1
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Wu R, Khamrui S, Dodatko T, Leandro J, Sabovic A, Violante S, Cross JR, Marsan E, Kumar K, DeVita RJ, Lazarus MB, Houten SM. Characterization, Structure, and Inhibition of the Human Succinyl-CoA:glutarate-CoA Transferase, a Putative Genetic Modifier of Glutaric Aciduria Type 1. ACS Chem Biol 2024; 19:1544-1553. [PMID: 38915184 PMCID: PMC11259535 DOI: 10.1021/acschembio.4c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Glutaric Aciduria Type 1 (GA1) is a serious inborn error of metabolism with no pharmacological treatments. A novel strategy to treat this disease is to divert the toxic biochemical intermediates to less toxic or nontoxic metabolites. Here, we report a putative novel target, succinyl-CoA:glutarate-CoA transferase (SUGCT), which we hypothesize suppresses the GA1 metabolic phenotype through decreasing glutaryl-CoA and the derived 3-hydroxyglutaric acid. SUGCT is a type III CoA transferase that uses succinyl-CoA and glutaric acid as substrates. We report the structure of SUGCT, develop enzyme- and cell-based assays, and identify valsartan and losartan carboxylic acid as inhibitors of the enzyme in a high-throughput screen of FDA-approved compounds. The cocrystal structure of SUGCT with losartan carboxylic acid revealed a novel pocket in the active site and further validated the high-throughput screening approach. These results may form the basis for the future development of new pharmacological intervention to treat GA1.
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Affiliation(s)
- Ruoxi Wu
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Susmita Khamrui
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Tetyana Dodatko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - João Leandro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Amanda Sabovic
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Sara Violante
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - Justin R Cross
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - Eric Marsan
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Kunal Kumar
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Robert J DeVita
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Michael B Lazarus
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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2
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Öster L, Castaldo M, de Vries E, Edfeldt F, Pemberton N, Gordon E, Cederblad L, Käck H. The structures of salt-inducible kinase 3 in complex with inhibitors reveal determinants for binding and selectivity. J Biol Chem 2024; 300:107201. [PMID: 38508313 PMCID: PMC11061224 DOI: 10.1016/j.jbc.2024.107201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024] Open
Abstract
The salt-inducible kinases (SIKs) 1 to 3, belonging to the AMPK-related kinase family, serve as master regulators orchestrating a diverse set of physiological processes such as metabolism, bone formation, immune response, oncogenesis, and cardiac rhythm. Owing to its key regulatory role, the SIK kinases have emerged as compelling targets for pharmacological intervention across a diverse set of indications. Therefore, there is interest in developing SIK inhibitors with defined selectivity profiles both to further dissect the downstream biology and for treating disease. However, despite a large pharmaceutical interest in the SIKs, experimental structures of SIK kinases are scarce. This is likely due to the challenges associated with the generation of proteins suitable for structural studies. By adopting a rational approach to construct design and protein purification, we successfully crystallized and subsequently solved the structure of SIK3 in complex with HG-9-91-01, a potent SIK inhibitor. To enable further SIK3-inhibitor complex structures we identified an antibody fragment that facilitated crystallization and enabled a robust protocol suitable for structure-based drug design. The structures reveal SIK3 in an active conformation, where the ubiquitin-associated domain is shown to provide further stabilization to this active conformation. We present four pharmacologically relevant and distinct SIK3-inhibitor complexes. These detail the key interaction for each ligand and reveal how different regions of the ATP site are engaged by the different inhibitors to achieve high affinity. Notably, the structure of SIK3 in complex with a SIK3 specific inhibitor offers insights into isoform selectivity.
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Affiliation(s)
- Linda Öster
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
| | - Marie Castaldo
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Emma de Vries
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | - Fredrik Edfeldt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Nils Pemberton
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Euan Gordon
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Linda Cederblad
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Helena Käck
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
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3
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Khamrui S, Dodatko T, Wu R, Leandro J, Sabovic A, Violante S, Cross JR, Marsan E, Kumar K, DeVita RJ, Lazarus MB, Houten SM. Characterization, structure and inhibition of the human succinyl-CoA:glutarate-CoA transferase, a genetic modifier of glutaric aciduria type 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.578422. [PMID: 38370847 PMCID: PMC10871334 DOI: 10.1101/2024.02.07.578422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Glutaric Aciduria Type 1 (GA1) is a serious inborn error of metabolism with no pharmacological treatments. A novel strategy to treat this disease is to divert the toxic biochemical intermediates to less toxic or non-toxic metabolites. Here, we report a novel target, SUGCT, which we hypothesize suppresses the GA1 metabolic phenotype through decreasing glutaryl-CoA. We report the structure of SUGCT, the first eukaryotic structure of a type III CoA transferase, develop a high-throughput enzyme assay and a cell-based assay, and identify valsartan and losartan carboxylic acid as inhibitors of the enzyme validating the screening approach. These results may form the basis for future development of new pharmacological intervention to treat GA1.
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Affiliation(s)
- Susmita Khamrui
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tetyana Dodatko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruoxi Wu
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - João Leandro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amanda Sabovic
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara Violante
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Justin R. Cross
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Eric Marsan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kunal Kumar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert J. DeVita
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B. Lazarus
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sander M. Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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4
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Lin DYW, Kueffer LE, Juneja P, Wales TE, Engen JR, Andreotti AH. Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states. eLife 2024; 12:RP89489. [PMID: 38189455 PMCID: PMC10945472 DOI: 10.7554/elife.89489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
Full-length Bruton's tyrosine kinase (BTK) has been refractory to structural analysis. The nearest full-length structure of BTK to date consists of the autoinhibited SH3-SH2-kinase core. Precisely how the BTK N-terminal domains (the Pleckstrin homology/Tec homology [PHTH] domain and proline-rich regions [PRR] contain linker) contribute to BTK regulation remains unclear. We have produced crystals of full-length BTK for the first time but despite efforts to stabilize the autoinhibited state, the diffraction data still reveal only the SH3-SH2-kinase core with no electron density visible for the PHTH-PRR segment. Cryo-electron microscopy (cryoEM) data of full-length BTK, on the other hand, provide the first view of the PHTH domain within full-length BTK. CryoEM reconstructions support conformational heterogeneity in the PHTH-PRR region wherein the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3-SH2-kinase core. On the way to activation, disassembly of the SH3-SH2-kinase core opens a new autoinhibitory site on the kinase domain for PHTH domain binding that is ultimately released upon interaction of PHTH with phosphatidylinositol (3,4,5)-trisphosphate. Membrane-induced dimerization activates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. Together, these data provide the first structural elucidation of full-length BTK and allow a deeper understanding of allosteric control over the BTK kinase domain during distinct stages of activation.
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Affiliation(s)
- David Yin-wei Lin
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Lauren E Kueffer
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Puneet Juneja
- Cryo-EM Facility, Office of Biotechnology, Iowa State UniversityAmesUnited States
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern UniversityBostonUnited States
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern UniversityBostonUnited States
| | - Amy H Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmesUnited States
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5
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Lin DYW, Kueffer LE, Juneja P, Wales TE, Engen JR, Andreotti AH. Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543453. [PMID: 37786675 PMCID: PMC10541622 DOI: 10.1101/2023.06.02.543453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Full-length BTK has been refractory to structural analysis. The nearest full-length structure of BTK to date consists of the autoinhibited SH3-SH2-kinase core. Precisely how the BTK N-terminal domains (the Pleckstrin homology/Tec homology (PHTH) domain and proline-rich regions (PRR) contain linker) contribute to BTK regulation remains unclear. We have produced crystals of full-length BTK for the first time but despite efforts to stabilize the autoinhibited state, the diffraction data still reveals only the SH3-SH2-kinase core with no electron density visible for the PHTH-PRR segment. CryoEM data of full-length BTK, on the other hand, provide the first view of the PHTH domain within full-length BTK. CryoEM reconstructions support conformational heterogeneity in the PHTH-PRR region wherein the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3-SH2-kinase core. On the way to activation, disassembly of the SH3-SH2-kinase core opens a new autoinhibitory site on the kinase domain for PHTH domain binding that is ultimately released upon interaction of PHTH with PIP3. Membrane-induced dimerizationactivates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to transautophosphorylation. Together, these data provide the first structural elucidation of full-length BTK and allow a deeper understanding of allosteric control over the BTK kinase domain during distinct stages of activation.
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6
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Zhu S, Fan S, Tang T, Huang J, Zhou H, Huang C, Chen Y, Qian F. Polymorphic nanobody crystals as long-acting intravitreal therapy for wet age-related macular degeneration. Bioeng Transl Med 2023; 8:e10523. [PMID: 38023710 PMCID: PMC10658565 DOI: 10.1002/btm2.10523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/23/2023] [Accepted: 03/29/2023] [Indexed: 12/01/2023] Open
Abstract
Wet age-related macular degeneration (wet AMD) is the most common cause of blindness, and chronic intravitreal injection of anti-vascular endothelial growth factor (VEGF) proteins has been the dominant therapeutic approach. Less intravitreal injection and a prolonged inter-injection interval are the main drivers behind new wet AMD drug innovations. By rationally engineering the surface residues of a model anti-VEGF nanobody, we obtained a series of anti-VEGF nanobodies with identical protein structures and VEGF binding affinities, while drastically different crystallization propensities and crystal lattice structures. Among these nanobody crystals, the P212121 lattice appeared to be denser and released protein slower than the P1 lattice, while nanobody crystals embedding zinc coordination further slowed the protein release rate. The polymorphic protein crystals could be a potentially breakthrough strategy for chronic intravitreal administration of anti-VEGF proteins.
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Affiliation(s)
- Shuqian Zhu
- School of Pharmaceutical Sciences, Beijing Advanced Innovation Center for Structural Biology, and Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Tsinghua UniversityBeijingPeople's Republic of China
| | - Shilong Fan
- Beijing Frontier Research Center for Biological StructureTsinghua UniversityBeijingPeople's Republic of China
| | - Tianxin Tang
- School of Pharmaceutical Sciences, Beijing Advanced Innovation Center for Structural Biology, and Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Tsinghua UniversityBeijingPeople's Republic of China
| | - Jinliang Huang
- Quaerite Biopharm ResearchBeijingPeople's Republic of China
| | - Heng Zhou
- Shuimu BioSciences Co. Ltd.BeijingPeople's Republic of China
| | - Chengnan Huang
- School of Pharmaceutical Sciences, Beijing Advanced Innovation Center for Structural Biology, and Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Tsinghua UniversityBeijingPeople's Republic of China
| | - Youxin Chen
- Peking Union Medical College HospitalBeijingPeople's Republic of China
| | - Feng Qian
- School of Pharmaceutical Sciences, Beijing Advanced Innovation Center for Structural Biology, and Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Tsinghua UniversityBeijingPeople's Republic of China
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7
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Fenwick M, Reers AR, Liu Y, Zigweid R, Sankaran B, Shin J, Hulverson MA, Hammerson B, Fernández Álvaro E, Myler PJ, Kaushansky A, Van Voorhis WC, Fan E, Staker BL. Identification of and Structural Insights into Hit Compounds Targeting N-Myristoyltransferase for Cryptosporidium Drug Development. ACS Infect Dis 2023; 9:1821-1833. [PMID: 37722671 PMCID: PMC10580320 DOI: 10.1021/acsinfecdis.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Indexed: 09/20/2023]
Abstract
Each year, approximately 50,000 children under 5 die as a result of diarrhea caused by Cryptosporidium parvum, a protozoan parasite. There are currently no effective drugs or vaccines available to cure or prevent Cryptosporidium infection, and there are limited tools for identifying and validating targets for drug or vaccine development. We previously reported a high throughput screening (HTS) of a large compound library against Plasmodium N-myristoyltransferase (NMT), a validated drug target in multiple protozoan parasite species. To identify molecules that could be effective against Cryptosporidium, we counter-screened hits from the Plasmodium NMT HTS against Cryptosporidium NMT. We identified two potential hit compounds and validated them against CpNMT to determine if NMT might be an attractive drug target also for Cryptosporidium. We tested the compounds against Cryptosporidium using both cell-based and NMT enzymatic assays. We then determined the crystal structure of CpNMT bound to Myristoyl-Coenzyme A (MyrCoA) and structures of ternary complexes with MyrCoA and the hit compounds to identify the ligand binding modes. The binding site architectures display different conformational states in the presence of the two inhibitors and provide a basis for rational design of selective inhibitors.
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Affiliation(s)
- Michael
K. Fenwick
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Alexandra R. Reers
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Yi Liu
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rachael Zigweid
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Banumathi Sankaran
- Berkeley
Center for Structural Biology, Advanced Light Source, Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Janis Shin
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Matthew A. Hulverson
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Bradley Hammerson
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | | | - Peter J. Myler
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98195, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98195, United States
| | - Alexis Kaushansky
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Wesley C. Van Voorhis
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Erkang Fan
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bart L. Staker
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
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8
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Rajoub N, Gerard CJJ, Pantuso E, Fontananova E, Caliandro R, Belviso BD, Curcio E, Nicoletta FP, Pullen J, Chen W, Heng JYY, Ruane S, Liddell J, Alvey N, Ter Horst JH, Di Profio G. A workflow for the development of template-assisted membrane crystallization downstream processing for monoclonal antibody purification. Nat Protoc 2023; 18:2998-3049. [PMID: 37697106 DOI: 10.1038/s41596-023-00869-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 06/06/2023] [Indexed: 09/13/2023]
Abstract
Monoclonal antibodies (mAbs) are commonly used biologic drugs for the treatment of diseases such as rheumatoid arthritis, multiple sclerosis, COVID-19 and various cancers. They are produced in Chinese hamster ovary cell lines and are purified via a number of complex and expensive chromatography-based steps, operated in batch mode, that rely heavily on protein A resin. The major drawback of conventional procedures is the high cost of the adsorption media and the extensive use of chemicals for the regeneration of the chromatographic columns, with an environmental cost. We have shown that conventional protein A chromatography can be replaced with a single crystallization step and gram-scale production can be achieved in continuous flow using the template-assisted membrane crystallization process. The templates are embedded in a membrane (e.g., porous polyvinylidene fluoride with a layer of polymerized polyvinyl alcohol) and serve as nucleants for crystallization. mAbs are flexible proteins that are difficult to crystallize, so it can be challenging to determine the optimal conditions for crystallization. The objective of this protocol is to establish a systematic and flexible approach for the design of a robust, economic and sustainable mAb purification platform to replace at least the protein A affinity stage in traditional chromatography-based purification platforms. The procedure provides details on how to establish the optimal parameters for separation (crystallization conditions, choice of templates, choice of membrane) and advice on analytical and characterization methods.
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Affiliation(s)
- Nazer Rajoub
- CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Technology and Innovation Centre, Glasgow, UK
| | - Charline J J Gerard
- CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Technology and Innovation Centre, Glasgow, UK
| | - Elvira Pantuso
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Tecnologia delle Membrane (ITM), Rende, Italy
| | - Enrica Fontananova
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Tecnologia delle Membrane (ITM), Rende, Italy
| | - Rocco Caliandro
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Cristallografia (IC), Bari, Italy
| | - Benny D Belviso
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Cristallografia (IC), Bari, Italy
| | - Efrem Curcio
- Department of Environmental Engineering, University of Calabria, Rende, Italy
| | - Fiore P Nicoletta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Edificio Polifunzionale, Rende, Italy
| | - James Pullen
- FUJIFILM Diosynth Biotechnologies, Billingham, UK
| | - Wenqian Chen
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Jerry Y Y Heng
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Sean Ruane
- Center for Process Innovation (CPI), Darlington, UK
| | - John Liddell
- Center for Process Innovation (CPI), Darlington, UK
| | | | - Joop H Ter Horst
- CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Technology and Innovation Centre, Glasgow, UK
| | - Gianluca Di Profio
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Tecnologia delle Membrane (ITM), Rende, Italy.
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9
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Zhu W, Qin L, Xu Y, Lu H, Wu Q, Li W, Zhang C, Li X. Three Molecular Modification Strategies to Improve the Thermostability of Xylanase XynA from Streptomyces rameus L2001. Foods 2023; 12:foods12040879. [PMID: 36832954 PMCID: PMC9957083 DOI: 10.3390/foods12040879] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Glycoside hydrolase family 11 (GH11) xylanases are the preferred candidates for the production of functional oligosaccharides. However, the low thermostability of natural GH11 xylanases limits their industrial applications. In this study, we investigated the following three strategies to modify the thermostability of xylanase XynA from Streptomyces rameus L2001 mutation to reduce surface entropy, intramolecular disulfide bond construction, and molecular cyclization. Changes in the thermostability of XynA mutants were analyzed using molecular simulations. All mutants showed improved thermostability and catalytic efficiency compared with XynA, except for molecular cyclization. The residual activities of high-entropy amino acid-replacement mutants Q24A and K104A increased from 18.70% to more than 41.23% when kept at 65 °C for 30 min. The catalytic efficiencies of Q24A and K143A increased to 129.99 and 92.26 mL/s/mg, respectively, compared with XynA (62.97 mL/s/mg) when using beechwood xylan as the substrate. The mutant enzyme with disulfide bonds formed between Val3 and Thr30 increased the t1/260 °C by 13.33-fold and the catalytic efficiency by 1.80-fold compared with the wild-type XynA. The high thermostabilities and hydrolytic activities of XynA mutants will be useful for enzymatic production of functional xylo-oligosaccharides.
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Affiliation(s)
- Weijia Zhu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Liqin Qin
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Youqiang Xu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Hongyun Lu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Qiuhua Wu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Weiwei Li
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Chengnan Zhang
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Xiuting Li
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
- Correspondence:
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10
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Gao L, Lam KH, Liu S, Przykopanski A, Lübke J, Qi R, Krüger M, Nowakowska MB, Selby K, Douillard FP, Dorner MB, Perry K, Lindström M, Dorner BG, Rummel A, Jin R. Crystal structures of OrfX1, OrfX2 and the OrfX1-OrfX3 complex from the orfX gene cluster of botulinum neurotoxin E1. FEBS Lett 2023; 597:524-537. [PMID: 36653893 PMCID: PMC10019085 DOI: 10.1002/1873-3468.14576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 01/20/2023]
Abstract
Botulinum neurotoxins (BoNTs) are among the most lethal toxins known to humans, comprising seven established serotypes termed BoNT/A-G encoded in two types of gene clusters (ha and orfX) in BoNT-producing clostridia. The ha cluster encodes four non-toxic neurotoxin-associated proteins (NAPs) that assemble with BoNTs to protect and enhance their oral toxicity. However, the structure and function of the orfX-type NAPs remain largely unknown. Here, we report the crystal structures for OrfX1, OrfX2, and an OrfX1-OrfX3 complex, which are encoded in the orfX cluster of a BoNT/E1-producing Clostridium botulinum strain associated with human foodborne botulism. These structures lay the foundation for future studies on the potential roles of OrfX proteins in oral intoxication and pathogenesis of BoNTs.
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Affiliation(s)
- Linfeng Gao
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Kwok-ho Lam
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Shun Liu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Adina Przykopanski
- Institute of Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Johanna Lübke
- Institute of Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Ruifeng Qi
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Maren Krüger
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestrasse 10, 13353 Berlin, Germany
| | - Maria B. Nowakowska
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P. O. Box 66, 00014 University of Helsinki, Finland
| | - Katja Selby
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P. O. Box 66, 00014 University of Helsinki, Finland
| | - François P. Douillard
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P. O. Box 66, 00014 University of Helsinki, Finland
| | - Martin B. Dorner
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestrasse 10, 13353 Berlin, Germany
| | - Kay Perry
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Miia Lindström
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P. O. Box 66, 00014 University of Helsinki, Finland
| | - Brigitte G. Dorner
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestrasse 10, 13353 Berlin, Germany
| | - Andreas Rummel
- Institute of Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Rongsheng Jin
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
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11
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Zhou X, Wei M, Nie W, Xi Y, Peng L, Zheng Q, Tang K, Satheesh V, Wang Y, Luo J, Du X, Liu R, Yang Z, La H, Zhong Y, Yang Y, Zhu JK, Du J, Lei M. The H3K9me2-binding protein AGDP3 limits DNA methylation and transcriptional gene silencing in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2385-2395. [PMID: 36149781 DOI: 10.1111/jipb.13369] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation, a conserved epigenetic mark, is critical for tuning temporal and spatial gene expression. The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1) initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci. However, how ROS1 is recruited to specific loci is not well understood. Here, we report the discovery of Arabidopsis AGENET Domain Containing Protein 3 (AGDP3) as a cellular factor that is required to prevent gene silencing and DNA hypermethylation. AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette. Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3K9 and unmodified H3K4 are specifically anchored into two different surface pockets. A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity. Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.
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Affiliation(s)
- Xuelin Zhou
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengwei Wei
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenfeng Nie
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yue Xi
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Qijie Zheng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Kai Tang
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, Idiana, 47906, USA
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yuhua Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jinyan Luo
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Xuan Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Rui Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhenlin Yang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Honggui La
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yingli Zhong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Yu Yang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, Idiana, 47906, USA
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
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12
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Yang C, Zhang L, Zhang W, Huang C, Zhu Y, Jiang X, Liu W, Zhao M, De BC, Zhang C. Biochemical and structural insights of multifunctional flavin-dependent monooxygenase FlsO1-catalyzed unexpected xanthone formation. Nat Commun 2022; 13:5386. [PMID: 36104338 PMCID: PMC9474520 DOI: 10.1038/s41467-022-33131-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
Xanthone-containing natural products display diverse pharmacological properties. The biosynthetic mechanisms of the xanthone formation have not been well documented. Here we show that the flavoprotein monooxygenase FlsO1 in the biosynthesis of fluostatins not only functionally compensates for the monooxygenase FlsO2 in converting prejadomycin to dehydrorabelomycin, but also unexpectedly converts prejadomycin to xanthone-containing products by catalyzing three successive oxidations including hydroxylation, epoxidation and Baeyer-Villiger oxidation. We also provide biochemical evidence to support the physiological role of FlsO1 as the benzo[b]-fluorene C5-hydrolase by using nenestatin C as a substrate mimic. Finally, we resolve the crystal structure of FlsO1 in complex with the cofactor flavin adenine dinucleotide close to the “in” conformation to enable the construction of reactive substrate-docking models to understand the basis of a single enzyme-catalyzed multiple oxidations. This study highlights a mechanistic perspective for the enzymatic xanthone formation in actinomycetes and sets an example for the versatile functions of flavoproteins. The biosynthesis of xanthones has not been well documented. Here, the authors report that monooxygenase FlsO1 catalyzes three successive oxidations – hydroxylation, epoxidation and Baeyer–Villiger oxidation—to form the xanthone scaffold in actinomycetes.
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13
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Fietze T, Wilk P, Kabinger F, Anoosheh S, Hofer A, Lundin D, Feiler CG, Weiss MS, Loderer C. HUG Domain Is Responsible for Active Dimer Stabilization in an NrdJd Ribonucleotide Reductase. Biochemistry 2022; 61:1633-1641. [PMID: 35856337 DOI: 10.1021/acs.biochem.2c00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides. The catalytic activity of most RNRs depends on the formation of a dimer of the catalytic subunits. The active site is located at the interface, and part of the substrate binding site and regulatory mechanisms work across the subunit in the dimer. In this study, we describe and characterize a novel domain responsible for forming the catalytic dimer in several class II RNRs. The 3D structure of the class II RNR from Rhodobacter sphaeroides reveals a so far undescribed α-helical domain in the dimer interface, which is embracing the other subunit. Genetic removal of this HUG domain leads to a severe reduction of activity paired with reduced dimerization capability. In comparison with other described RNRs, the enzyme with this domain is less dependent on the presence of nucleotides to act as allosteric effectors in the formation of dimers. The HUG domain appears to serve as an interlock to keep the dimer intact and functional even at low enzyme and/or effector concentrations.
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Affiliation(s)
- Tobias Fietze
- Chair of Molecular Biotechnology, Technische Universität Dresden, Dresden 01217, Germany
| | - Piotr Wilk
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany.,Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 31-007, Poland
| | - Florian Kabinger
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Saber Anoosheh
- Department of Medical Biochemistry, Umeå University, Umeå 1965, Sweden
| | - Anders Hofer
- Department of Medical Biochemistry, Umeå University, Umeå 1965, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 114 19, Sweden
| | - Christian G Feiler
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany
| | - Christoph Loderer
- Chair of Molecular Biotechnology, Technische Universität Dresden, Dresden 01217, Germany
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14
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Zhou X, Zeng X, Wang L, Zheng Y, Zhang G, Cheng W. The Structure and Function of Biomaterial Endolysin EFm1 from E. faecalis Phage. MATERIALS 2022; 15:ma15144879. [PMID: 35888345 PMCID: PMC9316690 DOI: 10.3390/ma15144879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/03/2022] [Accepted: 07/08/2022] [Indexed: 01/17/2023]
Abstract
The endolysin EFm1 from the E. faecalis 002 (002) phage IME-EF1 efficiently lyses E. faecalis, a gram-positive bacterium that severely threatens human health. Here, the structure and lytic activity of EFm1 toward E. faecalis were further investigated. Lytic activity shows that EFm1 specifically lyses 002 and 22 other clinically isolated E. faecalis, but not E. faecalis 945. Therefore, EFm1 may be an alternative biomaterial to prevent and treat diseases caused by E. faecalis. A structural analysis showed that EFm1D166Q is a tetramer consisting of one full-length unit with additional C-terminal domains (CTDs), while EFm1166–237 aa is an octamer in an asymmetric unit. Several crucial domains and novel residues affecting the lytic activity of EFm1 were identified, including calcium-binding sites (D20, D22 and D31), a putative classic amidohydrolase catalytic triad (C29, H90 and D108), a tetramerization site (M168 and M227), putative ion channel sites (IGGK, 186–198 aa), and other residues (R208 and Y209). Furthermore, EFm1 exhibited no significant activity when expressed alone in vivo, and IME-EF1 lytic activity decreased when efm1 was knocked down. These findings provide valuable insights into the molecule mechanism of a potential functional biomaterial for the treatment of the disease caused by the opportunistic pathogen E. faecalis.
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Affiliation(s)
- Xuerong Zhou
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China; (X.Z.); (L.W.)
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China; (X.Z.); (Y.Z.)
| | - Li Wang
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China; (X.Z.); (L.W.)
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China; (X.Z.); (Y.Z.)
| | - Guixiang Zhang
- Laboratory of Bariatric and Metabolic Surgery, Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, No. 37, Chengdu 610041, China;
| | - Wei Cheng
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China; (X.Z.); (L.W.)
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China; (X.Z.); (Y.Z.)
- Correspondence:
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15
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Boyd RJ, Olson TL, Zook JD, Stein D, Aceves M, Lin WH, Craciunescu FM, Hansen DT, Anastasiadis PZ, Singharoy A, Fromme P. Characterization and computational simulation of human Syx, a RhoGEF implicated in glioblastoma. FASEB J 2022; 36:e22378. [PMID: 35639414 PMCID: PMC9262375 DOI: 10.1096/fj.202101808rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 12/04/2022]
Abstract
Structural discovery of guanine nucleotide exchange factor (GEF) protein complexes is likely to become increasingly relevant with the development of new therapeutics targeting small GTPases and development of new classes of small molecules that inhibit protein‐protein interactions. Syx (also known as PLEKHG5 in humans) is a RhoA GEF implicated in the pathology of glioblastoma (GBM). Here we investigated protein expression and purification of ten different human Syx constructs and performed biophysical characterizations and computational studies that provide insights into why expression of this protein was previously intractable. We show that human Syx can be expressed and isolated and Syx is folded as observed by circular dichroism (CD) spectroscopy and actively binds to RhoA as determined by co‐elution during size exclusion chromatography (SEC). This characterization may provide critical insights into the expression and purification of other recalcitrant members of the large class of oncogenic—Diffuse B‐cell lymphoma (Dbl) homology GEF proteins. In addition, we performed detailed homology modeling and molecular dynamics simulations on the surface of a physiologically realistic membrane. These simulations reveal novel insights into GEF activity and allosteric modulation by the plekstrin homology (PH) domain. These newly revealed interactions between the GEF PH domain and the membrane embedded region of RhoA support previously unexplained experimental findings regarding the allosteric effects of the PH domain from numerous activity studies of Dbl homology GEF proteins. This work establishes new hypotheses for structural interactivity and allosteric signal modulation in Dbl homology RhoGEFs.
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Affiliation(s)
- Ryan J Boyd
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA
| | - Tien L Olson
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA
| | - James D Zook
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA
| | - Derek Stein
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA
| | - Manuel Aceves
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA
| | - Wan-Hsin Lin
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Felicia M Craciunescu
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA
| | - Debra T Hansen
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA.,Center for Innovations in Medicine, Arizona State University, Tempe, Arizona, USA
| | | | - Abhishek Singharoy
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA
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16
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Zhang J, Hou X, Chen Z, Ko Y, Ruszczycky MW, Chen Y, Zhou J, Liu HW. Dioxane Bridge Formation during the Biosynthesis of Spectinomycin Involves a Twitch Radical S-Adenosyl Methionine Dehydrogenase That May Have Evolved from an Epimerase. J Am Chem Soc 2022; 144:9910-9919. [PMID: 35622017 DOI: 10.1021/jacs.2c02676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Spectinomycin is a dioxane-bridged, tricyclic aminoglycoside produced by Streptomyces spectabilis ATCC 27741. While the spe biosynthetic gene cluster for spectinomycin has been reported, the chemistry underlying construction of the dioxane ring is unknown. The twitch radical SAM enzyme SpeY from the spe cluster is shown here to catalyze dehydrogenation of the C2' alcohol of (2'R,3'S)-tetrahydrospectinomycin to yield (3'S)-dihydrospectinomycin as a likely biosynthetic intermediate. This reaction is radical-mediated and initiated via H atom abstraction from C2' of the substrate by the 5'-deoxyadenosyl radical equivalent generated upon reductive cleavage of SAM. Crystallographic analysis of the ternary Michaelis complex places serine-183 adjacent to C2' of the bound substrate opposite C5' of SAM. Mutation of this residue to cysteine converts SpeY to the corresponding C2' epimerase mirroring the opposite phenomenon observed in the homologous twitch radical SAM epimerase HygY from the hygromycin B biosynthetic pathway. Phylogenetic analysis suggests a relatively recent evolutionary branching of putative twitch radical SAM epimerases bearing homologous cysteine residues to generate the SpeY clade of enzymes.
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Affiliation(s)
- Jiawei Zhang
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Xueli Hou
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, China.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhang Chen
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yeonjin Ko
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Mark W Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yutian Chen
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jiahai Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.,Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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17
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Lv Y, Wang J, Yang H, Li N, Farzaneh M, Wei S, Zhai H, Zhang S, Hu Y. Lysine 2-hydroxyisobutyrylation orchestrates cell development and aflatoxin biosynthesis in Aspergillus flavus. Environ Microbiol 2022; 24:4356-4368. [PMID: 35621059 DOI: 10.1111/1462-2920.16077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib ) is a recently identified post-translational modifications (PTM) that regulates numerous cellular metabolic processes. In pathogenic microorganism, although glycolysis and fungal virulence are regulated by Khib , its potential roles in fungi remains to be elusive. Our preliminary results showed that levels of Khib fluctuate over time in Aspergillus flavus, which frequently contaminates crops and produces carcinogenic aflatoxins. However, the perception of Khib function in A. flavus is limited, especially in mycotoxin-producing strains. Here, we performed a comprehensive analysis of Khib in A. flavus, and 7156 Khib sites were identified in 1473 proteins. Notably, we demonstrated that Khib of AflM, a key enzyme in aflatoxin biosynthesis, affected conidia production and sclerotia formation. Furthermore, aflM deletion impaired aflatoxin biosynthesis, and more importantly, strains in which Khib was mimicked by K to T mutation at K49, K179 and K180 sites showed reduced aflatoxin production compared with wild type and ΔaflM complementation strains. These results indicate that Khib at these sites of AflM negatively regulates aflatoxin biosynthesis in A. flavus. In summary, our study revealed the potential roles of Khib in A. flavus, and particularly shed light on a new way to regulate aflatoxin production via Khib . This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yangyong Lv
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Jing Wang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Haojie Yang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Na Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Mohsen Farzaneh
- Department of Agriculture, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, 1983969411, Tehran, Iran
| | - Shan Wei
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Huanchen Zhai
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Shuaibing Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
| | - Yuansen Hu
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.,Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou, 450001, People's Republic of China
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18
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Insights into methionine S-methylation in diverse organisms. Nat Commun 2022; 13:2947. [PMID: 35618717 PMCID: PMC9135737 DOI: 10.1038/s41467-022-30491-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/02/2022] [Indexed: 12/04/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is an important marine anti-stress compound, with key roles in global nutrient cycling, chemotaxis and, potentially, climate regulation. Recently, diverse marine Actinobacteria, α- and γ-proteobacteria were shown to initiate DMSP synthesis via the methionine (Met) S-methyltransferase enzyme (MmtN), generating S-methyl-Met (SMM). Here we characterize a roseobacterial MmtN, providing structural and mechanistic insights into this DMSP synthesis enzyme. We propose that MmtN uses the proximity and desolvation mechanism for Met S-methylation with two adjacent MmtN monomers comprising the Met binding site. We also identify diverse functional MmtN enzymes in potentially symbiotic archaeal Candidatus Woesearchaeota and Candidate Phyla Radiation (CPR) bacteria, and the animalcule Adineta steineri, not anticipated to produce SMM and/or DMSP. These diverse MmtN enzymes, alongside the larger plant MMT enzyme with an N-terminus homologous to MmtN, likely utilize the same proximity and desolvation mechanism. This study provides important insights into the catalytic mechanism of SMM and/or DMSP production, and proposes roles for these compounds in secondary metabolite production, and SMM cycling in diverse organisms and environments. S-methyl methionine (SMM) is a key molecule in production of dimethylsulfoniopropionate (DMSP), an important marine anti-stress compound, with roles in global nutrient cycling. Here, the authors determine the mechanism of SMM synthesis and uncover unexpected roles for SMM in archaea, CPR bacteria and animals.
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19
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Du X, Yang Z, Ariza AJF, Wang Q, Xie G, Li S, Du J. Structure of plant RNA-DEPENDENT RNA POLYMERASE 2, an enzyme involved in small interfering RNA production. THE PLANT CELL 2022; 34:2140-2149. [PMID: 35188193 PMCID: PMC9134047 DOI: 10.1093/plcell/koac067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
In plants, the biogenesis of small interfering RNA (siRNA) requires a family of RNA-dependent RNA polymerases that convert single-stranded RNA (ssRNA) into double-stranded RNA (dsRNA), which is subsequently cleaved into defined lengths by Dicer endonucleases. Here, we determined the structure of maize (Zea mays) RNA-DEPENDENT RNA POLYMERASE 2 (ZmRDR2) in the closed and open conformations. The core catalytic region of ZmRDR2 possesses the canonical DNA-dependent RNA polymerase (DdRP) catalytic sites, pointing to a shared RNA production mechanism between DdRPs and plant RDR-family proteins. Apo-ZmRDR2 adopts a highly compact structure, representing an inactive closed conformation. By contrast, adding RNA induced a significant conformational change in the ZmRDR2 Head domain that opened the RNA binding tunnel, suggesting this is an active elongation conformation of ZmRDR2. Overall, our structural studies trapped both the active and inactive conformations of ZmRDR2, providing insights into the molecular mechanism of dsRNA synthesis during plant siRNA production.
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Affiliation(s)
| | | | - Alfredo Jose Florez Ariza
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
| | - Qian Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guohui Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Sisi Li
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen 518060, China
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20
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Sluchanko NN. Recent advances in structural studies of 14-3-3 protein complexes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:289-324. [PMID: 35534110 DOI: 10.1016/bs.apcsb.2021.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Being phosphopeptide-binding hubs, 14-3-3 proteins coordinate multiple cellular processes in eukaryotes, including the regulation of apoptosis, cell cycle, ion channels trafficking, transcription, signal transduction, and hormone biosynthesis. Forming constitutive α-helical dimers, 14-3-3 proteins predominantly recognize specifically phosphorylated Ser/Thr sites within their partners; this generally stabilizes phosphotarget conformation and affects its activity, intracellular distribution, dephosphorylation, degradation and interactions with other proteins. Not surprisingly, 14-3-3 complexes are involved in the development of a range of diseases and are considered promising drug targets. The wide interactome of 14-3-3 proteins encompasses hundreds of different phosphoproteins, for many of which the interaction is well-documented in vitro and in vivo but lack the structural data that would help better understand underlying regulatory mechanisms and develop new drugs. Despite obtaining structural information on 14-3-3 complexes is still lagging behind the research of 14-3-3 interactions on a proteome-wide scale, recent works provided some advances, including methodological improvements and accumulation of new interesting structural data, that are discussed in this review.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russian Federation.
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21
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Guo J, Liu B, Thorikay M, Yu M, Li X, Tong Z, Salmon RM, Read RJ, Ten Dijke P, Morrell NW, Li W. Crystal structures of BMPRII extracellular domain in binary and ternary receptor complexes with BMP10. Nat Commun 2022; 13:2395. [PMID: 35504921 PMCID: PMC9064986 DOI: 10.1038/s41467-022-30111-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/12/2022] [Indexed: 12/23/2022] Open
Abstract
Heterozygous mutations in BMPR2 (bone morphogenetic protein (BMP) receptor type II) cause pulmonary arterial hypertension. BMPRII is a receptor for over 15 BMP ligands, but why BMPR2 mutations cause lung-specific pathology is unknown. To elucidate the molecular basis of BMP:BMPRII interactions, we report crystal structures of binary and ternary BMPRII receptor complexes with BMP10, which contain an ensemble of seven different BMP10:BMPRII 1:1 complexes. BMPRII binds BMP10 at the knuckle epitope, with the A-loop and β4 strand making BMPRII-specific interactions. The BMPRII binding surface on BMP10 is dynamic, and the affinity is weaker in the ternary complex than in the binary complex. Hydrophobic core and A-loop interactions are important in BMPRII-mediated signalling. Our data reveal how BMPRII is a low affinity receptor, implying that forming a signalling complex requires high concentrations of BMPRII, hence mutations will impact on tissues with highest BMPR2 expression such as the lung vasculature.
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Affiliation(s)
- Jingxu Guo
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom
| | - Bin Liu
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom
| | - Midory Thorikay
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands
| | - Minmin Yu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Xiaoyan Li
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom
| | - Zhen Tong
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom
| | - Richard M Salmon
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom
| | - Randy J Read
- Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Peter Ten Dijke
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands
| | - Nicholas W Morrell
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom
| | - Wei Li
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom.
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22
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A mixed-valent Fe(II)Fe(III) species converts cysteine to an oxazolone/thioamide pair in methanobactin biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2123566119. [PMID: 35320042 PMCID: PMC9060507 DOI: 10.1073/pnas.2123566119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methanobactins (Mbns), copper-binding peptidic compounds produced by some bacteria, are candidate therapeutics for human diseases of copper overload. The paired oxazolone-thioamide bidentate ligands of methanobactins are generated from cysteine residues in a precursor peptide, MbnA, by the MbnBC enzyme complex. MbnBC activity depends on the presence of iron and oxygen, but the catalytically active form has not been identified. Here, we provide evidence that a dinuclear Fe(II)Fe(III) center in MbnB, which is the only representative of a >13,000-member protein family to be characterized, is responsible for this reaction. These findings expand the known roles of diiron enzymes in biology and set the stage for mechanistic understanding, and ultimately engineering, of the MbnBC biosynthetic complex. The iron-containing heterodimeric MbnBC enzyme complex plays a central role in the biosynthesis of methanobactins (Mbns), ribosomally synthesized, posttranslationally modified natural products that bind copper with high affinity. MbnBC catalyzes a four-electron oxidation of a cysteine residue in its precursor-peptide substrate, MbnA, to an oxazolone ring and an adjacent thioamide group. Initial studies of MbnBC indicated the presence of both diiron and triiron species, complicating identification of the catalytically active species. Here, we present evidence through activity assays combined with electron paramagnetic resonance (EPR) and Mössbauer spectroscopic analysis that the active species is a mixed-valent, antiferromagnetically coupled Fe(II)Fe(III) center. Consistent with this assignment, heterologous expression of the MbnBC complex in culture medium containing less iron yielded purified protein with less bound iron but greater activity in vitro. The maximally activated MbnBC prepared in this manner could modify both cysteine residues in MbnA, in contrast to prior findings that only the first cysteine could be processed. Site-directed mutagenesis and multiple crystal structures clearly identify the two essential Fe ions in the active cluster as well as the location of the previously detected third Fe site. Moreover, structural modeling indicates a role for MbnC in recognition of the MbnA leader peptide. These results add a biosynthetic oxidative rearrangement reaction to the repertoire of nonheme diiron enzymes and provide a foundation for elucidating the MbnBC mechanism.
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Deamidation of the human eye lens protein γS-crystallin accelerates oxidative aging. Structure 2022; 30:763-776.e4. [PMID: 35338852 PMCID: PMC9081212 DOI: 10.1016/j.str.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 11/23/2022]
Abstract
Cataract, a clouding of the eye lens from protein precipitation, affects millions of people every year. The lens proteins, the crystallins, show extensive post-translational modifications (PTMs) in cataractous lenses. The most common PTMs, deamidation and oxidation, promote crystallin aggregation; however, it is not clear precisely how these PTMs contribute to crystallin insolubilization. Here, we report six crystal structures of the lens protein γS-crystallin (γS): one of the wild-type and five of deamidated γS variants, from three to nine deamidation sites, after sample aging. The deamidation mutations do not change the overall fold of γS; however, increasing deamidation leads to accelerated disulfide-bond formation. Addition of deamidated sites progressively destabilized protein structure, and the deamidated variants display an increased propensity for aggregation. These results suggest that the deamidated variants are useful as models for accelerated aging; the structural changes observed provide support for redox activity of γS-crystallin in the lens.
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Daneshian L, Renggli I, Hanaway R, Offermann LR, Schlachter CR, Hernandez Arriaza R, Henry S, Prakash R, Wybouw N, Dermauw W, Shimizu LS, Van Leeuwen T, Makris TM, Grbic V, Grbic M, Chruszcz M. Structural and functional characterization of β-cyanoalanine synthase from Tetranychus urticae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 142:103722. [PMID: 35063675 DOI: 10.1016/j.ibmb.2022.103722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Tetranychus urticae is a polyphagous spider mite that can feed on more than 1100 plant species including cyanogenic plants. The herbivore genome contains a horizontally acquired gene tetur10g01570 (TuCAS) that was previously shown to participate in cyanide detoxification. To understand the structure and determine the function of TuCAS in T. urticae, crystal structures of the protein with lysine conjugated pyridoxal phosphate (PLP) were determined. These structures reveal extensive TuCAS homology with the β-substituted alanine synthase family, and they show that this enzyme utilizes a similar chemical mechanism involving a stable α-aminoacrylate intermediate in β-cyanoalanine and cysteine synthesis. We demonstrate that TuCAS is more efficient in the synthesis of β-cyanoalanine, which is a product of the detoxification reaction between cysteine and cyanide, than in the biosynthesis of cysteine. Also, the enzyme carries additional enzymatic activities that were not previously described. We show that TuCAS can detoxify cyanide using O-acetyl-L-serine as a substrate, leading to the direct formation of β-cyanoalanine. Moreover, it catalyzes the reaction between the TuCAS-bound α-aminoacrylate intermediate and aromatic compounds with a thiol group. In addition, we have tested several compounds as TuCAS inhibitors. Overall, this study identifies additional functions for TuCAS and provides new molecular insight into the xenobiotic metabolism of T. urticae.
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Affiliation(s)
- Leily Daneshian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Isabella Renggli
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Ryan Hanaway
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Lesa R Offermann
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Caleb R Schlachter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | | | - Shannon Henry
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Rahul Prakash
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Nicky Wybouw
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, 9000, Belgium
| | - Wannes Dermauw
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke, 9820, Belgium; Department of Plants and Crops, Ghent University, Ghent, 9000, Belgium
| | - Linda S Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | | | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA; Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, 27607, USA
| | - Vojislava Grbic
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada
| | - Miodrag Grbic
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada; University of La Rioja, Logrono, Spain
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA.
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25
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Matsui D, Muraki N, Chen K, Mori T, Ingram AA, Oike K, Gröger H, Aono S, Asano Y. Crystal structural analysis of aldoxime dehydratase from Bacillus sp. OxB-1: Importance of surface residues in optimization for crystallization. J Inorg Biochem 2022; 230:111770. [DOI: 10.1016/j.jinorgbio.2022.111770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 11/28/2022]
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26
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Dalle Vedove A, Cazzanelli G, Corsi J, Sedykh M, D’Agostino VG, Caflisch A, Lolli G. Identification of a BAZ2A Bromodomain Hit Compound by Fragment Joining. ACS BIO & MED CHEM AU 2021; 1:5-10. [PMID: 36147311 PMCID: PMC9484724 DOI: 10.1021/acsbiomedchemau.1c00016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Andrea Dalle Vedove
- Department of Cellular, Computational and Integrative Biology - CIBio, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Giulia Cazzanelli
- Department of Cellular, Computational and Integrative Biology - CIBio, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Jessica Corsi
- Department of Cellular, Computational and Integrative Biology - CIBio, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Maria Sedykh
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Vito Giuseppe D’Agostino
- Department of Cellular, Computational and Integrative Biology - CIBio, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Graziano Lolli
- Department of Cellular, Computational and Integrative Biology - CIBio, University of Trento, via Sommarive 9, 38123 Trento, Italy
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Sluchanko NN, Tugaeva KV, Gushchin I, Remeeva A, Kovalev K, Cooley RB. Crystal structure of human 14-3-3ζ complexed with the noncanonical phosphopeptide from proapoptotic BAD. Biochem Biophys Res Commun 2021; 583:100-105. [PMID: 34735870 DOI: 10.1016/j.bbrc.2021.10.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
Abstract
Several signaling pathways control phosphorylation of the proapoptotic protein BAD and its phosphorylation-dependent association with 14-3-3 proteins in the cytoplasm. The stability of the 14-3-3/BAD complex determines the cell fate: unphosphorylated BAD escapes from 14-3-3, migrates to the mitochondria and initiates apoptosis. While the 14-3-3/BAD interaction represents a promising drug target, it lacks structural characterization. Among several phosphosites identified in vivo, Ser75 and Ser99 of human BAD match the consensus sequence RXXpSXP recognized by 14-3-3 and, therefore, represent canonical 14-3-3-binding sites. Yet, BAD contains other serines phosphorylatable in vivo, whose role is less understood. Here, we report a 2.36 Å crystal structure of 14-3-3ζ complexed with a BAD fragment which includes residues Ser74 and Ser75, both being substrates for protein kinases. While the BAD peptide is anchored to 14-3-3 by phosphoserine as expected, the BAD peptide was unexpectedly phosphorylated at Ser74 instead of Ser75, revealing noncanonical binding within the amphipathic groove and leading to a one-step positional shift and reorganization of the interface. This observation exemplifies plasticity of the amphipathic 14-3-3 groove in accommodating various peptides and suggests the redundancy of Ser74 and Ser75 phosphosites with respect to binding of BAD to 14-3-3.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia; European Molecular Biology Laboratory, 22607, Hamburg, Germany
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
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Grininger C, Leypold M, Aschauer P, Pavkov-Keller T, Riegler-Berket L, Breinbauer R, Oberer M. Structural Changes in the Cap of Rv0183/mtbMGL Modulate the Shape of the Binding Pocket. Biomolecules 2021; 11:1299. [PMID: 34572512 PMCID: PMC8472722 DOI: 10.3390/biom11091299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis continues to be a major threat to the human population. Global efforts to eradicate the disease are ongoing but are hampered by the increasing occurrence of multidrug-resistant strains of Mycobacterium tuberculosis. Therefore, the development of new treatment, and the exploration of new druggable targets and treatment strategies, are of high importance. Rv0183/mtbMGL, is a monoacylglycerol lipase of M. tuberculosis and it is involved in providing fatty acids and glycerol as building blocks and as an energy source. Since the lipase is expressed during the dormant and active phase of an infection, Rv0183/mtbMGL is an interesting target for inhibition. In this work, we determined the crystal structures of a surface-entropy reduced variant K74A Rv0183/mtbMGL in its free form and in complex with a substrate mimicking inhibitor. The two structures reveal conformational changes in the cap region that forms a major part of the substrate/inhibitor binding region. We present a completely closed conformation in the free form and semi-closed conformation in the ligand-bound form. These conformations differ from the previously published, completely open conformation of Rv0183/mtbMGL. Thus, this work demonstrates the high conformational plasticity of the cap from open to closed conformations and provides useful insights into changes in the substrate-binding pocket, the target of potential small-molecule inhibitors.
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Affiliation(s)
- Christoph Grininger
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; (C.G.); (P.A.); (T.P.-K.); (L.R.-B.)
| | - Mario Leypold
- Institute of Organic Chemistry, Graz University of Technology, 8010 Graz, Austria; (M.L.); (R.B.)
| | - Philipp Aschauer
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; (C.G.); (P.A.); (T.P.-K.); (L.R.-B.)
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; (C.G.); (P.A.); (T.P.-K.); (L.R.-B.)
- BioHealth Graz, 8010 Graz, Austria
- BioTechMed Graz, 8010 Graz, Austria
| | - Lina Riegler-Berket
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; (C.G.); (P.A.); (T.P.-K.); (L.R.-B.)
| | - Rolf Breinbauer
- Institute of Organic Chemistry, Graz University of Technology, 8010 Graz, Austria; (M.L.); (R.B.)
- BioTechMed Graz, 8010 Graz, Austria
| | - Monika Oberer
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; (C.G.); (P.A.); (T.P.-K.); (L.R.-B.)
- BioHealth Graz, 8010 Graz, Austria
- BioTechMed Graz, 8010 Graz, Austria
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29
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Subramanian RH, Zhu J, Bailey JB, Chiong JA, Li Y, Golub E, Tezcan FA. Design of metal-mediated protein assemblies via hydroxamic acid functionalities. Nat Protoc 2021; 16:3264-3297. [PMID: 34050338 DOI: 10.1038/s41596-021-00535-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/15/2021] [Indexed: 02/05/2023]
Abstract
The self-assembly of proteins into sophisticated multicomponent assemblies is a hallmark of all living systems and has spawned extensive efforts in the construction of novel synthetic protein architectures with emergent functional properties. Protein assemblies in nature are formed via selective association of multiple protein surfaces through intricate noncovalent protein-protein interactions, a challenging task to accurately replicate in the de novo design of multiprotein systems. In this protocol, we describe the application of metal-coordinating hydroxamate (HA) motifs to direct the metal-mediated assembly of polyhedral protein architectures and 3D crystalline protein-metal-organic frameworks (protein-MOFs). This strategy has been implemented using an asymmetric cytochrome cb562 monomer through selective, concurrent association of Fe3+ and Zn2+ ions to form polyhedral cages. Furthermore, the use of ditopic HA linkers as bridging ligands with metal-binding protein nodes has allowed the construction of crystalline 3D protein-MOF lattices. The protocol is divided into two major sections: (1) the development of a Cys-reactive HA molecule for protein derivatization and self-assembly of protein-HA conjugates into polyhedral cages and (2) the synthesis of ditopic HA bridging ligands for the construction of ferritin-based protein-MOFs using symmetric metal-binding protein nodes. Protein cages are analyzed using analytical ultracentrifugation, transmission electron microscopy and single-crystal X-ray diffraction techniques. HA-mediated protein-MOFs are formed in sitting-drop vapor diffusion crystallization trays and are probed via single-crystal X-ray diffraction and multi-crystal small-angle X-ray scattering measurements. Ligand synthesis, construction of HA-mediated assemblies, and post-assembly analysis as described in this protocol can be performed by a graduate-level researcher within 6 weeks.
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Affiliation(s)
- Rohit H Subramanian
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Jie Zhu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Jake B Bailey
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Jerika A Chiong
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Eyal Golub
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA. .,Materials Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
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30
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Daneshian L, Schlachter C, Timmers LFSM, Radford T, Kapingidza B, Dias T, Liese J, Sperotto RA, Grbic V, Grbic M, Chruszcz M. Delta class glutathione S-transferase (TuGSTd01) from the two-spotted spider mite Tetranychus urticae is inhibited by abamectin. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 176:104873. [PMID: 34119218 DOI: 10.1016/j.pestbp.2021.104873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
GSTs (Glutathione S-transferases) are known to catalyze the nucleophilic attack of the sulfhydryl group of reduced glutathione (GSH) on electrophilic centers of xenobiotic compounds, including insecticides and acaricides. Genome analyses of the polyphagous spider mite herbivore Tetranychus urticae (two-spotted spider mite) revealed the presence of a set of 32 genes that code for secreted proteins belonging to the GST family of enzymes. To better understand the role of these proteins in T. urticae, we have functionally characterized TuGSTd01. Moreover, we have modeled the structure of the enzyme in apo form, as well as in the form with bound inhibitor. We demonstrated that this protein is a glutathione S-transferase that can conjugate glutathione to 1-chloro-2,4-dinitrobenzene (CDNB). We have tested TuGSTd01 activity with a range of potential substrates such as cinnamic acid, cumene hydroperoxide, and allyl isothiocyanate; however, the enzyme was unable to process these compounds. Using mutagenesis, we showed that putative active site variants S11A, E66A, S67A, and R68A mutants, which were residues predicted to interact directly with GSH, have no measurable activity, and these residues are required for the enzymatic activity of TuGSTd01. There are several reports that associate some T. urticae acaricide resistance with increased activity of GSTs . However, we found that TuGSTd01 is not able to detoxify abamectin; in fact, the acaricide inhibits the enzyme with Ki = 101 μM. Therefore, we suggest that the increased GST activity observed in abamectin resistant T. urticae field populations is a part of the compensatory feedback loop. In this case, the increased production of GSTs and relatively high concentration of GSH in cells allow GSTs to maintain physiological functions despite the presence of the acaricide.
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Affiliation(s)
- Leily Daneshian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Caleb Schlachter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | | | - Taylor Radford
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Brenda Kapingidza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Travis Dias
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Jana Liese
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Raul Antonio Sperotto
- Graduate Program in Biotechnology, University of Taquari Valley - Univates, Lajeado, Rio Grande do Sul, Brazil
| | - Vojislava Grbic
- Department of Biology, Western University, London, Ontario N6A 5B7, Canada; The University of La Rioja, Logrono, Spain
| | - Miodrag Grbic
- Department of Biology, Western University, London, Ontario N6A 5B7, Canada; The University of La Rioja, Logrono, Spain
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
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Chesterman C, Arnold E. Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry. Structure 2021; 29:598-605.e3. [PMID: 33636101 PMCID: PMC8178225 DOI: 10.1016/j.str.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 10/05/2020] [Accepted: 02/08/2021] [Indexed: 01/09/2023]
Abstract
This work presents a method for introducing synthetic symmetry into protein crystallization samples using an antibody fragment termed a diabody (Dab). These Dabs contain two target binding sites, and engineered disulfide bonds have been included to modulate Dab flexibility. The impacts of Dab engineering have been observed through assessment of thermal stability, small-angle X-ray scattering, and high-resolution crystal structures. Complexes between the engineered Dabs and HIV-1 reverse transcriptase (RT) bound to a high-affinity DNA aptamer were also generated to explore the capacity of engineered Dabs to enable the crystallization of bound target proteins. This strategy increased the crystallization hit frequency obtained for RT-aptamer, and the structure of a Dab-RT-aptamer complex was determined to 3.0-Å resolution. Introduction of synthetic symmetry using a Dab could be a broadly applicable strategy, especially when monoclonal antibodies for a target have previously been identified.
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Affiliation(s)
- Chelsy Chesterman
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA; GSK, Rockville, MD 20850, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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Structural Basis for the Diminished Ligand Binding and Catalytic Ability of Human Fetal-Specific CYP3A7. Int J Mol Sci 2021; 22:ijms22115831. [PMID: 34072457 PMCID: PMC8198134 DOI: 10.3390/ijms22115831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 3A7 (CYP3A7) is a fetal/neonatal liver enzyme that participates in estriol synthesis, clearance of all-trans retinoic acid, and xenobiotic metabolism. Compared to the closely related major drug-metabolizing enzyme in adult liver, CYP3A4, the ligand binding and catalytic capacity of CYP3A7 are substantially reduced. To better understand the structural basis for these functional differences, the 2.15 Å crystal structure of CYP3A7 has been solved. Comparative analysis of CYP3A enzymes shows that decreased structural plasticity rather than the active site microenvironment defines the ligand binding ability of CYP3A7. In particular, a rotameric switch in the gatekeeping amino acid F304 triggers local and long-range rearrangements that transmit to the F-G fragment and alter its interactions with the I-E-D-helical core, resulting in a more rigid structure. Elongation of the β3-β4 strands, H-bond linkage in the substrate channel, and steric constraints in the C-terminal loop further increase the active site rigidity and limit conformational ensemble. Collectively, these structural distinctions lower protein plasticity and change the heme environment, which, in turn, could impede the spin-state transition essential for optimal reactivity and oxidation of substrates.
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33
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Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts. CRYSTALS 2021. [DOI: 10.3390/cryst11060588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein crystallization can function as an effective method for protein purification or formulation. Such an application requires a comprehensive understanding of the intermolecular protein–protein interactions that drive and stabilize protein crystal formation to ensure a reproducible process. Using alcohol dehydrogenase from Lactobacillus brevis (LbADH) as a model system, we probed in our combined experimental and computational study the effect of residue substitutions at the protein crystal contacts on the crystallizability and the contact stability. Increased or decreased contact stability was calculated using molecular dynamics (MD) free energy simulations and showed excellent qualitative correlation with experimentally determined increased or decreased crystallizability. The MD simulations allowed us to trace back the changes to their physical origins at the atomic level. Engineered charge–charge interactions as well as engineered hydrophobic effects could be characterized and were found to improve crystallizability. For example, the simulations revealed a redesigning of a water mediated electrostatic interaction (“wet contact”) into a water depleted hydrophobic effect (“dry contact”) and the optimization of a weak hydrogen bonding contact towards a strong one. These findings explained the experimentally found improved crystallizability. Our study emphasizes that it is difficult to derive simple rules for engineering crystallizability but that free energy simulations could be a very useful tool for understanding the contribution of crystal contacts for stability and furthermore could help guide protein engineering strategies to enhance crystallization for technical purposes.
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Manakova E, Mikutenaite M, Golovenko D, Gražulis S, Tamulaitiene G. Crystal structure of restriction endonuclease Kpn2I of CCGG-family. Biochim Biophys Acta Gen Subj 2021; 1865:129926. [PMID: 33965438 DOI: 10.1016/j.bbagen.2021.129926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/02/2021] [Accepted: 05/04/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Restriction endonucleases belong to prokaryotic restriction-modification systems, that protect host cells from invading DNA. Type II restriction endonucleases recognize short 4-8 bp sequences in the target DNA and cut both DNA strands producing double strand breaks. Type II restriction endonuclease Kpn2I cleaves 5'-T/CCGGA DNA sequence ("/" marks the cleavage position). Analysis of protein sequences suggested that Kpn2I belongs to the CCGG-family, which contains ten enzymes that recognize diverse nucleotides outside the conserved 5'-CCGG core and share similar motifs for the 5'-CCGG recognition and cleavage. METHODS We solved a crystal structure of Kpn2I in a DNA-free form at 2.88 Å resolution. From the crystal structure we predicted active center and DNA recognition residues and tested them by mutational analysis. We estimated oligomeric state of Kpn2I by SEC-MALS and performed plasmid DNA cleavage assay to elucidate DNA cleavage mechanism. RESULTS Structure comparison confirmed that Kpn2I shares a conserved active site and structural determinants for the 5'-CCGG tetranucleotide recognition with other restriction endonucleases of the CCGG-family. Guided by structural similarity between Kpn2I and the CCGG-family restriction endonucleases PfoI and AgeI, Kpn2I residues involved in the outer base pair recognition were proposed. CONCLUSIONS Kpn2I is an orthodox Type IIP restriction endonuclease, which acts as a dimer. Kpn2I shares structural similarity to the CCGG-family restriction endonucleases PfoI, AgeI and PspGI. GENERAL SIGNIFICANCE The Kpn2I structure concluded the studies of the CCGG-family, covering detailed structural and biochemical characterization of eleven restriction enzymes and their complexes with DNA.
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Affiliation(s)
- Elena Manakova
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Migle Mikutenaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Dmitrij Golovenko
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Saulius Gražulis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania.
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Gogl G, Tugaeva KV, Eberling P, Kostmann C, Trave G, Sluchanko NN. Hierarchized phosphotarget binding by the seven human 14-3-3 isoforms. Nat Commun 2021; 12:1677. [PMID: 33723253 PMCID: PMC7961048 DOI: 10.1038/s41467-021-21908-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
The seven 14-3-3 isoforms are highly abundant human proteins encoded by similar yet distinct genes. 14-3-3 proteins recognize phosphorylated motifs within numerous human and viral proteins. Here, we analyze by X-ray crystallography, fluorescence polarization, mutagenesis and fusicoccin-mediated modulation the structural basis and druggability of 14-3-3 binding to four E6 oncoproteins of tumorigenic human papillomaviruses. 14-3-3 isoforms bind variant and mutated phospho-motifs of E6 and unrelated protein RSK1 with different affinities, albeit following an ordered affinity ranking with conserved relative KD ratios. Remarkably, 14-3-3 isoforms obey the same hierarchy when binding to most of their established targets, as supported by literature and a recent human complexome map. This knowledge allows predicting proportions of 14-3-3 isoforms engaged with phosphoproteins in various tissues. Notwithstanding their individual functions, cellular concentrations of 14-3-3 may be collectively adjusted to buffer the strongest phosphorylation outbursts, explaining their expression variations in different tissues and tumors.
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Affiliation(s)
- Gergo Gogl
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France.
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Pascal Eberling
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Camille Kostmann
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Gilles Trave
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
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36
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Chung IYW, Li L, Tyurin O, Gagarinova A, Wibawa R, Li P, Hartland EL, Cygler M. Structural and functional study of Legionella pneumophila effector RavA. Protein Sci 2021; 30:940-955. [PMID: 33660322 DOI: 10.1002/pro.4057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 01/20/2023]
Abstract
Legionella pneumophila is an intracellular pathogen that causes Legionnaire's disease in humans. This bacterium can be found in freshwater environments as a free-living organism, but it is also an intracellular parasite of protozoa. Human infection occurs when inhaled aerosolized pathogen comes into contact with the alveolar mucosa and replicates in alveolar macrophages. Legionella enters the host cell by phagocytosis and redirects the Legionella-containing phagosomes from the phagocytic maturation pathway. These nascent phagosomes fuse with ER-derived secretory vesicles and membranes forming the Legionella-containing vacuole. Legionella subverts many host cellular processes by secreting over 300 effector proteins into the host cell via the Dot/Icm type IV secretion system. The cellular function for many Dot/Icm effectors is still unknown. Here, we present a structural and functional study of L. pneumophila effector RavA (Lpg0008). Structural analysis revealed that the RavA consists of four ~85 residue long α-helical domains with similar folds, which show only a low level of structural similarity to other protein domains. The ~90 residues long C-terminal segment is predicted to be natively unfolded. We show that during L. pneumophila infection of human cells, RavA localizes to the Golgi apparatus and to the plasma membrane. The same localization is observed when RavA is expressed in human cells. The localization signal resides within the C-terminal sequence C409 WTSFCGLF417 . Yeast-two-hybrid screen using RavA as bait identified RAB11A as a potential binding partner. RavA is present in L. pneumophila strains but only distant homologs are found in other Legionella species, where the number of repeats varies.
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Affiliation(s)
- Ivy Y W Chung
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lei Li
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Oleg Tyurin
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Symvivo Corporation, Burnaby, British Columbia, Canada
| | - Alla Gagarinova
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Raissa Wibawa
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, and Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Pengfei Li
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, and Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Elizabeth L Hartland
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, and Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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37
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Yan R, Wang W, Vuong TV, Xiu Y, Skarina T, Di Leo R, Gatenholm P, Toriz G, Tenkanen M, Stogios PJ, Master ER. Structural characterization of the family GH115 α-glucuronidase from Amphibacillus xylanus yields insight into its coordinated action with α-arabinofuranosidases. N Biotechnol 2021; 62:49-56. [PMID: 33486119 DOI: 10.1016/j.nbt.2021.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 01/01/2023]
Abstract
The coordinated action of carbohydrate-active enzymes has mainly been evaluated for the purpose of complete saccharification of plant biomass (lignocellulose) to sugars. By contrast, the coordinated action of accessory hemicellulases on xylan debranching and recovery is less well characterized. Here, the activity of two family GH115 α-glucuronidases (SdeAgu115A from Saccharophagus degradans, and AxyAgu115A from Amphibacillus xylanus) on spruce arabinoglucuronoxylan (AGX) was evaluated in combination with an α-arabinofuranosidase from families GH51 (AniAbf51A, aka E-AFASE from Aspergillus niger) and GH62 (SthAbf62A from Streptomyces thermoviolaceus). The α-arabinofuranosidases boosted (methyl)-glucuronic acid release by SdeAgu115A by approximately 50 % and 30 %, respectively. The impact of the α-arabinofuranosidases on AxyAgu115A activity was comparatively low, motivating its structural characterization. The crystal structure of AxyAgu115A revealed increased length and flexibility of the active site loop compared to SdeAgu115A. This structural difference could explain the ability of AxyAgu115A to accommodate more highly substituted arabinoglucuronoxylan, and inform enzyme selections for improved AGX recovery and use.
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Affiliation(s)
- Ruoyu Yan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Yang Xiu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Paul Gatenholm
- Department of Chemistry and Chemical Engineering, Wallenberg Wood Science Center and Biopolymer Technology, Chalmers University of Technology, Kemivägen 4, Gothenburg, 412 96, Sweden
| | - Guillermo Toriz
- Department of Wood, Cellulose and Paper Research, University of Guadalajara, Guadalajara, 44100, Mexico
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki, 00014, Finland
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada; Department of Bioproducts and Biosystems, Aalto University, FI-00076, Aalto, Kemistintie 1, Espoo, Finland.
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Shah M, Taylor VL, Bona D, Tsao Y, Stanley SY, Pimentel-Elardo SM, McCallum M, Bondy-Denomy J, Howell PL, Nodwell JR, Davidson AR, Moraes TF, Maxwell KL. A phage-encoded anti-activator inhibits quorum sensing in Pseudomonas aeruginosa. Mol Cell 2021; 81:571-583.e6. [PMID: 33412111 DOI: 10.1016/j.molcel.2020.12.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/19/2020] [Accepted: 12/03/2020] [Indexed: 11/28/2022]
Abstract
The arms race between bacteria and phages has led to the evolution of diverse anti-phage defenses, several of which are controlled by quorum-sensing pathways. In this work, we characterize a quorum-sensing anti-activator protein, Aqs1, found in Pseudomonas phage DMS3. We show that Aqs1 inhibits LasR, the master regulator of quorum sensing, and present the crystal structure of the Aqs1-LasR complex. The 69-residue Aqs1 protein also inhibits PilB, the type IV pilus assembly ATPase protein, which blocks superinfection by phages that require the pilus for infection. This study highlights the remarkable ability of small phage proteins to bind multiple host proteins and disrupt key biological pathways. As quorum sensing influences various anti-phage defenses, Aqs1 provides a mechanism by which infecting phages might simultaneously dampen multiple defenses. Because quorum-sensing systems are broadly distributed across bacteria, this mechanism of phage counter-defense may play an important role in phage-host evolutionary dynamics.
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Affiliation(s)
- Megha Shah
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Véronique L Taylor
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Diane Bona
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Yvonne Tsao
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Sabrina Y Stanley
- Department of Molecular Genetics, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Sheila M Pimentel-Elardo
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Matthew McCallum
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - P Lynne Howell
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Molecular Genetics, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
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Cockburn DW, Cerqueira FM, Bahr C, Koropatkin NM. The structures of the GH13_36 amylases from Eubacterium rectale and Ruminococcus bromii reveal subsite architectures that favor maltose production. ACTA ACUST UNITED AC 2020. [DOI: 10.1515/amylase-2020-0003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractBacteria in the human gut including Ruminococcus bromii and Eubacterium rectale encode starch-active enzymes that dictate how these bacteria interact with starch to initiate a metabolic cascade that leads to increased butyrate. Here, we determined the structures of two predicted secreted glycoside hydrolase 13 subfamily 36 (GH13_36) enzymes: ErAmy13B complexed with maltotetraose from E. rectale and RbAmy5 from R. bromii. The structures show a limited binding pocket extending from –2 through +2 subsites with limited possibilities for substrate interaction beyond this, which contributes to the propensity for members of this family to produce maltose as their main product. The enzyme structures reveal subtle differences in the +1/+2 subsites that may restrict the recognition of larger starch polymers by ErAmy13B. Our bioinformatic analysis of the biochemically characterized members of the GH13_36 subfamily, which includes the cell-surface GH13 SusG from Bacteroides thetaiotaomicron, suggests that these maltogenic amylases (EC 3.2.1.133) are usually localized to the outside of the cell, display a range of substrate preferences, and most likely contribute to maltose liberation at the cell surface during growth on starch. A broader comparison between GH13_36 and other maltogenic amylase subfamilies explain how the activity profiles of these enzymes are influenced by their structures.
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Affiliation(s)
- Darrell W. Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Food Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Filipe M. Cerqueira
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Constance Bahr
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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40
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Zhang Y, Prach LM, O'Brien TE, DiMaio F, Prigozhin DM, Corn JE, Alber T, Siegel JB, Tantillo DJ. Crystal Structure and Mechanistic Molecular Modeling Studies of Mycobacterium tuberculosis Diterpene Cyclase Rv3377c. Biochemistry 2020; 59:4507-4515. [PMID: 33182997 DOI: 10.1021/acs.biochem.0c00762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Terpenes make up the largest class of natural products, with extensive chemical and structural diversity. Diterpenes, mostly isolated from plants and rarely prokaryotes, exhibit a variety of important biological activities and valuable applications, including providing antitumor and antibiotic pharmaceuticals. These natural products are constructed by terpene synthases, a class of enzymes that catalyze one of the most complex chemical reactions in biology: converting simple acyclic oligo-isoprenyl diphosphate substrates to complex polycyclic products via carbocation intermediates. Here we obtained the second ever crystal structure of a class II diterpene synthase from bacteria, tuberculosinol pyrophosphate synthase (i.e., Halimadienyl diphosphate synthase, MtHPS, or Rv3377c) from Mycobacterium tuberculosis (Mtb). This enzyme transforms (E,E,E)-geranylgeranyl diphosphate into tuberculosinol pyrophosphate (Halimadienyl diphosphate). Rv3377c is part of the Mtb diterpene pathway along with Rv3378c, which converts tuberculosinol pyrophosphate to 1-tuberculosinyl adenosine (1-TbAd). This pathway was shown to exist only in virulent Mycobacterium species, but not in closely related avirulent species, and was proposed to be involved in phagolysosome maturation arrest. To gain further insight into the reaction pathway and the mechanistically relevant enzyme substrate binding orientation, electronic structure calculation and docking studies of reaction intermediates were carried out. Results reveal a plausible binding mode of the substrate that can provide the information to guide future drug design and anti-infective therapies of this biosynthetic pathway.
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Affiliation(s)
- Yue Zhang
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Lisa M Prach
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Terrence E O'Brien
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jacob E Corn
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tom Alber
- Department of Molecular & Cell Biology and QB3 Institute, University of California, Berkeley, California 94720, United States
| | - Justin B Siegel
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States.,Department of Biochemistry and Molecular Medicine, University of California-Davis, Davis, California 95616, United States.,Genome Center, University of California-Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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42
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High-resolution crystal structure and biochemical characterization of a GH11 endoxylanase from Nectria haematococca. Sci Rep 2020; 10:15658. [PMID: 32973265 PMCID: PMC7519127 DOI: 10.1038/s41598-020-72644-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/28/2020] [Indexed: 11/08/2022] Open
Abstract
Enzymatic degradation of vegetal biomass offers versatile procedures to improve the production of alternative fuels and other biomass-based products. Here we present the three-dimensional structure of a xylanase from Nectria haematococca (NhGH11) at 1.0 Å resolution and its functional properties. The atomic resolution structure provides details and insights about the complex hydrogen bonding network of the active site region and allowed a detailed comparison with homologous structures. Complementary biochemical studies showed that the xylanase can catalyze the hydrolysis of complex xylan into simple xylose aldopentose subunits of different lengths. NhGH11 can catalyze the efficient breakdown of beechwood xylan, xylan polysaccharide, and wheat arabinoxylan with turnover numbers of 1730.6 ± 318.1 min-1, 1648.2 ± 249.3 min-1 and 2410.8 ± 517.5 min-1 respectively. NhGH11 showed maximum catalytic activity at pH 6.0 and 45 °C. The mesophilic character of NhGH11 can be explained by distinct structural features in comparison to thermophilic GH11 enzymes, including the number of hydrogen bonds, side chain interactions and number of buried water molecules. The enzymatic activity of NhGH11 is not very sensitive to metal ions and chemical reagents that are typically present in associated industrial production processes. The data we present highlights the potential of NhGH11 to be applied in industrial biomass degradation processes.
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43
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Current pivotal strategies leading a difficult target protein to a sample suitable for crystallographic analysis. Biochem Soc Trans 2020; 48:1661-1673. [PMID: 32677661 DOI: 10.1042/bst20200106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/26/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022]
Abstract
Crystallographic structural analysis is an essential method for the determination of protein structure. However, crystallization of a protein of interest is the most difficult process in the analysis. The process is often hampered during the sample preparation, including expression and purification. Even after a sample has been purified, not all candidate proteins crystallize. In this mini-review, the current methodologies used to overcome obstacles encountered during protein crystallization are sorted. Specifically, the strategy for an effective crystallization is compared with a pipeline where various expression hosts and constructs, purification and crystallization conditions, and crystallization chaperones as target-specific binder proteins are assessed by a precrystallization screening. These methodologies are also developed continuously to improve the process. The described methods are useful for sample preparation in crystallographic analysis and other structure determination techniques, such as cryo-electron microscopy.
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Chamberlain TC, Cheung ST, Yoon JSJ, Ming-Lum A, Gardill BR, Shakibakho S, Dzananovic E, Ban F, Samiea A, Jawanda K, Priatel J, Krystal G, Ong CJ, Cherkasov A, Andersen RJ, McKenna SA, Van Petegem F, Mui ALF. Interleukin-10 and Small Molecule SHIP1 Allosteric Regulators Trigger Anti-inflammatory Effects through SHIP1/STAT3 Complexes. iScience 2020; 23:101433. [PMID: 32823063 PMCID: PMC7452241 DOI: 10.1016/j.isci.2020.101433] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/07/2020] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
The anti-inflammatory actions of interleukin-10 (IL10) are thought to be mediated primarily by the STAT3 transcription factor, but pro-inflammatory cytokines such as interleukin-6 (IL6) also act through STAT3. We now report that IL10, but not IL6 signaling, induces formation of a complex between STAT3 and the inositol polyphosphate-5-phosphatase SHIP1 in macrophages. Both SHIP1 and STAT3 translocate to the nucleus in macrophages. Remarkably, sesquiterpenes of the Pelorol family, which we previously described as allosteric activators of SHIP1 phosphatase activity, could induce SHIP1/STAT3 complex formation in cells and mimic the anti-inflammatory action of IL10 in a mouse model of colitis. Using crystallography and docking studies we identified a drug-binding pocket in SHIP1. Our studies reveal new mechanisms of action for both STAT3 and SHIP1 and provide a rationale for use of allosteric SHIP1-activating compounds, which mimic the beneficial anti-inflammatory actions of IL10. Video Abstract
Loss of normal interleukin-10 (IL10) function results in inflammatory diseases IL10 or SHIP1 agonists induce formation of SHIP1/STAT3 complexes SHIP1 Y190 phosphorylation is required for SHIP1/STAT3 complex formation SHIP1 agonists mimic IL10 anti-inflammatory action in a mouse model of colitis
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Affiliation(s)
- Thomas C Chamberlain
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC V6H 3Z6, Canada; Department of Surgery, University of British Columbia, Vancouver, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Sylvia T Cheung
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC V6H 3Z6, Canada; Department of Surgery, University of British Columbia, Vancouver, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Jeff S J Yoon
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC V6H 3Z6, Canada; Department of Surgery, University of British Columbia, Vancouver, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Andrew Ming-Lum
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC V6H 3Z6, Canada; Department of Surgery, University of British Columbia, Vancouver, Canada
| | - Bernd R Gardill
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Soroush Shakibakho
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC V6H 3Z6, Canada; Department of Surgery, University of British Columbia, Vancouver, Canada
| | - Edis Dzananovic
- Department of Chemistry, University of Manitoba, Winnipeg, Canada
| | - Fuqiang Ban
- Department of Urological Sciences, University of British Columbia, Vancouver, Canada
| | - Abrar Samiea
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC V6H 3Z6, Canada; Department of Surgery, University of British Columbia, Vancouver, Canada
| | - Kamaldeep Jawanda
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC V6H 3Z6, Canada; Department of Surgery, University of British Columbia, Vancouver, Canada
| | - John Priatel
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Gerald Krystal
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher J Ong
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC V6H 3Z6, Canada; Department of Surgery, University of British Columbia, Vancouver, Canada; Department of Urological Sciences, University of British Columbia, Vancouver, Canada
| | - Artem Cherkasov
- Department of Urological Sciences, University of British Columbia, Vancouver, Canada
| | - Raymond J Andersen
- Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Alice L-F Mui
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC V6H 3Z6, Canada; Department of Surgery, University of British Columbia, Vancouver, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.
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An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity. Nat Struct Mol Biol 2020; 27:829-835. [PMID: 32719456 DOI: 10.1038/s41594-020-0464-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 06/17/2020] [Indexed: 12/17/2022]
Abstract
Multidrug efflux pumps present a challenge to the treatment of bacterial infections, making it vitally important to understand their mechanism of action. Here, we investigate the nature of substrate binding within Lactococcus lactis LmrP, a prototypical multidrug transporter of the major facilitator superfamily. We determined the crystal structure of LmrP in a ligand-bound outward-open state and observed an embedded lipid in the binding cavity of LmrP, an observation supported by native mass spectrometry analyses. Molecular dynamics simulations suggest that the anionic lipid stabilizes the observed ligand-bound structure. Mutants engineered to disrupt binding of the embedded lipid display reduced transport of some, but not all, antibiotic substrates. Our results suggest that a lipid within the binding cavity could provide a malleable hydrophobic component that allows adaptation to the presence of different substrates, helping to explain the broad specificity of this protein and possibly other multidrug transporters.
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A Sulfoglycolytic Entner-Doudoroff Pathway in Rhizobium leguminosarum bv. trifolii SRDI565. Appl Environ Microbiol 2020; 86:AEM.00750-20. [PMID: 32444469 DOI: 10.1128/aem.00750-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/14/2020] [Indexed: 01/05/2023] Open
Abstract
Rhizobia are nitrogen-fixing bacteria that engage in symbiotic relationships with plant hosts but can also persist as free-living bacteria in the soil and rhizosphere. Here, we show that free-living Rhizobium leguminosarum SRDI565 can grow on the sulfosugar sulfoquinovose (SQ) or the related glycoside SQ-glycerol using a sulfoglycolytic Entner-Doudoroff (sulfo-ED) pathway, resulting in production of sulfolactate (SL) as the major metabolic end product. Comparative proteomics supports the involvement of a sulfo-ED operon encoding an ABC transporter, sulfo-ED enzymes, and an SL exporter. Consistent with an oligotrophic lifestyle, proteomics data revealed little change in expression of the sulfo-ED proteins during growth on SQ versus mannitol, a result confirmed through biochemical assay of sulfoquinovosidase activity in cell lysates. Metabolomics analysis showed that growth on SQ involves gluconeogenesis to satisfy metabolic requirements for glucose-6-phosphate and fructose-6-phosphate. Metabolomics analysis also revealed the unexpected production of small amounts of sulfofructose and 2,3-dihydroxypropanesulfonate, which are proposed to arise from promiscuous activities of the glycolytic enzyme phosphoglucose isomerase and a nonspecific aldehyde reductase, respectively. The discovery of a rhizobium isolate with the ability to degrade SQ builds our knowledge of how these important symbiotic bacteria persist within soil.IMPORTANCE Sulfonate sulfur is a major form of organic sulfur in soils but requires biomineralization before it can be utilized by plants. Very little is known about the biochemical processes used to mobilize sulfonate sulfur. We show that a rhizobial isolate from soil, Rhizobium leguminosarum SRDI565, possesses the ability to degrade the abundant phototroph-derived carbohydrate sulfonate SQ through a sulfoglycolytic Entner-Doudoroff pathway. Proteomics and metabolomics demonstrated the utilization of this pathway during growth on SQ and provided evidence for gluconeogenesis. Unexpectedly, off-cycle sulfoglycolytic species were also detected, pointing to the complexity of metabolic processes within cells under conditions of sulfoglycolysis. Thus, rhizobial metabolism of the abundant sulfosugar SQ may contribute to persistence of the bacteria in the soil and to mobilization of sulfur in the pedosphere.
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Design, expression, purification and crystallization of human 14-3-3ζ protein chimera with phosphopeptide from proapoptotic protein BAD. Protein Expr Purif 2020; 175:105707. [PMID: 32682909 DOI: 10.1016/j.pep.2020.105707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/02/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
14-3-3 protein isoforms regulate multiple processes in eukaryotes, including apoptosis and cell division. 14-3-3 proteins preferentially recognize phosphorylated unstructured motifs, justifying the protein-peptide binding approach to study 14-3-3/phosphotarget complexes. Tethering of human 14-3-3σ with partner phosphopeptides via a short linker has provided structural information equivalent to the use of synthetic phosphopeptides, simultaneously facilitating purification and crystallization. Nevertheless, the broader applicability to other 14-3-3 isoforms and phosphopeptides was unclear. Here, we designed a novel 14-3-3ζ chimera with a conserved phosphopeptide from BAD, whose complex with 14-3-3 is a gatekeeper of apoptosis regulation. The chimera could be bacterially expressed and purified without affinity tags. Co-expressed PKA efficiently phosphorylates BAD within the chimera and blocks its interaction with a known 14-3-3 phosphotarget, suggesting occupation of the 14-3-3 grooves by the tethered BAD phosphopeptide. Efficient crystallization of the engineered protein suggests suitability of the "chimeric" approach for studies of other relevant 14-3-3 complexes.
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48
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Jones CS, Sychantha D, Howell PL, Clarke AJ. Structural basis for the O-acetyltransferase function of the extracytoplasmic domain of OatA from Staphylococcus aureus. J Biol Chem 2020; 295:8204-8213. [PMID: 32350117 DOI: 10.1074/jbc.ra120.013108] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/27/2020] [Indexed: 02/03/2023] Open
Abstract
Many bacteria possess enzymes that modify the essential cell-wall polymer peptidoglycan by O-acetylation. This modification occurs in numerous Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus, a common cause of human infections. O-Acetylation of peptidoglycan protects bacteria from the lytic activity of lysozyme, a mammalian innate immune enzyme, and as such is important for bacterial virulence. The O-acetylating enzyme in Gram-positive bacteria, O-acetyltransferase A (OatA), is a two-domain protein consisting of an N-terminal integral membrane domain and a C-terminal extracytoplasmic domain. Here, we present the X-ray crystal structure at 1.71 Å resolution and the biochemical characterization of the C-terminal domain of S. aureus OatA. The structure revealed that this OatA domain adopts an SGNH-hydrolase fold and possesses a canonical catalytic triad. Site-specific replacement of active-site amino acids revealed the presence of a water-coordinating aspartate residue that limits esterase activity. This residue, although conserved in staphyloccocal OatA and most other homologs, is not present in the previously characterized streptococcal OatA. These results provide insights into the mechanism of acetyl transfer in the SGNH/GDSL hydrolase family and highlight important evolutionary differences between homologous OatA enzymes. Furthermore, this study enhances our understanding of PG O-acetyltransferases, which could guide the development of novel antibacterial drugs to combat infections with multidrug-resistant bacterial pathogens.
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Affiliation(s)
- Carys S Jones
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - David Sychantha
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Anthony J Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada .,Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada
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Klünemann T, Henke S, Blankenfeldt W. The crystal structure of the heme d 1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo. Acta Crystallogr D Struct Biol 2020; 76:375-384. [PMID: 32254062 PMCID: PMC7137109 DOI: 10.1107/s2059798320003101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/05/2020] [Indexed: 11/10/2022] Open
Abstract
Monoheme c-type cytochromes are important electron transporters in all domains of life. They possess a common fold hallmarked by three α-helices that surround a covalently attached heme. An intriguing feature of many monoheme c-type cytochromes is their capacity to form oligomers by exchanging at least one of their α-helices, which is often referred to as 3D domain swapping. Here, the crystal structure of NirC, a c-type cytochrome co-encoded with other proteins involved in nitrite reduction by the opportunistic pathogen Pseudomonas aeruginosa, has been determined. The crystals diffracted anisotropically to a maximum resolution of 2.12 Å (spherical resolution of 2.83 Å) and initial phases were obtained by Fe-SAD phasing, revealing the presence of 11 NirC chains in the asymmetric unit. Surprisingly, these protomers arrange into one monomer and two different types of 3D domain-swapped dimers, one of which shows pronounced asymmetry. While the simultaneous observation of monomers and dimers probably reflects the interplay between the high protein concentration required for crystallization and the structural plasticity of monoheme c-type cytochromes, the identification of conserved structural motifs in the monomer together with a comparison with similar proteins may offer new leads to unravel the unknown function of NirC.
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Affiliation(s)
- Thomas Klünemann
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Steffi Henke
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
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50
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Barczewski AH, Ragusa MJ, Mierke DF, Pellegrini M. Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO. J Vis Exp 2019. [PMID: 31929506 DOI: 10.3791/60339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
NEMO is a scaffolding protein which plays an essential role in the NF-κB pathway by assembling the IKK-complex with the kinases IKKα and IKKβ. Upon activation, the IKK complex phosphorylates the IκB molecules leading to NF-κB nuclear translocation and activation of target genes. Inhibition of the NEMO/IKK interaction is an attractive therapeutic paradigm for the modulation of NF-κB pathway activity, making NEMO a target for inhibitors design and discovery. To facilitate the process of discovery and optimization of NEMO inhibitors, we engineered an improved construct of the IKK-binding domain of NEMO that would allow for structure determination of the protein in the apo form and while bound to small molecular weight inhibitors. Here, we present the strategy utilized for the design, expression and structural characterization of the IKK-binding domain of NEMO. The protein is expressed in E. coli cells, solubilized under denaturing conditions and purified through three chromatographic steps. We discuss the protocols for obtaining crystals for structure determination and describe data acquisition and analysis strategies. The protocols will find wide applicability to the structure determination of complexes of NEMO and small molecule inhibitors.
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