloramphenicol. Surprisingly, the acetylation of these two substrates by PA4794 is catalyzed by the enzyme using different active site residues and different kinetic mechanisms. Although it was expected that the GNATs would play a major role in protein acetylation, much of the lysine acetylation observed in bacteria is actually due to the metabolite acetylphosphate (1,2). Crystal structures and proteomics experiments revealed what makes some lysine residues particularly sensitive to acetylphosphate dependent lysine acetylation and what is required for subsequent enzymatic deacetylation. CSGID is funded with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contracts No. HHSN272200700058C and HHSN272201200026C and Midwest Center for Structural Genomics by grant GM094585
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Hoyland CN, Aldridge C, Cleverley RM, Duchêne MC, Minasov G, Onopriyenko O, Sidiq K, Stogios PJ, Anderson WF, Daniel RA, Savchenko A, Vollmer W, Lewis RJ. Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition. Structure 2014; 22:949-60. [PMID: 24909784 PMCID: PMC4087270 DOI: 10.1016/j.str.2014.04.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/24/2014] [Accepted: 04/29/2014] [Indexed: 01/30/2023]
Abstract
Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like β-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.
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Affiliation(s)
- Christopher N Hoyland
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Christine Aldridge
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Robert M Cleverley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marie-Clémence Duchêne
- Institut des Sciences de la Vie, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - George Minasov
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Olena Onopriyenko
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Karzan Sidiq
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Peter J Stogios
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Wayne F Anderson
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Richard A Daniel
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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Kuhn ML, Zemaitaitis B, Hu LI, Sahu A, Sorensen D, Minasov G, Lima BP, Scholle M, Mrksich M, Anderson WF, Gibson BW, Schilling B, Wolfe AJ. Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation. PLoS One 2014; 9:e94816. [PMID: 24756028 PMCID: PMC3995681 DOI: 10.1371/journal.pone.0094816] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 03/19/2014] [Indexed: 01/27/2023] Open
Abstract
The emerging view of Nε-lysine acetylation in eukaryotes is of a relatively abundant post-translational modification (PTM) that has a major impact on the function, structure, stability and/or location of thousands of proteins involved in diverse cellular processes. This PTM is typically considered to arise by the donation of the acetyl group from acetyl-coenzyme A (acCoA) to the ε-amino group of a lysine residue that is reversibly catalyzed by lysine acetyltransferases and deacetylases. Here, we provide genetic, mass spectrometric, biochemical and structural evidence that Nε-lysine acetylation is an equally abundant and important PTM in bacteria. Applying a recently developed, label-free and global mass spectrometric approach to an isogenic set of mutants, we detected acetylation of thousands of lysine residues on hundreds of Escherichia coli proteins that participate in diverse and often essential cellular processes, including translation, transcription and central metabolism. Many of these acetylations were regulated in an acetyl phosphate (acP)-dependent manner, providing compelling evidence for a recently reported mechanism of bacterial Nε-lysine acetylation. These mass spectrometric data, coupled with observations made by crystallography, biochemistry, and additional mass spectrometry showed that this acP-dependent acetylation is both non-enzymatic and specific, with specificity determined by the accessibility, reactivity and three-dimensional microenvironment of the target lysine. Crystallographic evidence shows acP can bind to proteins in active sites and cofactor binding sites, but also potentially anywhere molecules with a phosphate moiety could bind. Finally, we provide evidence that acP-dependent acetylation can impact the function of critical enzymes, including glyceraldehyde-3-phosphate dehydrogenase, triosephosphate isomerase, and RNA polymerase.
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Affiliation(s)
- Misty L. Kuhn
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bozena Zemaitaitis
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Linda I. Hu
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Alexandria Sahu
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Dylan Sorensen
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bruno P. Lima
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Michael Scholle
- Departments of Biomedical Engineering, Chemistry, and Cell & Molecular Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Milan Mrksich
- Departments of Biomedical Engineering, Chemistry, and Cell & Molecular Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bradford W. Gibson
- Buck Institute for Research on Aging, Novato, California, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
- * E-mail:
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Grum‐Tokars V, Roy S, Minasov G, Anderson W, Watterson D. A protein crystallography and small molecule informatics‐based discovery engine for the development of selective chemical probes for in vivo investigations of protein kinases (968.3). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.968.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Valerie Grum‐Tokars
- Molecular Pharmacology & Biological Chemistry Northwestern UniversityChicagoILUnited States
| | - Saktimayee Roy
- Molecular Pharmacology & Biological Chemistry Northwestern UniversityChicagoILUnited States
| | - George Minasov
- Molecular Pharmacology & Biological Chemistry Northwestern UniversityChicagoILUnited States
| | - Wayne Anderson
- Molecular Pharmacology & Biological Chemistry Northwestern UniversityChicagoILUnited States
| | - D. Watterson
- Molecular Pharmacology & Biological Chemistry Northwestern UniversityChicagoILUnited States
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Light SH, Minasov G, Duban ME, Anderson WF. Adherence to Bürgi-Dunitz stereochemical principles requires significant structural rearrangements in Schiff-base formation: insights from transaldolase complexes. Acta Crystallogr D Biol Crystallogr 2014; 70:544-52. [PMID: 24531488 PMCID: PMC3940192 DOI: 10.1107/s1399004713030666] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/08/2013] [Indexed: 11/10/2022]
Abstract
The Bürgi-Dunitz angle (αBD) describes the trajectory of approach of a nucleophile to an electrophile. The adoption of a stereoelectronically favorable αBD can necessitate significant reactive-group repositioning over the course of bond formation. In the context of enzyme catalysis, interactions with the protein constrain substrate rotation, which could necessitate structural transformations during bond formation. To probe this theoretical framework vis-à-vis biocatalysis, Schiff-base formation was analysed in Francisella tularensis transaldolase (TAL). Crystal structures of wild-type and Lys→Met mutant TAL in covalent and noncovalent complexes with fructose 6-phosphate and sedoheptulose 7-phosphate clarify the mechanism of catalysis and reveal that substrate keto moieties undergo significant conformational changes during Schiff-base formation. Structural changes compelled by the trajectory considerations discussed here bear relevance to bond formation in a variety of constrained enzymic/engineered systems and can inform the design of covalent therapeutics.
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Affiliation(s)
- Samuel H. Light
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mark-Eugene Duban
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Chemistry and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60201, USA
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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Kuhn ML, Prachi P, Minasov G, Shuvalova L, Ruan J, Dubrovska I, Winsor J, Giraldi M, Biagini M, Liberatori S, Savino S, Bagnoli F, Anderson WF, Grandi G. Structure and protective efficacy of the Staphylococcus aureus autocleaving protease EpiP. FASEB J 2014; 28:1780-93. [PMID: 24421400 DOI: 10.1096/fj.13-241737] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Despite the global medical needs associated with Staphylococcus aureus infections, no licensed vaccines are currently available. We identified and characterized a protein annotated as an epidermin leader peptide processing serine protease (EpiP), as a novel S. aureus vaccine candidate. In addition, we determined the structure of the recombinant protein (rEpiP) by X-ray crystallography. The crystal structure revealed that rEpiP was cleaved somewhere between residues 95 and 100, and we found that the cleavage occurs through an autocatalytic intramolecular mechanism. The protein expressed by S. aureus cells also appeared to undergo a similar processing event. To determine whether the protein acts as a serine protease, we mutated the hypothesized catalytic serine 393 residue to alanine, generating rEpiP-S393A. The crystal structure of this mutant protein showed that the polypeptide chain was not cleaved and was not interacting stably with the active site. Indeed, rEpiP-S393A was shown to be impaired in its protease activity. Mice vaccinated with rEpiP were protected from S. aureus infection (34% survival, P=0.0054). Moreover, the protective efficacy generated by rEpiP and rEpiP-S393A was comparable, implying that the noncleaving mutant could be used for vaccination purposes.
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Affiliation(s)
- Misty L Kuhn
- 2G.G., Novartis Vaccines, via Fiorentina 1, 53100, Siena, Italy.
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Vorontsov II, Wu Y, DeLucia M, Minasov G, Mehrens J, Shuvalova L, Anderson WF, Ahn J. Mechanisms of allosteric activation and inhibition of the deoxyribonucleoside triphosphate triphosphohydrolase from Enterococcus faecalis. J Biol Chem 2013; 289:2815-24. [PMID: 24338016 DOI: 10.1074/jbc.m113.524207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
EF1143 from Enterococcus faecalis, a life-threatening pathogen that is resistant to common antibiotics, is a homo-tetrameric deoxyribonucleoside triphosphate (dNTP) triphosphohydrolase (dNTPase), converting dNTPs into the deoxyribonucleosides and triphosphate. The dNTPase activity of EF1143 is regulated by canonical dNTPs, which simultaneously act as substrates and activity modulators. Previous crystal structures of apo-EF1143 and the protein bound to both dGTP and dATP suggested allosteric regulation of its enzymatic activity by dGTP binding at four identical allosteric sites. However, whether and how other canonical dNTPs regulate the enzyme activity was not defined. Here, we present the crystal structure of EF1143 in complex with dGTP and dTTP. The new structure reveals that the tetrameric EF1143 contains four additional secondary allosteric sites adjacent to the previously identified dGTP-binding primary regulatory sites. Structural and enzyme kinetic studies indicate that dGTP binding to the first allosteric site, with nanomolar affinity, is a prerequisite for substrate docking and hydrolysis. Then, the presence of a particular dNTP in the second site either enhances or inhibits the dNTPase activity of EF1143. Our results provide the first mechanistic insight into dNTP-mediated regulation of dNTPase activity.
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Affiliation(s)
- Ivan I Vorontsov
- From the Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611 and
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48
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Seo HS, Minasov G, Seepersaud R, Doran KS, Dubrovska I, Shuvalova L, Anderson WF, Iverson TM, Sullam PM. Characterization of fibrinogen binding by glycoproteins Srr1 and Srr2 of Streptococcus agalactiae. J Biol Chem 2013; 288:35982-96. [PMID: 24165132 PMCID: PMC3861647 DOI: 10.1074/jbc.m113.513358] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The serine-rich repeat glycoproteins of Gram-positive bacteria comprise a large family of cell wall proteins. Streptococcus agalactiae (group B streptococcus, GBS) expresses either Srr1 or Srr2 on its surface, depending on the strain. Srr1 has recently been shown to bind fibrinogen, and this interaction contributes to the pathogenesis of GBS meningitis. Although strains expressing Srr2 appear to be hypervirulent, no ligand for this adhesin has been described. We now demonstrate that Srr2 also binds human fibrinogen and that this interaction promotes GBS attachment to endothelial cells. Recombinant Srr1 and Srr2 bound fibrinogen in vitro, with affinities of KD = 2.1 × 10−5 and 3.7 × 10−6m, respectively, as measured by surface plasmon resonance spectroscopy. The binding site for Srr1 and Srr2 was localized to tandem repeats 6–8 of the fibrinogen Aα chain. The structures of both the Srr1 and Srr2 binding regions were determined and, in combination with mutagenesis studies, suggest that both Srr1 and Srr2 interact with a segment of these repeats via a “dock, lock, and latch” mechanism. Moreover, properties of the latch region may account for the increased affinity between Srr2 and fibrinogen. Together, these studies identify how greater affinity of Srr2 for fibrinogen may contribute to the increased virulence associated with Srr2-expressing strains.
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Affiliation(s)
- Ho Seong Seo
- From the Division of Infectious Diseases, Veterans Affairs Medical Center, University of California at San Francisco and the Northern California Institute for Research and Education, San Francisco, California 94121
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Watterson DM, Grum-Tokars VL, Roy SM, Schavocky JP, Bradaric BD, Bachstetter AD, Xing B, Dimayuga E, Saeed F, Zhang H, Staniszewski A, Pelletier JC, Minasov G, Anderson WF, Arancio O, Van Eldik LJ. Development of Novel In Vivo Chemical Probes to Address CNS Protein Kinase Involvement in Synaptic Dysfunction. PLoS One 2013; 8:e66226. [PMID: 23840427 PMCID: PMC3694096 DOI: 10.1371/journal.pone.0066226] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/02/2013] [Indexed: 12/23/2022] Open
Abstract
Serine-threonine protein kinases are critical to CNS function, yet there is a dearth of highly selective, CNS-active kinase inhibitors for in vivo investigations. Further, prevailing assumptions raise concerns about whether single kinase inhibitors can show in vivo efficacy for CNS pathologies, and debates over viable approaches to the development of safe and efficacious kinase inhibitors are unsettled. It is critical, therefore, that these scientific challenges be addressed in order to test hypotheses about protein kinases in neuropathology progression and the potential for in vivo modulation of their catalytic activity. Identification of molecular targets whose in vivo modulation can attenuate synaptic dysfunction would provide a foundation for future disease-modifying therapeutic development as well as insight into cellular mechanisms. Clinical and preclinical studies suggest a critical link between synaptic dysfunction in neurodegenerative disorders and the activation of p38αMAPK mediated signaling cascades. Activation in both neurons and glia also offers the unusual potential to generate enhanced responses through targeting a single kinase in two distinct cell types involved in pathology progression. However, target validation has been limited by lack of highly selective inhibitors amenable to in vivo use in the CNS. Therefore, we employed high-resolution co-crystallography and pharmacoinformatics to design and develop a novel synthetic, active site targeted, CNS-active, p38αMAPK inhibitor (MW108). Selectivity was demonstrated by large-scale kinome screens, functional GPCR agonist and antagonist analyses of off-target potential, and evaluation of cellular target engagement. In vitro and in vivo assays demonstrated that MW108 ameliorates beta-amyloid induced synaptic and cognitive dysfunction. A serendipitous discovery during co-crystallographic analyses revised prevailing models about active site targeting of inhibitors, providing insights that will facilitate future kinase inhibitor design. Overall, our studies deliver highly selective in vivo probes appropriate for CNS investigations and demonstrate that modulation of p38αMAPK activity can attenuate synaptic dysfunction.
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Affiliation(s)
- D. Martin Watterson
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
- * E-mail:
| | - Valerie L. Grum-Tokars
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - Saktimayee M. Roy
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - James P. Schavocky
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - Brinda Desai Bradaric
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - Adam D. Bachstetter
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - Bin Xing
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - Edgardo Dimayuga
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - Faisal Saeed
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Hong Zhang
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Agnieszka Staniszewski
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Jeffrey C. Pelletier
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - George Minasov
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - Wayne F. Anderson
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - Ottavio Arancio
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Linda J. Van Eldik
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
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Egli M, Minasov G, Tereshko V, Pallan PS, Teplova M, Inamati GB, Lesnik EA, Owens SR, Ross BS, Prakash TP, Manoharan M. Correction to Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2′- O-Ribonucleic Acid Modifications. Biochemistry 2013. [DOI: 10.1021/bi4002166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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