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Long-range structural defects by pathogenic mutations in most severe glucose-6-phosphate dehydrogenase deficiency. Proc Natl Acad Sci U S A 2021; 118:2022790118. [PMID: 33468660 PMCID: PMC7848525 DOI: 10.1073/pnas.2022790118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mechanism of the loss of activity of the most severe patient-derived mutants of glucose-6-phosphate dehydrogenase (G6PD) deficiency has remained elusive despite the availability of the G6PD structures for decades. Structural and biophysical investigations have revealed a common mechanism and dynamics of how these mutations hinder the substrate-binding site, reducing enzymatic activity. These are triggered by a long-distance propagation of structural defects at the dimer interface and the binding site of the noncatalytic cofactor. These structural distortions are found among all of the class I mutants investigated, providing critical clues for drug design to address G6PD deficiency by correcting the structural defects. Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common blood disorder, presenting multiple symptoms, including hemolytic anemia. It affects 400 million people worldwide, with more than 160 single mutations reported in G6PD. The most severe mutations (about 70) are classified as class I, leading to more than 90% loss of activity of the wild-type G6PD. The crystal structure of G6PD reveals these mutations are located away from the active site, concentrating around the noncatalytic NADP+-binding site and the dimer interface. However, the molecular mechanisms of class I mutant dysfunction have remained elusive, hindering the development of efficient therapies. To resolve this, we performed integral structural characterization of five G6PD mutants, including four class I mutants, associated with the noncatalytic NADP+ and dimerization, using crystallography, small-angle X-ray scattering (SAXS), cryogenic electron microscopy (cryo-EM), and biophysical analyses. Comparisons with the structure and properties of the wild-type enzyme, together with molecular dynamics simulations, bring forward a universal mechanism for this severe G6PD deficiency due to the class I mutations. We highlight the role of the noncatalytic NADP+-binding site that is crucial for stabilization and ordering two β-strands in the dimer interface, which together communicate these distant structural aberrations to the active site through a network of additional interactions. This understanding elucidates potential paths for drug development targeting G6PD deficiency.
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52
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Absmeier E, Vester K, Ghane T, Burakovskiy D, Milon P, Imhof P, Rodnina MV, Santos KF, Wahl MC. Long-range allostery mediates cooperative adenine nucleotide binding by the Ski2-like RNA helicase Brr2. J Biol Chem 2021; 297:100829. [PMID: 34048711 PMCID: PMC8220420 DOI: 10.1016/j.jbc.2021.100829] [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: 01/28/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022] Open
Abstract
Brr2 is an essential Ski2-like RNA helicase that exhibits a unique structure among the spliceosomal helicases. Brr2 harbors a catalytically active N-terminal helicase cassette and a structurally similar but enzymatically inactive C-terminal helicase cassette connected by a linker region. Both cassettes contain a nucleotide-binding pocket, but it is unclear whether nucleotide binding in these two pockets is related. Here we use biophysical and computational methods to delineate the functional connectivity between the cassettes and determine whether occupancy of one nucleotide-binding site may influence nucleotide binding at the other cassette. Our results show that Brr2 exhibits high specificity for adenine nucleotides, with both cassettes binding ADP tighter than ATP. Adenine nucleotide affinity for the inactive C-terminal cassette is more than two orders of magnitude higher than that of the active N-terminal cassette, as determined by slow nucleotide release. Mutations at the intercassette surfaces and in the connecting linker diminish the affinity of adenine nucleotides for both cassettes. Moreover, we found that abrogation of nucleotide binding at the C-terminal cassette reduces nucleotide binding at the N-terminal cassette 70 Å away. Molecular dynamics simulations identified structural communication lines that likely mediate these long-range allosteric effects, predominantly across the intercassette interface. Together, our results reveal intricate networks of intramolecular interactions in the complex Brr2 RNA helicase, which fine-tune its nucleotide affinities and which could be exploited to regulate enzymatic activity during splicing.
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Affiliation(s)
- Eva Absmeier
- Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Karen Vester
- Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Tahereh Ghane
- Computational Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Dmitry Burakovskiy
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Pohl Milon
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Petra Imhof
- Computational Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Karine F Santos
- Structural Biochemistry, Freie Universität Berlin, Berlin, Germany.
| | - Markus C Wahl
- Structural Biochemistry, Freie Universität Berlin, Berlin, Germany; Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany.
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53
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Saxton RA, Henneberg LT, Calafiore M, Su L, Jude KM, Hanash AM, Garcia KC. The tissue protective functions of interleukin-22 can be decoupled from pro-inflammatory actions through structure-based design. Immunity 2021; 54:660-672.e9. [PMID: 33852830 PMCID: PMC8054646 DOI: 10.1016/j.immuni.2021.03.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/17/2021] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Interleukin-22 (IL-22) acts on epithelial cells to promote tissue protection and regeneration, but can also elicit pro-inflammatory effects, contributing to disease pathology. Here, we engineered a high-affinity IL-22 super-agonist that enabled the structure determination of the IL-22-IL-22Rα-IL-10Rβ ternary complex to a resolution of 2.6 Å. Using structure-based design, we systematically destabilized the IL-22-IL-10Rβ binding interface to create partial agonist analogs that decoupled downstream STAT1 and STAT3 signaling. The extent of STAT bias elicited by a single ligand varied across tissues, ranging from full STAT3-biased agonism to STAT1/3 antagonism, correlating with IL-10Rβ expression levels. In vivo, this tissue-selective signaling drove tissue protection in the pancreas and gastrointestinal tract without inducing local or systemic inflammation, thereby uncoupling these opposing effects of IL-22 signaling. Our findings provide insight into the mechanisms underlying the cytokine pleiotropy and illustrate how differential receptor expression levels and STAT response thresholds can be synthetically exploited to endow pleiotropic cytokines with enhanced functional specificity.
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Affiliation(s)
- Robert A Saxton
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Lukas T Henneberg
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Marco Calafiore
- Departments of Medicine, Human Oncology and Pathogenesis Program, and Immunology and Microbial Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY 10065, USA
| | - Leon Su
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Alan M Hanash
- Departments of Medicine, Human Oncology and Pathogenesis Program, and Immunology and Microbial Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY 10065, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA.
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54
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Yu CH, Bhattacharya A, Persaud M, Taylor AB, Wang Z, Bulnes-Ramos A, Xu J, Selyutina A, Martinez-Lopez A, Cano K, Demeler B, Kim B, Hardies SC, Diaz-Griffero F, Ivanov DN. Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification. Nat Commun 2021; 12:731. [PMID: 33531504 PMCID: PMC7854603 DOI: 10.1038/s41467-021-21023-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 01/08/2021] [Indexed: 12/26/2022] Open
Abstract
SAMHD1 impedes infection of myeloid cells and resting T lymphocytes by retroviruses, and the enzymatic activity of the protein-dephosphorylation of deoxynucleotide triphosphates (dNTPs)-implicates enzymatic dNTP depletion in innate antiviral immunity. Here we show that the allosteric binding sites of the enzyme are plastic and can accommodate oligonucleotides in place of the allosteric activators, GTP and dNTP. SAMHD1 displays a preference for oligonucleotides containing phosphorothioate bonds in the Rp configuration located 3' to G nucleotides (GpsN), the modification pattern that occurs in a mechanism of antiviral defense in prokaryotes. In the presence of GTP and dNTPs, binding of GpsN-containing oligonucleotides promotes formation of a distinct tetramer with mixed occupancy of the allosteric sites. Mutations that impair formation of the mixed-occupancy complex abolish the antiretroviral activity of SAMHD1, but not its ability to deplete dNTPs. The findings link nucleic acid binding to the antiretroviral activity of SAMHD1, shed light on the immunomodulatory effects of synthetic phosphorothioated oligonucleotides and raise questions about the role of nucleic acid phosphorothioation in human innate immunity.
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Affiliation(s)
- Corey H Yu
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Akash Bhattacharya
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Mirjana Persaud
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander B Taylor
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Zhonghua Wang
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Angel Bulnes-Ramos
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joella Xu
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | - Anastasia Selyutina
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alicia Martinez-Lopez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kristin Cano
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, USA
| | - Baek Kim
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | - Stephen C Hardies
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Dmitri N Ivanov
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA.
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55
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A Thermophilic Bacterial Esterase for Scavenging Nerve Agents: A Kinetic, Biophysical and Structural Study. Molecules 2021; 26:molecules26030657. [PMID: 33513869 PMCID: PMC7865465 DOI: 10.3390/molecules26030657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/23/2021] [Accepted: 01/23/2021] [Indexed: 12/02/2022] Open
Abstract
Organophosphorous nerve agents (OPNA) pose an actual and major threat for both military and civilians alike, as an upsurge in their use has been observed in the recent years. Currently available treatments mitigate the effect of the nerve agents, and could be vastly improved by means of scavengers of the nerve agents. Consequently, efforts have been made over the years into investigating enzymes, also known as bioscavengers, which have the potential either to trap or hydrolyze these toxic compounds. We investigated the previously described esterase 2 from Thermogutta terrifontis (TtEst2) as a potential bioscavenger of nerve agents. As such, we assessed its potential against G-agents (tabun, sarin, and cyclosarin), VX, as well as the pesticide paraoxon. We report that TtEst2 is a good bioscavenger of paraoxon and G-agents, but is rather slow at scavenging VX. X-ray crystallography studies showed that TtEst2 forms an irreversible complex with the aforementioned agents, and allowed the identification of amino-acids, whose mutagenesis could lead to better scavenging properties for VX. In conjunction with its cheap production and purification processes, as well as a robust structural backbone, further engineering of TtEst2 could lead to a stopgap bioscavenger useful for in corpo scavenging or skin decontamination.
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56
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Torabi SF, Vaidya AT, Tycowski KT, DeGregorio SJ, Wang J, Shu MD, Steitz TA, Steitz JA. RNA stabilization by a poly(A) tail 3'-end binding pocket and other modes of poly(A)-RNA interaction. Science 2021; 371:science.abe6523. [PMID: 33414189 DOI: 10.1126/science.abe6523] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022]
Abstract
Polyadenylate [poly(A)] tail addition to the 3' end of a wide range of RNAs is a highly conserved modification that plays a central role in cellular RNA function. Elements for nuclear expression (ENEs) are cis-acting RNA elements that stabilize poly(A) tails by sequestering them in RNA triplex structures. A crystal structure of a double ENE from a rice hAT transposon messenger RNA complexed with poly(A)28 at a resolution of 2.89 angstroms reveals multiple modes of interaction with poly(A), including major-groove triple helices, extended minor-groove interactions with RNA double helices, a quintuple-base motif that transitions poly(A) from minor-groove associations to major-groove triple helices, and a poly(A) 3'-end binding pocket. Our findings both expand the repertoire of motifs involved in long-range RNA interactions and provide insights into how polyadenylation can protect an RNA's extreme 3' end.
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Affiliation(s)
- Seyed-Fakhreddin Torabi
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Anand T Vaidya
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA.,TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Suzanne J DeGregorio
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Mei-Di Shu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA. .,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
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57
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Shock Damage Analysis in Serial Femtosecond Crystallography Data Collected at MHz X-ray Free-Electron Lasers. CRYSTALS 2020. [DOI: 10.3390/cryst10121145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Serial femtosecond crystallography (SFX) data were recorded at the European X-ray free-electron laser facility (EuXFEL) with protein microcrystals delivered via a microscopic liquid jet. An XFEL beam striking such a jet may launch supersonic shock waves up the jet, compromising the oncoming sample. To investigate this efficiently, we employed a novel XFEL pulse pattern to nominally expose the sample to between zero and four shock waves before being probed. Analyzing hit rate, indexing rate, and resolution for diffraction data recorded at MHz pulse rates, we found no evidence of damage. Notably, however, this conclusion could only be drawn after careful identification and assimilation of numerous interrelated experimental factors, which we describe in detail. Failure to do so would have led to an erroneous conclusion. Femtosecond photography of the sample-carrying jet revealed critically different jet behavior from that of all homogeneous liquid jets studied to date in this manner.
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58
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Di Mattia T, Martinet A, Ikhlef S, McEwen AG, Nominé Y, Wendling C, Poussin-Courmontagne P, Voilquin L, Eberling P, Ruffenach F, Cavarelli J, Slee J, Levine TP, Drin G, Tomasetto C, Alpy F. FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts. EMBO J 2020; 39:e104369. [PMID: 33124732 PMCID: PMC7705450 DOI: 10.15252/embj.2019104369] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 11/13/2022] Open
Abstract
Organelles are physically connected in membrane contact sites. The endoplasmic reticulum possesses three major receptors, VAP‐A, VAP‐B, and MOSPD2, which interact with proteins at the surface of other organelles to build contacts. VAP‐A, VAP‐B, and MOSPD2 contain an MSP domain, which binds a motif named FFAT (two phenylalanines in an acidic tract). In this study, we identified a non‐conventional FFAT motif where a conserved acidic residue is replaced by a serine/threonine. We show that phosphorylation of this serine/threonine is critical for non‐conventional FFAT motifs (named Phospho‐FFAT) to be recognized by the MSP domain. Moreover, structural analyses of the MSP domain alone or in complex with conventional and Phospho‐FFAT peptides revealed new mechanisms of interaction. Based on these new insights, we produced a novel prediction algorithm, which expands the repertoire of candidate proteins with a Phospho‐FFAT that are able to create membrane contact sites. Using a prototypical tethering complex made by STARD3 and VAP, we showed that phosphorylation is instrumental for the formation of ER‐endosome contacts, and their sterol transfer function. This study reveals that phosphorylation acts as a general switch for inter‐organelle contacts.
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Affiliation(s)
- Thomas Di Mattia
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Arthur Martinet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Souade Ikhlef
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, CNRS, Valbonne, France
| | - Alastair G McEwen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Yves Nominé
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Corinne Wendling
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Pierre Poussin-Courmontagne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Laetitia Voilquin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Pascal Eberling
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Frank Ruffenach
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jean Cavarelli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - John Slee
- UCL Institute of Ophthalmology, London, UK
| | | | - Guillaume Drin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, CNRS, Valbonne, France
| | - Catherine Tomasetto
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Fabien Alpy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
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59
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Lolicato M, Natale AM, Abderemane-Ali F, Crottès D, Capponi S, Duman R, Wagner A, Rosenberg JM, Grabe M, Minor DL. K 2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions. SCIENCE ADVANCES 2020; 6:6/44/eabc9174. [PMID: 33127683 PMCID: PMC7608817 DOI: 10.1126/sciadv.abc9174] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/10/2020] [Indexed: 05/05/2023]
Abstract
K2P potassium channels regulate cellular excitability using their selectivity filter (C-type) gate. C-type gating mechanisms, best characterized in homotetrameric potassium channels, remain controversial and are attributed to selectivity filter pinching, dilation, or subtle structural changes. The extent to which such mechanisms control C-type gating of innately heterodimeric K2Ps is unknown. Here, combining K2P2.1 (TREK-1) x-ray crystallography in different potassium concentrations, potassium anomalous scattering, molecular dynamics, and electrophysiology, we uncover unprecedented, asymmetric, potassium-dependent conformational changes that underlie K2P C-type gating. These asymmetric order-disorder transitions, enabled by the K2P heterodimeric architecture, encompass pinching and dilation, disrupt the S1 and S2 ion binding sites, require the uniquely long K2P SF2-M4 loop and conserved "M3 glutamate network," and are suppressed by the K2P C-type gate activator ML335. These findings demonstrate that two distinct C-type gating mechanisms can operate in one channel and underscore the SF2-M4 loop as a target for K2P channel modulator development.
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Affiliation(s)
- Marco Lolicato
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Andrew M Natale
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Fayal Abderemane-Ali
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - David Crottès
- Department of Physiology, University of California, San Francisco, CA 93858-2330, USA
| | - Sara Capponi
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Ramona Duman
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Armin Wagner
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - John M Rosenberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Michael Grabe
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 93858-2330, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA.
- Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 93858-2330, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 93858-2330, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA, 93858-2330, USA
- Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
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60
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Roslova M, Smeets S, Wang B, Thersleff T, Xu H, Zou X. InsteaDMatic: towards cross-platform automated continuous rotation electron diffraction. J Appl Crystallogr 2020; 53:1217-1224. [PMID: 33117109 PMCID: PMC7534539 DOI: 10.1107/s1600576720009590] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/14/2020] [Indexed: 11/26/2022] Open
Abstract
A DigitalMicrograph script named InsteaDMatic has been developed for automated continuous rotation electron diffraction (cRED) data acquisition. InsteaDMatic coordinates functions of the transmission electron microscope goniometer and camera in order to tune up diffraction-frame recording simultaneously with crystal rotation. Exploiting fast and automated data collection, the influence of the electron dose rate on the quality of cRED data was studied, and structural models obtained for two different parallel-beam illumination modes (aperture selection and nanoprobe) were compared. A DigitalMicrograph script, InsteaDMatic, has been developed to facilitate rapid automated 3D electron diffraction/microcrystal electron diffraction data acquisition by continuous rotation of a crystal with a constant speed, denoted as continuous rotation electron diffraction. The script coordinates microscope functions, such as stage rotation, and camera functions relevant for data collection, and stores the experiment metadata. The script is compatible with any microscope that can be controlled by DigitalMicrograph and has been tested on both JEOL and Thermo Fisher Scientific microscopes. A proof of concept has been performed through employing InsteaDMatic for data collection and structure determination of a ZSM-5 zeolite. The influence of illumination settings and electron dose rate on the quality of diffraction data, unit-cell determination and structure solution has been investigated in order to optimize the data acquisition procedure.
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Affiliation(s)
- Maria Roslova
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Stef Smeets
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Bin Wang
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Thomas Thersleff
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
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61
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Watson ZL, Ward FR, Méheust R, Ad O, Schepartz A, Banfield JF, Cate JH. Structure of the bacterial ribosome at 2 Å resolution. eLife 2020; 9:60482. [PMID: 32924932 DOI: 10.1101/2020.06.26.174334] [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: 06/27/2020] [Accepted: 09/11/2020] [Indexed: 05/24/2023] Open
Abstract
Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.
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Affiliation(s)
- Zoe L Watson
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Fred R Ward
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
- Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, United States
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
- Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, United States
| | - Jamie Hd Cate
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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62
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Watson ZL, Ward FR, Méheust R, Ad O, Schepartz A, Banfield JF, Cate JHD. Structure of the bacterial ribosome at 2 Å resolution. eLife 2020; 9:e60482. [PMID: 32924932 PMCID: PMC7550191 DOI: 10.7554/elife.60482] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/11/2020] [Indexed: 12/31/2022] Open
Abstract
Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.
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Affiliation(s)
- Zoe L Watson
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Fred R Ward
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Earth and Planetary Science, University of California, BerkeleyBerkeleyUnited States
| | - Omer Ad
- Department of Chemistry, Yale UniversityNew HavenUnited States
| | - Alanna Schepartz
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Earth and Planetary Science, University of California, BerkeleyBerkeleyUnited States
- Environmental Science, Policy and Management, University of California BerkeleyBerkeleyUnited States
| | - Jamie HD Cate
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
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63
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A chemical interpretation of protein electron density maps in the worldwide protein data bank. PLoS One 2020; 15:e0236894. [PMID: 32785279 PMCID: PMC7423092 DOI: 10.1371/journal.pone.0236894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/15/2020] [Indexed: 11/29/2022] Open
Abstract
High-quality three-dimensional structural data is of great value for the functional interpretation of biomacromolecules, especially proteins; however, structural quality varies greatly across the entries in the worldwide Protein Data Bank (wwPDB). Since 2008, the wwPDB has required the inclusion of structure factors with the deposition of x-ray crystallographic structures to support the independent evaluation of structures with respect to the underlying experimental data used to derive those structures. However, interpreting the discrepancies between the structural model and its underlying electron density data is difficult, since derived sigma-scaled electron density maps use arbitrary electron density units which are inconsistent between maps from different wwPDB entries. Therefore, we have developed a method that converts electron density values from sigma-scaled electron density maps into units of electrons. With this conversion, we have developed new methods that can evaluate specific regions of an x-ray crystallographic structure with respect to a physicochemical interpretation of its corresponding electron density map. We have systematically compared all deposited x-ray crystallographic protein models in the wwPDB with their underlying electron density maps, if available, and characterized the electron density in terms of expected numbers of electrons based on the structural model. The methods generated coherent evaluation metrics throughout all PDB entries with associated electron density data, which are consistent with visualization software that would normally be used for manual quality assessment. To our knowledge, this is the first attempt to derive units of electrons directly from electron density maps without the aid of the underlying structure factors. These new metrics are biochemically-informative and can be extremely useful for filtering out low-quality structural regions from inclusion into systematic analyses that span large numbers of PDB entries. Furthermore, these new metrics will improve the ability of non-crystallographers to evaluate regions of interest within PDB entries, since only the PDB structure and the associated electron density maps are needed. These new methods are available as a well-documented Python package on GitHub and the Python Package Index under a modified Clear BSD open source license.
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64
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Goepfert A, Lehmann S, Blank J, Kolbinger F, Rondeau JM. Structural Analysis Reveals that the Cytokine IL-17F Forms a Homodimeric Complex with Receptor IL-17RC to Drive IL-17RA-Independent Signaling. Immunity 2020; 52:499-512.e5. [PMID: 32187518 DOI: 10.1016/j.immuni.2020.02.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 11/25/2019] [Accepted: 02/18/2020] [Indexed: 12/30/2022]
Abstract
Interleukin-17A (IL-17A), IL-17F, and IL-17A/F heterodimers are key cytokines of the innate and adaptive immune response. Dysregulation of the IL-17 pathway contributes to immune pathology, and it is therefore important to elucidate the molecular mechanisms that govern IL-17 recognition and signaling. The receptor IL-17RC is thought to act in concert with IL-17RA to transduce IL-17A-, IL-17F-, and IL-17A/F-mediated signals. We report the crystal structure of the extracellular domain of human IL-17RC in complex with IL-17F. In contrast to the expected model, we found that IL-17RC formed a symmetrical 2:1 complex with IL-17F, thus competing with IL-17RA for cytokine binding. Using biophysical techniques, we showed that IL-17A and IL-17A/F also form 2:1 complexes with IL-17RC, suggesting the possibility of IL-17RA-independent IL-17 signaling pathways. The crystal structure of the IL-17RC:IL-17F complex provides a structural basis for IL-17F signaling through IL-17RC, with potential therapeutic applications for respiratory allergy and inflammatory bowel diseases.
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Affiliation(s)
- Arnaud Goepfert
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Sylvie Lehmann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Jutta Blank
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Frank Kolbinger
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Jean-Michel Rondeau
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland.
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65
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Malý M, Diederichs K, Dohnálek J, Kolenko P. Paired refinement under the control of PAIREF. IUCRJ 2020; 7:681-692. [PMID: 32695415 PMCID: PMC7340264 DOI: 10.1107/s2052252520005916] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/29/2020] [Indexed: 05/08/2023]
Abstract
Crystallographic resolution is a key characteristic of diffraction data and represents one of the first decisions an experimenter has to make in data evaluation. Conservative approaches to the high-resolution cutoff determination are based on a number of criteria applied to the processed X-ray diffraction data only. However, high-resolution data that are weaker than arbitrary cutoffs can still result in the improvement of electron-density maps and refined structure models. Therefore, the impact of reflections from resolution shells higher than those previously used in conservative structure refinement should be analysed by the paired refinement protocol. For this purpose, a tool called PAIREF was developed to provide automation of this protocol. As a new feature, a complete cross-validation procedure has also been implemented. Here, the design, usage and control of the program are described, and its application is demonstrated on six data sets. The results prove that the inclusion of high-resolution data beyond the conventional criteria can lead to more accurate structure models.
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Affiliation(s)
- Martin Malý
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, Prague 11519, Czech Republic
- Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, Vestec 25250, Czech Republic
| | - Kay Diederichs
- University of Konstanz, Box M647, Konstanz 78457, Germany
| | - Jan Dohnálek
- Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, Vestec 25250, Czech Republic
| | - Petr Kolenko
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, Prague 11519, Czech Republic
- Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, Vestec 25250, Czech Republic
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66
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Abstract
Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.
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67
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Aminobenzosuberone derivatives as PfA-M1 inhibitors: Molecular recognition and antiplasmodial evaluation. Bioorg Chem 2020; 98:103750. [DOI: 10.1016/j.bioorg.2020.103750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/27/2020] [Accepted: 03/09/2020] [Indexed: 12/16/2022]
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68
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Beale EV, Warren AJ, Trincão J, Beilsten-Edmands J, Crawshaw AD, Sutton G, Stuart D, Evans G. Scanning electron microscopy as a method for sample visualization in protein X-ray crystallography. IUCRJ 2020; 7:500-508. [PMID: 32431833 PMCID: PMC7201292 DOI: 10.1107/s2052252520003875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/16/2020] [Indexed: 05/24/2023]
Abstract
Developing methods to determine high-resolution structures from micrometre- or even submicrometre-sized protein crystals has become increasingly important in recent years. This applies to both large protein complexes and membrane proteins, where protein production and the subsequent growth of large homogeneous crystals is often challenging, and to samples which yield only micro- or nanocrystals such as amyloid or viral polyhedrin proteins. The versatile macromolecular crystallography microfocus (VMXm) beamline at Diamond Light Source specializes in X-ray diffraction measurements from micro- and nanocrystals. Because of the possibility of measuring data from crystalline samples that approach the resolution limit of visible-light microscopy, the beamline design includes a scanning electron microscope (SEM) to visualize, locate and accurately centre crystals for X-ray diffraction experiments. To ensure that scanning electron microscopy is an appropriate method for sample visualization, tests were carried out to assess the effect of SEM radiation on diffraction quality. Cytoplasmic polyhedrosis virus polyhedrin protein crystals cryocooled on electron-microscopy grids were exposed to SEM radiation before X-ray diffraction data were collected. After processing the data with DIALS, no statistically significant difference in data quality was found between datasets collected from crystals exposed and not exposed to SEM radiation. This study supports the use of an SEM as a tool for the visualization of protein crystals and as an integrated visualization tool on the VMXm beamline.
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Affiliation(s)
- Emma V. Beale
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Anna J. Warren
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - José Trincão
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - James Beilsten-Edmands
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Adam D. Crawshaw
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Geoff Sutton
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, Oxfordshire OX3 7BN, UK
| | - David Stuart
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, Oxfordshire OX3 7BN, UK
| | - Gwyndaf Evans
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
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69
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Benavides BS, Valandro S, Cioloboc D, Taylor AB, Schanze KS, Kurtz DM. Structure of a Zinc Porphyrin-Substituted Bacterioferritin and Photophysical Properties of Iron Reduction. Biochemistry 2020; 59:1618-1629. [PMID: 32283930 PMCID: PMC7927158 DOI: 10.1021/acs.biochem.9b01103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The iron storage protein bacterioferritin (Bfr) binds up to 12 hemes b at specific sites in its protein shell. The heme b can be substituted with the photosensitizer Zn(II)-protoporphyrin IX (ZnPP), and photosensitized reductive iron release from the ferric oxyhydroxide {[FeO(OH)]n} core inside the ZnPP-Bfr protein shell was demonstrated [Cioloboc, D., et al. (2018) Biomacromolecules 19, 178-187]. This report describes the X-ray crystal structure of ZnPP-Bfr and the effects of loaded iron on the photophysical properties of the ZnPP. The crystal structure of ZnPP-Bfr shows a unique six-coordinate zinc in the ZnPP with two axial methionine sulfur ligands. Steady state and transient ultraviolet-visible absorption and luminescence spectroscopies show that irradiation with light overlapping the Soret absorption causes oxidation of ZnPP to the cation radical ZnPP•+ only when the ZnPP-Bfr is loaded with [FeO(OH)]n. Femtosecond transient absorption spectroscopy shows that this photooxidation occurs from the singlet excited state (1ZnPP*) on the picosecond time scale and is consistent with two oxidizing populations of Fe3+, which do not appear to involve the ferroxidase center iron. We propose that [FeO(OH)]n clusters at or near the inner surface of the protein shell are responsible for ZnPP photooxidation. Hopping of the photoinjected electrons through the [FeO(OH)]n would effectively cause migration of Fe2+ through the inner cavity to pores where it exits the protein. Reductive iron mobilization is presumed to be a physiological function of Bfrs. The phototriggered Fe3+ reduction could be used to identify the sites of iron mobilization within the Bfr protein shell.
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Affiliation(s)
- Brenda S Benavides
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Silvano Valandro
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Daniela Cioloboc
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Alexander B Taylor
- Department of Biochemistry and Structural Biology and X-ray Crystallography Core Laboratory, University of Texas Health Science Center at San Antonio (UT Health San Antonio), San Antonio, Texas 78229, United States
| | - Kirk S Schanze
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Donald M Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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70
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Manna D, Cordara G, Krengel U. Crystal structure of MOA in complex with a peptide fragment: A protease caught in flagranti. Curr Res Struct Biol 2020; 2:56-67. [PMID: 34235469 PMCID: PMC8244254 DOI: 10.1016/j.crstbi.2020.04.003] [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: 12/21/2019] [Revised: 03/28/2020] [Accepted: 04/06/2020] [Indexed: 11/20/2022] Open
Abstract
The Marasmius oreades agglutinin (MOA) is the holotype of an emerging family of fungal chimerolectins and an active Ca2+/Mn2+-dependent protease, which exhibits a unique papain-like fold with special active site features. Here we investigated the functional significance of the structural elements differentiating MOA from other papain-like cysteine proteases. X-ray crystal structures of MOA co-crystallized with two synthetic substrates reveal cleaved peptides bound to the catalytic site, corresponding to the final products of the proteolytic reaction. Anomalous diffraction data on crystals grown in the presence of calcium and manganese, cadmium or zinc resolve the calcium/manganese preference of MOA and elucidate the inhibitory roles of zinc and cadmium towards papain-like cysteine proteases in general. The reported structures, together with activity data of MOA active site variants, point to a conservation of the general proteolysis mechanism established for papain. Ultimately, the findings suggest that papain and the papain-like domain of MOA are the product of convergent evolution.
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Affiliation(s)
- Dipankar Manna
- Department of Chemistry, University of Oslo, PO Box 1033 Blindern, 0315, Oslo, Norway
| | - Gabriele Cordara
- Department of Chemistry, University of Oslo, PO Box 1033 Blindern, 0315, Oslo, Norway
| | - Ute Krengel
- Department of Chemistry, University of Oslo, PO Box 1033 Blindern, 0315, Oslo, Norway
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71
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Noske GD, Gawriljuk VO, Fernandes RS, Furtado ND, Bonaldo MC, Oliva G, Godoy AS. Structural characterization and polymorphism analysis of the NS2B-NS3 protease from the 2017 Brazilian circulating strain of Yellow Fever virus. Biochim Biophys Acta Gen Subj 2020; 1864:129521. [DOI: 10.1016/j.bbagen.2020.129521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 01/03/2020] [Accepted: 01/09/2020] [Indexed: 12/15/2022]
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72
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Vollmar M, Parkhurst JM, Jaques D, Baslé A, Murshudov GN, Waterman DG, Evans G. The predictive power of data-processing statistics. IUCRJ 2020; 7:342-354. [PMID: 32148861 PMCID: PMC7055369 DOI: 10.1107/s2052252520000895] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
This study describes a method to estimate the likelihood of success in determining a macromolecular structure by X-ray crystallography and experimental single-wavelength anomalous dispersion (SAD) or multiple-wavelength anomalous dispersion (MAD) phasing based on initial data-processing statistics and sample crystal properties. Such a predictive tool can rapidly assess the usefulness of data and guide the collection of an optimal data set. The increase in data rates from modern macromolecular crystallography beamlines, together with a demand from users for real-time feedback, has led to pressure on computational resources and a need for smarter data handling. Statistical and machine-learning methods have been applied to construct a classifier that displays 95% accuracy for training and testing data sets compiled from 440 solved structures. Applying this classifier to new data achieved 79% accuracy. These scores already provide clear guidance as to the effective use of computing resources and offer a starting point for a personalized data-collection assistant.
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Affiliation(s)
- Melanie Vollmar
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - James M. Parkhurst
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Dominic Jaques
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 1HH, England
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - David G. Waterman
- Science Technology and Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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73
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Crawshaw AD, Baslé A, Salgado PS. A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study. Acta Crystallogr D Struct Biol 2020; 76:261-271. [PMID: 32133990 PMCID: PMC7057214 DOI: 10.1107/s2059798320000467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/14/2020] [Indexed: 12/02/2022] Open
Abstract
Many biologists are now routinely seeking to determine the three-dimensional structures of their proteins of choice, illustrating the importance of this knowledge, but also of the simplification and streamlining of structure-determination processes. Despite the fact that most software packages offer simple pipelines, for the non-expert navigating the outputs and understanding the key aspects can be daunting. Here, the structure determination of the type IV pili (TFP) protein PilA1 from Clostridioides difficile is used to illustrate the different steps involved, the key decision criteria and important considerations when using the most common pipelines and software. Molecular-replacement pipelines within CCP4i2 are presented to illustrate the more commonly used processes. Previous knowledge of the biology and structure of TFP pilins, particularly the presence of a long, N-terminal α-helix required for pilus formation, allowed informed decisions to be made during the structure-determination strategy. The PilA1 structure was finally successfully determined using ARCIMBOLDO and the ab initio MR strategy used is described.
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Affiliation(s)
- Adam D. Crawshaw
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, England
| | - Arnaud Baslé
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, England
| | - Paula S. Salgado
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, England
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74
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Huang YH, Said N, Loll B, Wahl MC. Structural basis for the function of SuhB as a transcription factor in ribosomal RNA synthesis. Nucleic Acids Res 2020; 47:6488-6503. [PMID: 31020314 PMCID: PMC6614801 DOI: 10.1093/nar/gkz290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/29/2019] [Accepted: 04/10/2019] [Indexed: 11/28/2022] Open
Abstract
Ribosomal RNA synthesis in Escherichia coli involves a transcription complex, in which RNA polymerase is modified by a signal element on the transcript, Nus factors A, B, E and G, ribosomal protein S4 and inositol mono-phosphatase SuhB. This complex is resistant to ρ-dependent termination and facilitates ribosomal RNA folding, maturation and subunit assembly. The functional contributions of SuhB and their structural bases are presently unclear. We show that SuhB directly binds the RNA signal element and the C-terminal AR2 domain of NusA, and we delineate the atomic basis of the latter interaction by macromolecular crystallography. SuhB recruitment to a ribosomal RNA transcription complex depends on the RNA signal element but not on the NusA AR2 domain. SuhB in turn is required for stable integration of the NusB/E dimer into the complex. In vitro transcription assays revealed that SuhB is crucial for delaying or suppressing ρ-dependent termination, that SuhB also can reduce intrinsic termination, and that SuhB-AR2 contacts contribute to these effects. Together, our results reveal functions of SuhB during ribosomal RNA synthesis and delineate some of the underlying molecular interactions.
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Affiliation(s)
- Yong-Heng Huang
- Freie Universität Berlin, Laboratory of Structural Biochemistry, Takustraβe 6, D-14195 Berlin, Germany
| | - Nelly Said
- Freie Universität Berlin, Laboratory of Structural Biochemistry, Takustraβe 6, D-14195 Berlin, Germany
| | - Bernhard Loll
- Freie Universität Berlin, Laboratory of Structural Biochemistry, Takustraβe 6, D-14195 Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Laboratory of Structural Biochemistry, Takustraβe 6, D-14195 Berlin, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
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75
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Bashiri G, Nigon LV, Jirgis ENM, Ho NAT, Stanborough T, Dawes SS, Baker EN, Bulloch EMM, Johnston JM. Allosteric regulation of menaquinone (vitamin K 2) biosynthesis in the human pathogen Mycobacterium tuberculosis. J Biol Chem 2020; 295:3759-3770. [PMID: 32029475 DOI: 10.1074/jbc.ra119.012158] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/01/2020] [Indexed: 11/06/2022] Open
Abstract
Menaquinone (vitamin K2) plays a vital role in energy generation and environmental adaptation in many bacteria, including the human pathogen Mycobacterium tuberculosis (Mtb). Although menaquinone levels are known to be tightly linked to the cellular redox/energy status of the cell, the regulatory mechanisms underpinning this phenomenon are unclear. The first committed step in menaquinone biosynthesis is catalyzed by MenD, a thiamine diphosphate-dependent enzyme comprising three domains. Domains I and III form the MenD active site, but no function has yet been ascribed to domain II. Here, we show that the last cytosolic metabolite in the menaquinone biosynthesis pathway, 1,4-dihydroxy-2-naphthoic acid (DHNA), binds to domain II of Mtb-MenD and inhibits its activity. Using X-ray crystallography of four apo- and cofactor-bound Mtb-MenD structures, along with several spectroscopy assays, we identified three arginine residues (Arg-97, Arg-277, and Arg-303) that are important for both enzyme activity and the feedback inhibition by DHNA. Among these residues, Arg-277 appeared to be particularly important for signal propagation from the allosteric site to the active site. This is the first evidence of feedback regulation of the menaquinone biosynthesis pathway in bacteria, identifying a protein-level regulatory mechanism that controls menaquinone levels within the cell and may therefore represent a good target for disrupting menaquinone biosynthesis in M. tuberculosis.
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Affiliation(s)
- Ghader Bashiri
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Laura V Nigon
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Ehab N M Jirgis
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Ngoc Anh Thu Ho
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), and Maurice Wilkins Centre for Molecular Biodiscovery, University of Canterbury, Christchurch 8041, New Zealand
| | - Tamsyn Stanborough
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), and Maurice Wilkins Centre for Molecular Biodiscovery, University of Canterbury, Christchurch 8041, New Zealand
| | - Stephanie S Dawes
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Edward N Baker
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Esther M M Bulloch
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Jodie M Johnston
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), and Maurice Wilkins Centre for Molecular Biodiscovery, University of Canterbury, Christchurch 8041, New Zealand
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76
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Leonarski F, Mozzanica A, Brückner M, Lopez-Cuenca C, Redford S, Sala L, Babic A, Billich H, Bunk O, Schmitt B, Wang M. JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:014305. [PMID: 32128347 PMCID: PMC7044001 DOI: 10.1063/1.5143480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/04/2020] [Indexed: 05/08/2023]
Abstract
In this paper, we present a data workflow developed to operate the adJUstiNg Gain detector FoR the Aramis User station (JUNGFRAU) adaptive gain charge integrating pixel-array detectors at macromolecular crystallography beamlines. We summarize current achievements for operating at 9 GB/s data-rate a JUNGFRAU with 4 Mpixel at 1.1 kHz frame-rate and preparations to operate at 46 GB/s data-rate a JUNGFRAU with 10 Mpixel at 2.2 kHz in the future. In this context, we highlight the challenges for computer architecture and how these challenges can be addressed with innovative hardware including IBM POWER9 servers and field-programmable gate arrays. We discuss also data science challenges, showing the effect of rounding and lossy compression schemes on the MX JUNGFRAU detector images.
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Affiliation(s)
- Filip Leonarski
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Aldo Mozzanica
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Martin Brückner
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Carlos Lopez-Cuenca
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Sophie Redford
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Leonardo Sala
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Andrej Babic
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Oliver Bunk
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Bernd Schmitt
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Meitian Wang
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
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77
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Vester K, Santos KF, Kuropka B, Weise C, Wahl MC. The inactive C-terminal cassette of the dual-cassette RNA helicase BRR2 both stimulates and inhibits the activity of the N-terminal helicase unit. J Biol Chem 2019; 295:2097-2112. [PMID: 31914407 DOI: 10.1074/jbc.ra119.010964] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/27/2019] [Indexed: 11/06/2022] Open
Abstract
The RNA helicase bad response to refrigeration 2 homolog (BRR2) is required for the activation of the spliceosome before the first catalytic step of RNA splicing. BRR2 represents a distinct subgroup of Ski2-like nucleic acid helicases whose members comprise tandem helicase cassettes. Only the N-terminal cassette of BRR2 is an active ATPase and can unwind substrate RNAs. The C-terminal cassette represents a pseudoenzyme that can stimulate RNA-related activities of the N-terminal cassette. However, the molecular mechanisms by which the C-terminal cassette modulates the activities of the N-terminal unit remain elusive. Here, we show that N- and C-terminal cassettes adopt vastly different relative orientations in a crystal structure of BRR2 in complex with an activating domain of the spliceosomal Prp8 protein at 2.4 Å resolution compared with the crystal structure of BRR2 alone. Likewise, inspection of BRR2 structures within spliceosomal complexes revealed that the cassettes occupy different relative positions and engage in different intercassette contacts during different splicing stages. Engineered disulfide bridges that locked the cassettes in two different relative orientations had opposite effects on the RNA-unwinding activity of the N-terminal cassette, with one configuration enhancing and the other configuration inhibiting RNA unwinding compared with the unconstrained protein. Moreover, we found that differences in relative positioning of the cassettes strongly influence RNA-stimulated ATP hydrolysis by the N-terminal cassette. Our results indicate that the inactive C-terminal cassette of BRR2 can both positively and negatively affect the activity of the N-terminal helicase unit from a distance.
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Affiliation(s)
- Karen Vester
- Structural Biochemistry Group, Department of Biochemistry, Freie Universität Berlin, Takustrasse 63, D-14195 Berlin, Germany
| | - Karine F Santos
- Structural Biochemistry Group, Department of Biochemistry, Freie Universität Berlin, Takustrasse 63, D-14195 Berlin, Germany
| | - Benno Kuropka
- Protein Biochemistry Group, Department of Biochemistry, Freie Universität Berlin, Thielallee 63, D-14195 Berlin, Germany
| | - Christoph Weise
- Protein Biochemistry Group, Department of Biochemistry, Freie Universität Berlin, Thielallee 63, D-14195 Berlin, Germany
| | - Markus C Wahl
- Structural Biochemistry Group, Department of Biochemistry, Freie Universität Berlin, Takustrasse 63, D-14195 Berlin, Germany; Macromolecular Crystallography Group, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany.
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78
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Molecular Mechanism Underlying Inhibition of Intrinsic ATPase Activity in a Ski2-like RNA Helicase. Structure 2019; 28:236-243.e3. [PMID: 31859026 DOI: 10.1016/j.str.2019.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/06/2019] [Accepted: 11/22/2019] [Indexed: 11/20/2022]
Abstract
RNA-dependent NTPases can act as RNA/RNA-protein remodeling enzymes and typically exhibit low NTPase activity in the absence of RNA/RNA-protein substrates. How futile intrinsic NTP hydrolysis is prevented is frequently not known. The ATPase/RNA helicase Brr2 belongs to the Ski2-like family of nucleic acid-dependent NTPases and is an integral component of the spliceosome. Comprehensive nucleotide binding and hydrolysis studies are not available for a member of the Ski2-like family. We present crystal structures of Chaetomium thermophilum Brr2 in the apo, ADP-bound, and ATPγS-bound states, revealing nucleotide-induced conformational changes and a hitherto unknown ATPγS binding mode. Our results in conjunction with Brr2 structures in other molecular contexts reveal multiple molecular mechanisms that contribute to the inhibition of intrinsic ATPase activity, including an N-terminal region that restrains the RecA-like domains in an open conformation and exclusion of an attacking water molecule, and suggest how RNA substrate binding can lead to ATPase stimulation.
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79
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Dacher M, Tachiwana H, Horikoshi N, Kujirai T, Taguchi H, Kimura H, Kurumizaka H. Incorporation and influence of Leishmania histone H3 in chromatin. Nucleic Acids Res 2019; 47:11637-11648. [PMID: 31722422 PMCID: PMC7145708 DOI: 10.1093/nar/gkz1040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022] Open
Abstract
Immunopathologies caused by Leishmania cause severe human morbidity and mortality. This protozoan parasite invades and persists inside host cells, resulting in disease development. Leishmania modifies the epigenomic status of the host cells, thus probably averting the host cell defense mechanism. To accomplish this, Leishmania may change the host cell chromatin structure. However, the mechanism by which the parasite changes the host cell chromatin has not been characterized. In the present study, we found that ectopically produced Leishmania histone H3, LmaH3, which mimics the secreted LmaH3 in infected cells, is incorporated into chromatin in human cells. A crystallographic analysis revealed that LmaH3 forms nucleosomes with human histones H2A, H2B and H4. We found that LmaH3 was less stably incorporated into the nucleosome, as compared to human H3.1. Consistently, we observed that LmaH3-H4 association was remarkably weakened. Mutational analyses revealed that the specific LmaH3 Trp35, Gln57 and Met98 residues, which correspond to the H3.1 Tyr41, Arg63 and Phe104 residues, might be responsible for the instability of the LmaH3 nucleosome. Nucleosomes containing LmaH3 resisted the Mg2+-mediated compaction of the chromatin fiber. These distinct physical characteristics of LmaH3 support the possibility that histones secreted by parasites during infection may modulate the host chromatin structure.
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Affiliation(s)
- Mariko Dacher
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroaki Tachiwana
- Department of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Naoki Horikoshi
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroyuki Taguchi
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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80
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Williamson A, Leiros HKS. Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation. Nucleic Acids Res 2019; 47:7147-7162. [PMID: 31312841 PMCID: PMC6698739 DOI: 10.1093/nar/gkz596] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/24/2019] [Accepted: 07/05/2019] [Indexed: 01/17/2023] Open
Abstract
DNA ligases join adjacent 5' phosphate (5'P) and 3' hydroxyl (3'OH) termini of double-stranded DNA via a three-step mechanism requiring a nucleotide cofactor and divalent metal ion. Although considerable structural detail is available for the first two steps, less is known about step 3 where the DNA-backbone is joined or about the cation role at this step. We have captured high-resolution structures of an adenosine triphosphate (ATP)-dependent DNA ligase from Prochlorococcus marinus including a Mn-bound pre-ternary ligase-DNA complex poised for phosphodiester bond formation, and a post-ternary intermediate retaining product DNA and partially occupied AMP in the active site. The pre-ternary structure unambiguously identifies the binding site of the catalytic metal ion and confirms both its role in activating the 3'OH terminus for nucleophilic attack on the 5'P group and stabilizing the pentavalent transition state. The post-ternary structure indicates that DNA distortion and most enzyme-AMP contacts remain after phosphodiester bond formation, implying loss of covalent linkage to the DNA drives release of AMP, rather than active site rearrangement. Additionally, comparisons of this cyanobacterial DNA ligase with homologs from bacteria and bacteriophage pose interesting questions about the structural origin of double-strand break joining activity and the evolution of these ATP-dependent DNA ligase enzymes.
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Affiliation(s)
- Adele Williamson
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø, N-9037, Norway.,School of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø, N-9037, Norway
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81
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Jeliazkov JR, Robinson AC, García-Moreno E. B, Berger JM, Gray JJ. Toward the computational design of protein crystals with improved resolution. Acta Crystallogr D Struct Biol 2019; 75:1015-1027. [PMID: 31692475 PMCID: PMC6834074 DOI: 10.1107/s2059798319013226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/26/2019] [Indexed: 11/10/2022] Open
Abstract
Substantial advances have been made in the computational design of protein interfaces over the last 20 years. However, the interfaces targeted by design have typically been stable and high-affinity. Here, we report the development of a generic computational design method to stabilize the weak interactions at crystallographic interfaces. Initially, we analyzed structures reported in the Protein Data Bank to determine whether crystals with more stable interfaces result in higher resolution structures. We found that for 22 variants of a single protein crystallized by a single individual, the Rosetta-calculated `crystal score' correlates with the reported diffraction resolution. We next developed and tested a computational design protocol, seeking to identify point mutations that would improve resolution in a highly stable variant of staphylococcal nuclease (SNase). Using a protocol based on fixed protein backbones, only one of the 11 initial designs crystallized, indicating modeling inaccuracies and forcing us to re-evaluate our strategy. To compensate for slight changes in the local backbone and side-chain environment, we subsequently designed on an ensemble of minimally perturbed protein backbones. Using this strategy, four of the seven designed proteins crystallized. By collecting diffraction data from multiple crystals per design and solving crystal structures, we found that the designed crystals improved the resolution modestly and in unpredictable ways, including altering the crystal space group. Post hoc, in silico analysis of the three observed space groups for SNase showed that the native space group was the lowest scoring for four of six variants (including the wild type), but that resolution did not correlate with crystal score, as it did in the preliminary results. Collectively, our results show that calculated crystal scores can correlate with reported resolution, but that the correlation is absent when the problem is inverted. This outcome suggests that more comprehensive modeling of the crystallographic state is necessary to design high-resolution protein crystals from poorly diffracting crystals.
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Affiliation(s)
| | - Aaron C. Robinson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Bertrand García-Moreno E.
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - James M. Berger
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeffrey J. Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA
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82
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Lan W, Zhou Z, Li J, Dou Y, Hao X, Yang L, Liu H, Li D, Liu Q, Zhang D. A cyanide-bridged Fe III-Mn II heterobimetallic one-dimensional coordination polymer: synthesis, crystal structure, experimental and theoretical magnetism investigation. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2019; 75:1475-1481. [PMID: 31686657 DOI: 10.1107/s2053229619013172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/24/2019] [Indexed: 11/10/2022]
Abstract
A new cyanide-bridged FeIII-MnII heterobimetallic coordination polymer (CP), namely catena-poly[[[N,N'-(1,2-phenylene)bis(pyridine-2-carboxamidato)-κ4N,N',N'',N''']iron(III)]-μ-cyanido-κ2C:N-[bis(4,4'-bipyridine-κN)bis(methanol-κO)manganese(II)]-μ-cyanido-κ2N:C], {[FeMn(C18H12N4O2)(CN)2(C10H8N2)2(CH3OH)2]ClO4}n, (1), was prepared by the self-assembly of the trans-dicyanidoiron(III)-containing building block [Fe(bpb)(CN)2]- [bpb2- = N,N'-(1,2-phenylene)bis(pyridine-2-carboxamidate)], [Mn(ClO4)2]·6H2O and 4,4'-bipyridine, and was structurally characterized by elemental analysis, IR spectroscopy, single-crystal X-ray crystallography and powder X-ray diffraction (PXRD). Single-crystal X-ray diffraction analysis shows that CP 1 possesses a cationic linear chain structure consisting of alternating cyanide-bridged Fe-Mn units, with free perchlorate as the charge-balancing anion, which can be further extended into a two-dimensional supramolecular sheet structure via inter-chain π-π interactions between the 4,4'-bipyridine ligands. Within the chain, each MnII ion is six-coordinated by an N6 unit and is involved in a slightly distorted octahedral coordination geometry. Investigation of the magnetic properties of 1 reveals an antiferromagnetic coupling between the cyanide-bridged FeIII and MnII ions. A best fit of the magnetic susceptibility based on the one-dimensional alternating chain model leads to the magnetic coupling constants J1 = -1.35 and J2 = -1.05 cm-1, and the antiferromagnetic coupling was further confirmed by spin Hamiltonian-based density functional theoretical (DFT) calculations.
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Affiliation(s)
- Wenlong Lan
- College of Chemical and Chemical Engineering, Shandong University of Technology, Zibo 255049, People's Republic of China
| | - Zhen Zhou
- College of Chemical and Chemical Engineering, Shandong University of Technology, Zibo 255049, People's Republic of China
| | - Jie Li
- College of Chemical and Chemical Engineering, Shandong University of Technology, Zibo 255049, People's Republic of China
| | - Yong Dou
- College of Chemical and Chemical Engineering, Shandong University of Technology, Zibo 255049, People's Republic of China
| | - Xiaoyun Hao
- College of Chemical and Chemical Engineering, Shandong University of Technology, Zibo 255049, People's Republic of China
| | - Lu Yang
- College of Chemical and Chemical Engineering, Shandong University of Technology, Zibo 255049, People's Republic of China
| | - Hui Liu
- College of Chemical and Chemical Engineering, Shandong University of Technology, Zibo 255049, People's Republic of China
| | - Dacheng Li
- College of Chemical and Chemical Engineering, Liaocheng University, Liaocheng 252059, People's Republic of China
| | - Qingyun Liu
- College of Chemical and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266510, People's Republic of China
| | - Daopeng Zhang
- College of Chemical and Chemical Engineering, Shandong University of Technology, Zibo 255049, People's Republic of China
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83
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Crystal structure of zinc-α2-glycoprotein in complex with a fatty acid reveals multiple different modes of protein-lipid binding. Biochem J 2019; 476:2815-2834. [PMID: 31506272 DOI: 10.1042/bcj20190354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 12/14/2022]
Abstract
Human zinc-α2-glycoprotein (ZAG) is a 42 kDa adipokine which regulates body fat mass and is associated with cachexia and obesity. ZAG belongs to the major histocompatibility complex class I protein family and binds long-chain polyunsaturated fatty acids in its groove formed from the α1 and α2 domains. To identify the molecular basis of its lipid-binding function, we determined the first crystal structure at 2.49 Å resolution for fatty acid-bound ZAG, where the ligand was the fluorescent 11-(dansylamino)undecanoic acid (DAUDA). The 192 kDa crystallographic asymmetric unit contained six ZAG and eight fatty acid molecules in unique conformations. Six fatty acid molecules were localised to the ZAG grooves, where their tails were bound in two distinct conformations. The carboxylate groups of three fatty acids projected out of the groove, while the fourth was hydrogen bonded with R73 inside the groove. Other ligand-residue contacts were primarily hydrophobic. A new fatty acid site was revealed for two further DAUDA molecules at the ZAG α3 domains. Following conformational changes from unbound ZAG, the α3 domains formed tetrameric β-barrel structures lined by fatty acid molecules that doubled the binding capacity of ZAG. Analytical ultracentrifugation revealed that ZAG in solution was a monomer in the absence of DAUDA, but formed small amounts of tetramers with DAUDA. By showing that ZAG binds fatty acids in different locations, we demonstrate an augmented mechanism for fatty acid binding in ZAG that is distinct from other known fatty acid binding proteins, and may be relevant to cachexia.
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84
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Harrison K, Wu Z, Juers DH. A comparison of gas stream cooling and plunge cooling of macromolecular crystals. J Appl Crystallogr 2019; 52:1222-1232. [PMID: 31636524 PMCID: PMC6782077 DOI: 10.1107/s1600576719010318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/18/2019] [Indexed: 01/17/2023] Open
Abstract
Cryocooling for macromolecular crystallography is usually performed via plunging the crystal into a liquid cryogen or placing the crystal in a cold gas stream. These two approaches are compared here for the case of nitro-gen cooling. The results show that gas stream cooling, which typically cools the crystal more slowly, yields lower mosaicity and, in some cases, a stronger anomalous signal relative to rapid plunge cooling. During plunging, moving the crystal slowly through the cold gas layer above the liquid surface can produce mosaicity similar to gas stream cooling. Annealing plunge cooled crystals by warming and recooling in the gas stream allows the mosaicity and anomalous signal to recover. For tetragonal thermolysin, the observed effects are less pronounced when the cryosolvent has smaller thermal contraction, under which conditions the protein structures from plunge cooled and gas stream cooled crystals are very similar. Finally, this work also demonstrates that the resolution dependence of the reflecting range is correlated with the cooling method, suggesting it may be a useful tool for discerning whether crystals are cooled too rapidly. The results support previous studies suggesting that slower cooling methods are less deleterious to crystal order, as long as ice formation is prevented and dehydration is limited.
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Affiliation(s)
- Kaitlin Harrison
- Department of Physics and Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Zhenguo Wu
- Department of Physics and Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Douglas H Juers
- Department of Physics and Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
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85
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Ojennus DD, Bratt NJ, Jones KL, Juers DH. Structural characterization of a prolyl aminodipeptidase (PepX) from Lactobacillus helveticus. Acta Crystallogr F Struct Biol Commun 2019; 75:625-633. [PMID: 31584010 PMCID: PMC6777133 DOI: 10.1107/s2053230x19011774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/26/2019] [Indexed: 01/25/2023] Open
Abstract
Prolyl aminodipeptidase (PepX) is an enzyme that hydrolyzes peptide bonds from the N-terminus of substrates when the penultimate amino-acid residue is a proline. Prolyl peptidases are of particular interest owing to their ability to hydrolyze food allergens that contain a high percentage of proline residues. PepX from Lactobacillus helveticus was cloned and expressed in Escherichia coli as an N-terminally His-tagged recombinant construct and was crystallized by hanging-drop vapor diffusion in a phosphate buffer using PEG 3350 as a precipitant. The structure was determined at 2.0 Å resolution by molecular replacement using the structure of PepX from Lactococcus lactis (PDB entry 1lns) as the starting model. Notable differences between the L. helveticus PepX structure and PDB entry 1lns include a cysteine instead of a phenylalanine at the substrate-binding site in the position which confers exopeptidase activity and the presence of a calcium ion coordinated by a calcium-binding motif with the consensus sequence DX(DN)XDG.
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Affiliation(s)
- Deanna Dahlke Ojennus
- Department of Chemistry, Whitworth University, 300 West Hawthorne Road, Spokane, WA 99251, USA
| | - Nicholas J. Bratt
- Department of Chemistry, Whitworth University, 300 West Hawthorne Road, Spokane, WA 99251, USA
| | - Kent L. Jones
- Department of Mathematics and Computer Science, Whitworth University, 300 West Hawthorne Road, Spokane, WA 99251, USA
| | - Douglas H. Juers
- Department of Physics and Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99632, USA
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86
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Bamford NC, Le Mauff F, Subramanian AS, Yip P, Millán C, Zhang Y, Zacharias C, Forman A, Nitz M, Codée JDC, Usón I, Sheppard DC, Howell PL. Ega3 from the fungal pathogen Aspergillus fumigatus is an endo-α-1,4-galactosaminidase that disrupts microbial biofilms. J Biol Chem 2019; 294:13833-13849. [PMID: 31416836 DOI: 10.1074/jbc.ra119.009910] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/01/2019] [Indexed: 11/06/2022] Open
Abstract
Aspergillus fumigatus is an opportunistic fungal pathogen that causes both chronic and acute invasive infections. Galactosaminogalactan (GAG) is an integral component of the A. fumigatus biofilm matrix and a key virulence factor. GAG is a heterogeneous linear α-1,4-linked exopolysaccharide of galactose and GalNAc that is partially deacetylated after secretion. A cluster of five co-expressed genes has been linked to GAG biosynthesis and modification. One gene in this cluster, ega3, is annotated as encoding a putative α-1,4-galactosaminidase belonging to glycoside hydrolase family 114 (GH114). Herein, we show that recombinant Ega3 is an active glycoside hydrolase that disrupts GAG-dependent A. fumigatus and Pel polysaccharide-dependent Pseudomonas aeruginosa biofilms at nanomolar concentrations. Using MS and functional assays, we demonstrate that Ega3 is an endo-acting α-1,4-galactosaminidase whose activity depends on the conserved acidic residues, Asp-189 and Glu-247. X-ray crystallographic structural analysis of the apo Ega3 and an Ega3-galactosamine complex, at 1.76 and 2.09 Å resolutions, revealed a modified (β/α)8-fold with a deep electronegative cleft, which upon ligand binding is capped to form a tunnel. Our structural analysis coupled with in silico docking studies also uncovered the molecular determinants for galactosamine specificity and substrate binding at the -2 to +1 binding subsites. The findings in this study increase the structural and mechanistic understanding of the GH114 family, which has >600 members encoded by plant and opportunistic human pathogens, as well as in industrially used bacteria and fungi.
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Affiliation(s)
- Natalie C Bamford
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - François Le Mauff
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, Quebec H3A 2B4, Canada.,Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec H3A 1Y2, Canada
| | - Adithya S Subramanian
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Patrick Yip
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Claudia Millán
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer Baldiri Reixac 15, 3 A17, Barcelona 08028, Spain
| | - Yongzhen Zhang
- Leiden Institute of Chemistry, Leiden University, 2300RA Leiden, The Netherlands
| | - Caitlin Zacharias
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, Quebec H3A 2B4, Canada.,Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec H3A 1Y2, Canada
| | - Adam Forman
- Department of Chemistry, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Mark Nitz
- Department of Chemistry, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, 2300RA Leiden, The Netherlands
| | - Isabel Usón
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer Baldiri Reixac 15, 3 A17, Barcelona 08028, Spain.,ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, E-08003 Barcelona, Spain
| | - Donald C Sheppard
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, Quebec H3A 2B4, Canada .,Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec H3A 1Y2, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada .,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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87
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Trachman RJ, Stagno JR, Conrad C, Jones CP, Fischer P, Meents A, Wang YX, Ferré-D’Amaré AR. Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser. Acta Crystallogr F Struct Biol Commun 2019; 75:547-551. [PMID: 31397326 PMCID: PMC6688663 DOI: 10.1107/s2053230x19010136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/15/2019] [Indexed: 11/10/2022] Open
Abstract
Turn-on aptamers are in vitro-selected RNAs that bind to conditionally fluorescent small molecules and enhance their fluorescence. Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold). This aptamer was generated by structure-guided engineering and functional reselection of the parental aptamer Mango-III. Structures of both Mango-III and iMango-III have previously been determined by conventional cryocrystallography using synchrotron X-radiation. Using an X-ray free-electron laser (XFEL), the room-temperature iMango-III-TO1-biotin co-crystal structure has now been determined at 3.0 Å resolution. This structural model, which was refined against a data set of ∼1300 diffraction images (each from a single crystal), is largely consistent with the structures determined from single-crystal data sets collected at 100 K. This constitutes a technical benchmark on the way to XFEL pump-probe experiments on fluorescent RNA-small molecule complexes.
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Affiliation(s)
- Robert J. Trachman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Jason R. Stagno
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Chelsie Conrad
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Christopher P. Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Pontus Fischer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- DESY Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- DESY Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
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88
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Meagher M, Epling LB, Enemark EJ. DNA translocation mechanism of the MCM complex and implications for replication initiation. Nat Commun 2019; 10:3117. [PMID: 31308367 PMCID: PMC6629641 DOI: 10.1038/s41467-019-11074-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 06/18/2019] [Indexed: 12/12/2022] Open
Abstract
The DNA translocation activity of the minichromosome maintenance (MCM) complex powers DNA strand separation of the replication forks of eukaryotes and archaea. Here we illustrate an atomic level mechanism for this activity with a crystal structure of an archaeal MCM hexamer bound to single-stranded DNA and nucleotide cofactors. Sequence conservation indicates this rotary mechanism is fully possible for all eukaryotes and archaea. The structure definitively demonstrates the ring orients during translocation with the N-terminal domain leading, indicating that the translocation activity could also provide the physical basis of replication initiation where a double-hexamer idly encircling double-stranded DNA transforms to single-hexamers that encircle only one strand. In this mechanism, each strand binds to the N-terminal tier of one hexamer and the AAA+ tier of the other hexamer such that one ring pulls on the other, aligning equivalent interfaces to enable each hexamer to pull its translocation strand outside of the opposing hexamer.
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Affiliation(s)
- Martin Meagher
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 311, Memphis, TN, 38105, USA
| | - Leslie B Epling
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 311, Memphis, TN, 38105, USA.,Incyte Research Institute, 1801 Augustine Cut-off, Wilmington, DE, 19803, USA
| | - Eric J Enemark
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 311, Memphis, TN, 38105, USA.
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89
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Chen Y, Cramer P. Structure of the super-elongation complex subunit AFF4 C-terminal homology domain reveals requirements for AFF homo- and heterodimerization. J Biol Chem 2019; 294:10663-10673. [PMID: 31147444 PMCID: PMC6615702 DOI: 10.1074/jbc.ra119.008577] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/27/2019] [Indexed: 12/12/2022] Open
Abstract
AF4/FMR2 family member 4 (AFF4) is the scaffold protein of the multisubunit super-elongation complex, which plays key roles in the release of RNA polymerase II from promoter-proximal pausing and in the transactivation of HIV-1 transcription. AFF4 consists of an intrinsically disordered N-terminal region that interacts with other super-elongation complex subunits and a C-terminal homology domain (CHD) that is conserved among AF4/FMR2 family proteins, including AFF1, AFF2, AFF3, and AFF4. Here, we solved the X-ray crystal structure of the CHD in human AFF4 (AFF4-CHD) to 2.2 Å resolution and characterized its biochemical properties. The structure disclosed that AFF4-CHD folds into a novel domain that consists of eight helices and is distantly related to tetratrico peptide repeat motifs. Our analyses further revealed that AFF4-CHD mediates the formation of an AFF4 homodimer or an AFF1-AFF4 heterodimer. Results from fluorescence anisotropy experiments suggested that AFF4-CHD interacts with both RNA and DNA in vitro Furthermore, we identified a surface loop region in AFF4-CHD as a substrate for the P-TEFb kinase cyclin-dependent kinase 9, which triggers release of polymerase II from promoter-proximal pausing sites. In conclusion, the AFF-CHD structure and biochemical analyses reported here reveal the molecular basis for the homo- and heterodimerization of AFF proteins and implicate the AFF4-CHD in nucleic acid interactions. The high conservation of the CHD among several other proteins suggests that our results are also relevant for understanding other CHD-containing proteins and their dimerization behavior.
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Affiliation(s)
- Ying Chen
- From the Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Patrick Cramer
- From the Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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90
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Halsted TP, Yamashita K, Gopalasingam CC, Shenoy RT, Hirata K, Ago H, Ueno G, Blakeley MP, Eady RR, Antonyuk SV, Yamamoto M, Hasnain SS. Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography. IUCRJ 2019; 6:761-772. [PMID: 31316819 PMCID: PMC6608623 DOI: 10.1107/s2052252519008285] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/12/2019] [Indexed: 05/31/2023]
Abstract
Copper-containing nitrite reductases (CuNiRs) that convert NO2 - to NO via a CuCAT-His-Cys-CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD-, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2 - a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed.
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Affiliation(s)
- Thomas P. Halsted
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Chai C. Gopalasingam
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Rajesh T. Shenoy
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Hideo Ago
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Go Ueno
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Masaki Yamamoto
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
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91
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Jones C, Tran B, Conrad C, Stagno J, Trachman R, Fischer P, Meents A, Ferré-D'Amaré A. Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:496-500. [PMID: 31282869 DOI: 10.1107/s2053230x19008549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/15/2019] [Indexed: 11/10/2022]
Abstract
Riboswitches are conformationally dynamic RNAs that regulate gene expression by binding specific small molecules. ZTP riboswitches bind the purine-biosynthetic intermediate 5-aminoimidazole-4-carboxamide riboside 5'-monophosphate (ZMP) and its triphosphorylated form (ZTP). Ligand binding to this riboswitch ultimately upregulates genes involved in folate and purine metabolism. Using an X-ray free-electron laser (XFEL), the room-temperature structure of the Fusobacterium ulcerans ZTP riboswitch bound to ZMP has now been determined at 4.1 Å resolution. This model, which was refined against a data set from ∼750 diffraction images (each from a single crystal), was found to be consistent with that previously obtained from data collected at 100 K using conventional synchrotron X-radiation. These experiments demonstrate the feasibility of time-resolved XFEL experiments to understand how the ZTP riboswitch accommodates cognate ligand binding.
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Affiliation(s)
- Christopher Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
| | - Brandon Tran
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
| | - Chelsie Conrad
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Jason Stagno
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Robert Trachman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
| | - Pontus Fischer
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Adrian Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
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92
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Structural Differences between the Woodchuck Hepatitis Virus Core Protein in the Dimer and Capsid States Are Consistent with Entropic and Conformational Regulation of Assembly. J Virol 2019; 93:JVI.00141-19. [PMID: 31043524 DOI: 10.1128/jvi.00141-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022] Open
Abstract
Hepadnaviruses are hepatotropic enveloped DNA viruses with an icosahedral capsid. Hepatitis B virus (HBV) causes chronic infection in an estimated 240 million people; woodchuck hepatitis virus (WHV), an HBV homologue, has been an important model system for drug development. The dimeric capsid protein (Cp) has multiple functions during the viral life cycle and thus has become an important target for a new generation of antivirals. Purified HBV and WHV Cp spontaneously assemble into 120-dimer capsids. Though they have 65% identity, WHV Cp has error-prone assembly with stronger protein-protein association. We have taken advantage of the differences in assemblies to investigate the basis of assembly regulation. We determined the structures of the WHV capsid to 4.5-Å resolution by cryo-electron microscopy (cryo-EM) and of the WHV Cp dimer to 2.9-Å resolution by crystallography and examined the biophysical properties of the dimer. We found, in dimer, that the subdomain that makes protein-protein interactions is partially disordered and rotated 21° from its position in capsid. This subdomain is susceptible to proteolysis, consistent with local disorder. WHV assembly shows similar susceptibility to HBV antiviral molecules, suggesting that HBV assembly follows similar transitions. These data show that there is an entropic cost for assembly that is compensated for by the energetic gain of burying hydrophobic interprotein contacts. We propose a series of stages in assembly that incorporate a disorder-to-order transition and structural shifts. We suggest that a cascade of structural changes may be a common mechanism for regulating high-fidelity capsid assembly in HBV and other viruses.IMPORTANCE Virus capsids assemble spontaneously with surprisingly high fidelity. This requires strict geometry and a narrow range of association energies for these protein-protein interactions. It was hypothesized that requiring subunits to undergo a conformational change to become assembly active could regulate assembly by creating an energetic barrier and attenuating association. We found that woodchuck hepatitis virus capsid protein undergoes structural transitions between its dimeric and its 120-dimer capsid states. It is likely that the closely related hepatitis B virus capsid protein undergoes similar structural changes, which has implications for drug design. Regulation of assembly by structural transition may be a common mechanism for many viruses.
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93
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Haji-Ghassemi O, Yuchi Z, Van Petegem F. The Cardiac Ryanodine Receptor Phosphorylation Hotspot Embraces PKA in a Phosphorylation-Dependent Manner. Mol Cell 2019; 75:39-52.e4. [PMID: 31078384 DOI: 10.1016/j.molcel.2019.04.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/05/2019] [Accepted: 04/11/2019] [Indexed: 12/22/2022]
Abstract
Ryanodine receptors (RyRs) are intracellular Ca2+ release channels controlling essential cellular functions. RyRs are targeted by cyclic AMP (cAMP)-dependent protein kinase A (PKA), a controversial regulation implicated in disorders ranging from heart failure to Alzheimer's. Using crystal structures, we show that the phosphorylation hotspot domain of RyR2 embraces the PKA catalytic subunit, with an extensive interface not seen in PKA complexes with peptides. We trapped an intermediary open-form PKA bound to the RyR2 domain and an ATP analog, showing that PKA can engage substrates in an open form. Phosphomimetics or prior phosphorylation at nearby sites in RyR2 either enhance or reduce the activity of PKA. Finally, we show that a phosphomimetic at S2813, a well-known target site for calmodulin-dependent kinase II, induces the formation of an alpha helix in the phosphorylation domain, resulting in increased interactions and PKA activity. This shows that the different phosphorylation sites in RyR2 are not independent.
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Affiliation(s)
- Omid Haji-Ghassemi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zhiguang Yuchi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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94
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Vidilaseris K, Kiriazis A, Turku A, Khattab A, Johansson NG, Leino TO, Kiuru PS, Boije af Gennäs G, Meri S, Yli-Kauhaluoma J, Xhaard H, Goldman A. Asymmetry in catalysis by Thermotoga maritima membrane-bound pyrophosphatase demonstrated by a nonphosphorus allosteric inhibitor. SCIENCE ADVANCES 2019; 5:eaav7574. [PMID: 31131322 PMCID: PMC6530997 DOI: 10.1126/sciadv.aav7574] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
Membrane-bound pyrophosphatases are homodimeric integral membrane proteins that hydrolyze pyrophosphate into orthophosphates, coupled to the active transport of protons or sodium ions across membranes. They are important in the life cycle of bacteria, archaea, plants, and parasitic protists, but no homologous proteins exist in vertebrates, making them a promising drug target. Here, we report the first nonphosphorus allosteric inhibitor of the thermophilic bacterium Thermotoga maritima membrane-bound pyrophosphatase and its bound structure together with the substrate analog imidodiphosphate. The unit cell contains two protein homodimers, each binding a single inhibitor dimer near the exit channel, creating a hydrophobic clamp that inhibits the movement of β-strand 1-2 during pumping, and thus prevents the hydrophobic gate from opening. This asymmetry of inhibitor binding with respect to each homodimer provides the first clear structural demonstration of asymmetry in the catalytic cycle of membrane-bound pyrophosphatases.
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Affiliation(s)
- Keni Vidilaseris
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
| | - Alexandros Kiriazis
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Ainoleena Turku
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Ayman Khattab
- Malaria Research Laboratory, Immunobiology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Niklas G. Johansson
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Teppo O. Leino
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Paula S. Kiuru
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Gustav Boije af Gennäs
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Seppo Meri
- Malaria Research Laboratory, Immunobiology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Henri Xhaard
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Adrian Goldman
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
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95
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Halby L, Marechal N, Pechalrieu D, Cura V, Franchini DM, Faux C, Alby F, Troffer-Charlier N, Kudithipudi S, Jeltsch A, Aouadi W, Decroly E, Guillemot JC, Page P, Ferroud C, Bonnefond L, Guianvarc'h D, Cavarelli J, Arimondo PB. Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0072. [PMID: 29685976 DOI: 10.1098/rstb.2017.0072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2017] [Indexed: 12/12/2022] Open
Abstract
DNA, RNA and histone methylation is implicated in various human diseases such as cancer or viral infections, playing a major role in cell process regulation, especially in modulation of gene expression. Here we developed a convergent synthetic pathway starting from a protected bromomethylcytosine derivative to synthesize transition state analogues of the DNA methyltransferases. This approach led to seven 5-methylcytosine-adenosine compounds that were, surprisingly, inactive against hDNMT1, hDNMT3Acat, TRDMT1 and other RNA human and viral methyltransferases. Interestingly, compound 4 and its derivative 2 showed an inhibitory activity against PRMT4 in the micromolar range. Crystal structures showed that compound 4 binds to the PRMT4 active site, displacing strongly the S-adenosyl-l-methionine cofactor, occupying its binding site, and interacting with the arginine substrate site through the cytosine moiety that probes the space filled by a substrate peptide methylation intermediate. Furthermore, the binding of the compounds induces important structural switches. These findings open new routes for the conception of new potent PRMT4 inhibitors based on the 5-methylcytosine-adenosine scaffold.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Ludovic Halby
- CNRS FRE3600 ETaC, bât. IBCG, 31062 Toulouse, France.,Maison Française d'Oxford, CNRS, MEAE, 2-10 Norham Road, Oxford, UK
| | - Nils Marechal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Vincent Cura
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Céline Faux
- CNRS FRE3600 ETaC, bât. IBCG, 31062 Toulouse, France
| | - Fréderic Alby
- Laboratoire Pierre Fabre, 3 avenue H. Curien, 31100 Toulouse, France
| | - Nathalie Troffer-Charlier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Srikanth Kudithipudi
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Wahiba Aouadi
- Laboratoire Architecture Fonction des Macromolécules Biologiques (AFMB-UMR 7257), Aix-Marseille Université & CNRS, 163 avenue de Luminy, 13288 Marseille cedex 09, France
| | - Etienne Decroly
- Laboratoire Architecture Fonction des Macromolécules Biologiques (AFMB-UMR 7257), Aix-Marseille Université & CNRS, 163 avenue de Luminy, 13288 Marseille cedex 09, France
| | - Jean-Claude Guillemot
- Laboratoire Architecture Fonction des Macromolécules Biologiques (AFMB-UMR 7257), Aix-Marseille Université & CNRS, 163 avenue de Luminy, 13288 Marseille cedex 09, France
| | - Patrick Page
- Epiremed SAS, 1 Rue des Pénitents Blancs, 31000 Toulouse, France
| | - Clotilde Ferroud
- Laboratoire de chimie moléculaire, CMGPCE, EA7341, Conservatoire National des Arts et Métiers, 2 rue Conté, 75003 Paris, France
| | - Luc Bonnefond
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Dominique Guianvarc'h
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France
| | - Jean Cavarelli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Paola B Arimondo
- CNRS FRE3600 ETaC, bât. IBCG, 31062 Toulouse, France .,Churchill College, CB3 0DS Cambridge, UK
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96
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Roncase EJ, González-Páez GE, Wolan DW. X-ray Structures of Two Bacteroides thetaiotaomicron C11 Proteases in Complex with Peptide-Based Inhibitors. Biochemistry 2019; 58:1728-1737. [PMID: 30835452 DOI: 10.1021/acs.biochem.9b00098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Commensal bacteria secrete proteins and metabolites to influence host intestinal homeostasis, and proteases represent a significant constituent of the components at the host:microbiome interface. Here, we determined the structures of the two secreted C11 cysteine proteases encoded by the established gut commensal Bacteroides thetaiotaomicron. We employed mutational analysis to demonstrate the two proteases, termed "thetapain" and "iotapain", undergo in trans autoactivation after lysine and/or arginine residues, as observed for other C11 proteases. We determined the structures of the active forms of thetapain and iotapain in complex with irreversible peptide inhibitors, Ac-VLTK-AOMK and biotin-VLTK-AOMK, respectively. Structural comparisons revealed key active-site interactions important for peptide recognition are more extensive for thetapain; however, both proteases employ a glutamate residue to preferentially bind small polar residues at the P2 position. Our results will aid in the design of protease-specific probes to ultimately understand the biological role of C11 proteases in bacterial fitness, elucidate their host and/or microbial substrates, and interrogate their involvement in microbiome-related diseases.
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Affiliation(s)
- Emily J Roncase
- Departments of Molecular Medicine and Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Gonzalo E González-Páez
- Departments of Molecular Medicine and Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Dennis W Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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97
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98
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Child SA, Flint KL, Bruning JB, Bell SG. The characterisation of two members of the cytochrome P450 CYP150 family: CYP150A5 and CYP150A6 from Mycobacterium marinum. Biochim Biophys Acta Gen Subj 2019; 1863:925-934. [PMID: 30826435 DOI: 10.1016/j.bbagen.2019.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/20/2019] [Accepted: 02/27/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Actinobacteria, including the Mycobacteria, have a large component of cytochrome P450 family monooxygenases. This includes Mycobacterium tuberculosis, M. ulcerans and M. marinum, and M. vanbaalenii. These enzymes can abstract CH bonds and have important roles in natural product biosynthesis. METHODS Two members of the bacterial CYP150 family, CYP150A5 and CYP150A6 from M. marinum, were produced, purified and characterised. The potential substrate ranges of both enzymes were analysed and the monooxygenase activity of CYP150A5 was reconstituted using a physiological electron transfer partner system. CYP150A6 was structurally characterised by X-ray crystallography. RESULTS CYP150A5 was shown to bind various norisoprenoids and terpenoids. It could regioselectively hydroxylate β-ionol. The X-ray crystal structure of substrate-free CYP150A6 was solved to 1.5 Å. This displayed an open conformation with short F and G helices, an unresolved F-G loop region and exposed active site pocket. The active site residues could be identified and important variations were found among the CYP150A enzymes. Haem-binding azole inhibitors were identified for both enzymes. CONCLUSIONS The structure of CYP150A6 will facilitate the identification of physiological substrates and the design of better inhibitors for members of this P450 family. Based on the observed differences in substrate binding preference and sequence variations among the active site residues, their roles are predicted to be different. GENERAL SIGNIFICANCE Multiple CYP150 family members were found in many bacteria and are prevalent in the Mycobacteria including several human pathogens. Inhibition and structural data are reported here for these enzymes for the first time.
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Affiliation(s)
- Stella A Child
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | - Kate L Flint
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA 5005, Australia.
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99
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Mendoza JL, Escalante NK, Jude KM, Sotolongo Bellon J, Su L, Horton TM, Tsutsumi N, Berardinelli SJ, Haltiwanger RS, Piehler J, Engleman EG, Garcia KC. Structure of the IFNγ receptor complex guides design of biased agonists. Nature 2019; 567:56-60. [PMID: 30814731 PMCID: PMC6561087 DOI: 10.1038/s41586-019-0988-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/25/2019] [Indexed: 01/09/2023]
Abstract
The cytokine interferon-γ (IFNγ) is a central coordinator of innate and adaptive immunity, but its highly pleiotropic actions have diminished its prospects for use as an immunotherapeutic agent. Here, we took a structure-based approach to decoupling IFNγ pleiotropy. We engineered an affinity-enhanced variant of the ligand-binding chain of the IFNγ receptor IFNγR1, which enabled us to determine the crystal structure of the complete hexameric (2:2:2) IFNγ-IFNγR1-IFNγR2 signalling complex at 3.25 Å resolution. The structure reveals the mechanism underlying deficits in IFNγ responsiveness in mycobacterial disease syndrome resulting from a T168N mutation in IFNγR2, which impairs assembly of the full signalling complex. The topology of the hexameric complex offers a blueprint for engineering IFNγ variants to tune IFNγ receptor signalling output. Unexpectedly, we found that several partial IFNγ agonists exhibited biased gene-expression profiles. These biased agonists retained the ability to induce upregulation of major histocompatibility complex class I antigen expression, but exhibited impaired induction of programmed death-ligand 1 expression in a wide range of human cancer cell lines, offering a route to decoupling immunostimulatory and immunosuppressive functions of IFNγ for therapeutic applications.
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Affiliation(s)
- Juan L Mendoza
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Molecular Engineering and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Nichole K Escalante
- Stanford Blood Center, Palo Alto, CA, USA
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Junel Sotolongo Bellon
- Division of Biophysics, Department of Biology, University of Osnabruck, Osnabruck, Germany
| | - Leon Su
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tim M Horton
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Naotaka Tsutsumi
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Jacob Piehler
- Division of Biophysics, Department of Biology, University of Osnabruck, Osnabruck, Germany
| | - Edgar G Engleman
- Stanford Blood Center, Palo Alto, CA, USA
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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100
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González-Páez GE, Roncase EJ, Wolan DW. X-ray structure of an inactive zymogen clostripain-like protease from Parabacteroides distasonis. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:325-332. [PMID: 30950403 DOI: 10.1107/s2059798319000809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/16/2019] [Indexed: 02/07/2023]
Abstract
The clostripain-like (C11) family of cysteine proteases are ubiquitously produced by the vast majority of the bacterial strains that make up the human distal gut microbiome. Recent reports show that some C11 proteases promote host immune responses and bacterial pathogenesis, including the induction of neutrophil phagocytosis and the activation of bacterial pathogenic toxins, respectively. The crystal structure of distapain, the only C11 protease predicted within the genome of the commensal bacterium Parabacteroides distasonis, was determined in the inactive zymogen state to 1.65 Å resolution. This is the first C11 protease structure of a zymogen, and the structure helped to uncover key unique conformations among critical active-site residues that are likely to assist in preserving the inactive protease. His135, a member of the catalytic dyad, is repositioned approximately 5.5 Å from the orientation found in active C11 structures and forms a hydrogen bond to Asp180 and a π-stacking interaction with Trp133. The structure sheds light on the potential importance of Asp180 and Trp133, as these residues are highly conserved across C11 proteases. Structure elucidation of C11 proteases will ultimately help to identify new ways to chemically and/or biologically regulate this family of enzymes, which represent potential drug-discovery targets in microbiome-related gastrointestinal diseases.
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Affiliation(s)
- Gonzalo E González-Páez
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Emily J Roncase
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dennis W Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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