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Li FKK, Worrall LJ, Gale RT, Brown ED, Strynadka NCJ. Cryo-EM analysis of S. aureus TarL, a polymerase in wall teichoic acid biogenesis central to virulence and antibiotic resistance. Sci Adv 2024; 10:eadj3864. [PMID: 38416829 PMCID: PMC10901376 DOI: 10.1126/sciadv.adj3864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/23/2024] [Indexed: 03/01/2024]
Abstract
Wall teichoic acid (WTA), a covalent adduct of Gram-positive bacterial cell wall peptidoglycan, contributes directly to virulence and antibiotic resistance in pathogenic species. Polymerization of the Staphylococcus aureus WTA ribitol-phosphate chain is catalyzed by TarL, a member of the largely uncharacterized TagF-like family of membrane-associated enzymes. We report the cryo-electron microscopy structure of TarL, showing a tetramer that forms an extensive membrane-binding platform of monotopic helices. TarL is composed of an amino-terminal immunoglobulin-like domain and a carboxyl-terminal glycosyltransferase-B domain for ribitol-phosphate polymerization. The active site of the latter is complexed to donor substrate cytidine diphosphate-ribitol, providing mechanistic insights into the catalyzed phosphotransfer reaction. Furthermore, the active site is surrounded by electropositive residues that serve to retain the lipid-linked acceptor for polymerization. Our data advance general insight into the architecture and membrane association of the still poorly characterized monotopic membrane protein class and present molecular details of ribitol-phosphate polymerization that may aid in the design of new antimicrobials.
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Affiliation(s)
- Franco K K Li
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert T Gale
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
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2
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Pérez-Vargas J, Worrall LJ, Olmstead AD, Ton AT, Lee J, Villanueva I, Thompson CAH, Dudek S, Ennis S, Smith JR, Shapira T, De Guzman J, Gang S, Ban F, Vuckovic M, Bielecki M, Kovacic S, Kenward C, Hong CY, Gordon DG, Levett PN, Krajden M, Leduc R, Boudreault PL, Niikura M, Paetzel M, Young RN, Cherkasov A, Strynadka NCJ, Jean F. A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants. Emerg Microbes Infect 2023; 12:2246594. [PMID: 37555275 PMCID: PMC10453993 DOI: 10.1080/22221751.2023.2246594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/10/2023]
Abstract
Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors (C2-C5a). Our lead direct-acting antiviral (DAA), C5a, is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro. The compounds C2-C5a exhibit broad-spectrum activity against Omicron subvariants (BA.5, BQ.1.1, and XBB.1.5) and seasonal human coronavirus-229E infection in human cells. Notably, C5a has median effective concentrations of 30-50 nM against BQ.1.1 and XBB.1.5 in two different human cell lines. X-ray crystallography has confirmed the unique binding modes of C2-C5a to the 3CLpro, which can limit virus cross-resistance to emerging Paxlovid-resistant variants. We tested the effect of C5a with two of our newly discovered host-directed antivirals (HDAs): N-0385, a TMPRSS2 inhibitor, and bafilomycin D (BafD), a human vacuolar H+-ATPase [V-ATPase] inhibitor. We demonstrated a synergistic action of C5a in combination with N-0385 and BafD against Omicron BA.5 infection in human Calu-3 lung cells. Our findings underscore that a SARS-CoV-2 multi-targeted treatment for circulating Omicron subvariants based on DAAs (C5a) and HDAs (N-0385 or BafD) can lead to therapeutic benefits by enhancing treatment efficacy. Furthermore, the high-resolution structures of SARS-CoV-2 3CLpro in complex with C2-C5a will facilitate future rational optimization of our novel broad-spectrum active-site-directed 3C-like protease inhibitors.
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Affiliation(s)
- Jimena Pérez-Vargas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Andrea D. Olmstead
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Ivan Villanueva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Connor A. H. Thompson
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Svenja Dudek
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Jason R. Smith
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Tirosh Shapira
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Joshua De Guzman
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Shutong Gang
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Michael Bielecki
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Suzana Kovacic
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Calem Kenward
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Christopher Yee Hong
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Danielle G. Gordon
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Paul N. Levett
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Robert N. Young
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - François Jean
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
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3
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Yu H, Worrall LJ, Berger T, Petric M, Lin BH, Vuckovic M, Robb CS, Le Q, Kenward C, Dai C, Wakeham A, Liu S, Snow B, Tobin C, Budylowski P, Guvenc F, You-Ten A, Haight J, Silvester J, Singh RP, Ahn SK, Sultana A, Poon B, Lam J, Christie-Holmes N, Ostrowski M, Gray-Owen SD, Kubli S, Mak T, Strynadka NCJ, Brunham RC. Identification of an Optimized Receptor-Binding Domain Subunit Vaccine against SARS-CoV-2. J Immunol 2023; 211:981-993. [PMID: 37493438 DOI: 10.4049/jimmunol.2300282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023]
Abstract
Current vaccine efforts to combat SARS-CoV-2 are focused on the whole spike protein administered as mRNA, viral vector, or protein subunit. However, the SARS-CoV-2 receptor-binding domain (RBD) is the immunodominant portion of the spike protein, accounting for 90% of serum neutralizing activity. In this study, we constructed several versions of RBD and together with aluminum hydroxide or DDA (dimethyldioctadecylammonium bromide)/TDB (d-(+)-trehalose 6,6'-dibehenate) adjuvant evaluated immunogenicity in mice. We generated human angiotensin-converting enzyme 2 knock-in mice to evaluate vaccine efficacy in vivo following viral challenge. We found that 1) subdomain (SD)1 was essential for the RBD to elicit maximal immunogenicity; 2) RBDSD1 produced in mammalian HEK cells elicited better immunogenicity than did protein produced in insect or yeast cells; 3) RBDSD1 combined with the CD4 Th1 adjuvant DDA/TDB produced higher neutralizing Ab responses and stronger CD4 T cell responses than did aluminum hydroxide; 4) addition of monomeric human Fc receptor to RBDSD1 (RBDSD1Fc) significantly enhanced immunogenicity and neutralizing Ab titers; 5) the Beta version of RBDSD1Fc provided a broad range of cross-neutralization to multiple antigenic variants of concern, including Omicron; and 6) the Beta version of RBDSD1Fc with DDA/TDB provided complete protection against virus challenge in the knock-in mouse model. Thus, we have identified an optimized RBD-based subunit vaccine suitable for clinical trials.
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Affiliation(s)
- Hong Yu
- British Columbia Centre for Disease Control, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thorsten Berger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Martin Petric
- British Columbia Centre for Disease Control, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bryan H Lin
- Department of Biochemistry and Molecular Biology, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig S Robb
- Department of Biochemistry and Molecular Biology, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Quan Le
- Department of Biochemistry and Molecular Biology, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Calem Kenward
- Department of Biochemistry and Molecular Biology, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chuanbin Dai
- British Columbia Centre for Disease Control, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Wakeham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shaofeng Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Bryan Snow
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Chantal Tobin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Patrick Budylowski
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Toronto High Containment Facility, University of Toronto, Toronto, Ontario, Canada
| | - Furkan Guvenc
- Toronto High Containment Facility, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Annick You-Ten
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jillian Haight
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jennifer Silvester
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rashim Pal Singh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sang Kyun Ahn
- Toronto High Containment Facility, University of Toronto, Toronto, Ontario, Canada
| | - Azmiri Sultana
- Toronto High Containment Facility, University of Toronto, Toronto, Ontario, Canada
| | - Betty Poon
- Toronto High Containment Facility, University of Toronto, Toronto, Ontario, Canada
| | - Jessica Lam
- Toronto High Containment Facility, University of Toronto, Toronto, Ontario, Canada
| | - Natasha Christie-Holmes
- Emerging and Pandemic Infections Consortium, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mario Ostrowski
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Scott D Gray-Owen
- Toronto High Containment Facility, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shawn Kubli
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Treadwell Therapeutics, Toronto, Ontario, Canada
| | - Tak Mak
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert C Brunham
- British Columbia Centre for Disease Control, University of British Columbia, Vancouver, British Columbia, Canada
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4
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Worrall LJ, Majewski DD, Strynadka NCJ. Structural Insights into Type III Secretion Systems of the Bacterial Flagellum and Injectisome. Annu Rev Microbiol 2023; 77:669-698. [PMID: 37713458 DOI: 10.1146/annurev-micro-032521-025503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
Two of the most fascinating bacterial nanomachines-the broadly disseminated rotary flagellum at the heart of cellular motility and the eukaryotic cell-puncturing injectisome essential to specific pathogenic species-utilize at their core a conserved export machinery called the type III secretion system (T3SS). The T3SS not only secretes the components that self-assemble into their extracellular appendages but also, in the case of the injectisome, subsequently directly translocates modulating effector proteins from the bacterial cell into the infected host. The injectisome is thought to have evolved from the flagellum as a minimal secretory system lacking motility, with the subsequent acquisition of additional components tailored to its specialized role in manipulating eukaryotic hosts for pathogenic advantage. Both nanomachines have long been the focus of intense interest, but advances in structural and functional understanding have taken a significant step forward since 2015, facilitated by the revolutionary advances in cryo-electron microscopy technologies. With several seminal structures of each nanomachine now captured, we review here the molecular similarities and differences that underlie their diverse functions.
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Affiliation(s)
- Liam J Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
| | - Dorothy D Majewski
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
- Current affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
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5
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Danby PM, Jeong A, Sim L, Sweeney RP, Wardman JF, Karimi R, Geissner A, Worrall LJ, Reid JP, Strynadka NCJ, Withers S. Vinyl Halide-Modified Unsaturated Cyclitols are Mechanism-Based Glycosidase Inhibitors. Angew Chem Int Ed Engl 2023; 62:e202301258. [PMID: 36940280 DOI: 10.1002/anie.202301258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023]
Abstract
Suitably configured allyl ethers of unsaturated cyclitols act as substrates of β-glycosidases, reacting via allylic cation transition states. Incorporation of halogens at the vinylic position of these carbasugars, along with an activated leaving group, generates potent inactivators of β-glycosidases. Enzymatic turnover of these halogenated cyclitols (F, Cl, Br) displayed a counter-intuitive trend wherein the most electronegative substituents yielded the most labile pseudo-glycosidic linkages. Structures of complexes with the Sulfolobus β-glucosidase revealed similar enzyme-ligand interactions to those seen in complexes with a 2-fluorosugar inhibitor, the lone exception being displacement of tyrosine 322 from the active site by the halogen. Mutation of Y322 to Y322F largely abolished glycosidase activity, consistent with lost interactions at O5, but minimally affected (7-fold) rates of carbasugar hydrolysis, yielding a more selective enzyme for unsaturated cyclitol ether hydrolysis.
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Affiliation(s)
| | - Andrew Jeong
- The University of British Columbia Faculty of Science, Chemistry, CANADA
| | - Lyann Sim
- The University of British Columbia, Chemistry, CANADA
| | - Ryan P Sweeney
- The University of British Columbia Faculty of Science, Chemistry, CANADA
| | - Jacob F Wardman
- The University of British Columbia Faculty of Science, Chemistry, CANADA
| | - Ryan Karimi
- The University of British Columbia, Chemistry, CANADA
| | | | - Liam J Worrall
- The University of British Columbia, Biochemistry, CANADA
| | - Jolene P Reid
- The University of British Columbia, Chemistry, CANADA
| | | | - Stephen Withers
- University of British Columbia, Chemistry, 2036 Main Mall, V6T 1Z1, Vancouver, CANADA
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6
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Garland O, Ton AT, Moradi S, Smith JR, Kovacic S, Ng K, Pandey M, Ban F, Lee J, Vuckovic M, Worrall LJ, Young RN, Pantophlet R, Strynadka NCJ, Cherkasov A. Large-Scale Virtual Screening for the Discovery of SARS-CoV-2 Papain-like Protease (PLpro) Non-covalent Inhibitors. J Chem Inf Model 2023; 63:2158-2169. [PMID: 36930801 DOI: 10.1021/acs.jcim.2c01641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
The rapid global spread of the SARS-CoV-2 virus facilitated the development of novel direct-acting antiviral agents (DAAs). The papain-like protease (PLpro) has been proposed as one of the major SARS-CoV-2 targets for DAAs due to its dual role in processing viral proteins and facilitating the host's immune suppression. This dual role makes identifying small molecules that can effectively neutralize SARS-CoV-2 PLpro activity a high-priority task. However, PLpro drug discovery faces a significant challenge due to the high mobility and induced-fit effects in the protease's active site. Herein, we virtually screened the ZINC20 database with Deep Docking (DD) to identify prospective noncovalent PLpro binders and combined ultra-large consensus docking with two pharmacophore (ph4)-filtering strategies. The analysis of active compounds revealed their somewhat-limited diversity, likely attributed to the induced-fit nature of PLpro's active site in the crystal structures, and therefore, the use of rigid docking protocols poses inherited limitations. The top hits were assessed against recombinant viral proteins and live viruses, demonstrating desirable inhibitory activities. The best compound VPC-300195 (IC50: 15 μM) ranks among the top noncovalent PLpro inhibitors discovered through in silico methodologies. In the search for novel SARS-CoV-2 PLpro-specific chemotypes, the identified inhibitors could serve as diverse templates for the development of effective noncovalent PLpro inhibitors.
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Affiliation(s)
- Olivia Garland
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Shoeib Moradi
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jason R Smith
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada.,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Suzana Kovacic
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Kurtis Ng
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Mohit Pandey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Robert N Young
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
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7
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Alexander JAN, Worrall LJ, Hu J, Vuckovic M, Satishkumar N, Poon R, Sobhanifar S, Rosell FI, Jenkins J, Chiang D, Mosimann WA, Chambers HF, Paetzel M, Chatterjee SS, Strynadka NCJ. Structural basis of broad-spectrum β-lactam resistance in Staphylococcus aureus. Nature 2023; 613:375-382. [PMID: 36599987 PMCID: PMC9834060 DOI: 10.1038/s41586-022-05583-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/18/2022] [Indexed: 01/05/2023]
Abstract
Broad-spectrum β-lactam antibiotic resistance in Staphylococcus aureus is a global healthcare burden1,2. In clinical strains, resistance is largely controlled by BlaR13, a receptor that senses β-lactams through the acylation of its sensor domain, inducing transmembrane signalling and activation of the cytoplasmic-facing metalloprotease domain4. The metalloprotease domain has a role in BlaI derepression, inducing blaZ (β-lactamase PC1) and mecA (β-lactam-resistant cell-wall transpeptidase PBP2a) expression3-7. Here, overcoming hurdles in isolation, we show that BlaR1 cleaves BlaI directly, as necessary for inactivation, with no requirement for additional components as suggested previously8. Cryo-electron microscopy structures of BlaR1-the wild type and an autocleavage-deficient F284A mutant, with or without β-lactam-reveal a domain-swapped dimer that we suggest is critical to the stabilization of the signalling loops within. BlaR1 undergoes spontaneous autocleavage in cis between Ser283 and Phe284 and we describe the catalytic mechanism and specificity underlying the self and BlaI cleavage. The structures suggest that allosteric signalling emanates from β-lactam-induced exclusion of the prominent extracellular loop bound competitively in the sensor-domain active site, driving subsequent dynamic motions, including a shift in the sensor towards the membrane and accompanying changes in the zinc metalloprotease domain. We propose that this enhances the expulsion of autocleaved products from the active site, shifting the equilibrium to a state that is permissive of efficient BlaI cleavage. Collectively, this study provides a structure of a two-component signalling receptor that mediates action-in this case, antibiotic resistance-through the direct cleavage of a repressor.
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Affiliation(s)
- J Andrew N Alexander
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
- HRMEM Facility, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jinhong Hu
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Nidhi Satishkumar
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA
- Institute of Marine and Environmental Technology, Baltimore, MD, USA
| | - Raymond Poon
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA
- Institute of Marine and Environmental Technology, Baltimore, MD, USA
| | - Solmaz Sobhanifar
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Federico I Rosell
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Joshua Jenkins
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel Chiang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Wesley A Mosimann
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Henry F Chambers
- Division of Infectious Diseases, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Som S Chatterjee
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA
- Institute of Marine and Environmental Technology, Baltimore, MD, USA
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada.
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada.
- HRMEM Facility, The University of British Columbia, Vancouver, British Columbia, Canada.
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8
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Fedoretz-Maxwell BP, Shin CH, MacNeil GA, Worrall LJ, Park R, Strynadka NCJ, Walsby CJ, Warren JJ. The Impact of Second Coordination Sphere Methionine-Aromatic Interactions in Copper Proteins. Inorg Chem 2022; 61:5563-5571. [DOI: 10.1021/acs.inorgchem.2c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brooklyn P. Fedoretz-Maxwell
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Catherine H. Shin
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Gregory A. MacNeil
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Rachel Park
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Charles J. Walsby
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jeffrey J. Warren
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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9
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Yu ACY, Volkers G, Jongkees SAK, Worrall LJ, Withers SG, Strynadka NCJ. Crystal structure of the Propionibacterium acnes surface sialidase, a drug target for P. acnes-associated diseases. Glycobiology 2021; 32:162-170. [PMID: 34792586 DOI: 10.1093/glycob/cwab094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 11/12/2022] Open
Abstract
Propionibacterium acnes, though generally considered part of the normal flora of human skin, is an opportunistic pathogen associated with acne vulgaris as well as other diseases, including endocarditis, endophthalmitis and prosthetic joint infections. Its virulence potential is also supported by knowledge gained from its sequenced genome. Indeed, a vaccine targeting a putative cell wall-anchored P. acnes sialidase has been shown to suppress cytotoxicity and pro-inflammatory cytokine release induced by the organism, and is proposed as an alternative treatment for P. acnes-associated diseases. Here, we report the crystal structures of the surface sialidase and its complex with the transition-state mimic Neu5Ac2en. Our structural and kinetic analyses, together with insight from a glycan array screen, which probes subtle specificities of the sialidase for α-2,3-sialosides, provide a basis for the structure-based design of novel small-molecule therapeutics against P. acnes infections.
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Affiliation(s)
- Angel C Y Yu
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, 2350 Health Sciences Mall, V6T 1Z3, Canada
| | - Gesa Volkers
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, 2350 Health Sciences Mall, V6T 1Z3, Canada
| | - Seino A K Jongkees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, 2350 Health Sciences Mall, V6T 1Z3, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, 2350 Health Sciences Mall, V6T 1Z3, Canada
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10
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Lee J, Worrall LJ, Vuckovic M, Rosell FI, Gentile F, Ton AT, Caveney NA, Ban F, Cherkasov A, Paetzel M, Strynadka NCJ. Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Nat Commun 2020; 11:5877. [PMID: 33208735 PMCID: PMC7674412 DOI: 10.1038/s41467-020-19662-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 10/15/2020] [Indexed: 12/29/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (Mpro) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on Mpro inhibition.
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Affiliation(s)
- Jaeyong Lee
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Federico I Rosell
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Francesco Gentile
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, BC, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, BC, Canada
| | - Nathanael A Caveney
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, BC, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, BC, Canada
| | - Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada.
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11
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Affiliation(s)
- Liam J. Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
- HRMEM Facility, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jinhong Hu
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
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12
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Hu J, Worrall LJ, Strynadka NCJ. Towards capture of dynamic assembly and action of the T3SS at near atomic resolution. Curr Opin Struct Biol 2020; 61:71-78. [DOI: 10.1016/j.sbi.2019.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 10/17/2019] [Indexed: 11/30/2022]
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13
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Hu J, Worrall LJ, Hong C, Vuckovic M, Atkinson CE, Caveney N, Yu Z, Strynadka NCJ. Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin. Nat Commun 2018; 9:3840. [PMID: 30242280 PMCID: PMC6155069 DOI: 10.1038/s41467-018-06298-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/20/2018] [Indexed: 11/09/2022] Open
Abstract
The bacterial type III secretion system, or injectisome, is a syringe shaped nanomachine essential for the virulence of many disease causing Gram-negative bacteria. At the core of the injectisome structure is the needle complex, a continuous channel formed by the highly oligomerized inner and outer membrane hollow rings and a polymerized helical needle filament which spans through and projects into the infected host cell. Here we present the near-atomic resolution structure of a needle complex from the prototypical Salmonella Typhimurium SPI-1 type III secretion system, with local masking protocols allowing for model building and refinement of the major membrane spanning components of the needle complex base in addition to an isolated needle filament. This work provides significant insight into injectisome structure and assembly and importantly captures the molecular basis for substrate induced gating in the giant outer membrane secretin portal family.
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Affiliation(s)
- J Hu
- Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - L J Worrall
- Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
- HRMEM facility, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - C Hong
- CryoEM Shared Resources, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, 20147, VA, USA
| | - M Vuckovic
- Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - C E Atkinson
- Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
- HRMEM facility, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - N Caveney
- Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - Z Yu
- CryoEM Shared Resources, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, 20147, VA, USA
| | - N C J Strynadka
- Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada.
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14
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Majewski DD, Worrall LJ, Strynadka NCJ. Secretins revealed: structural insights into the giant gated outer membrane portals of bacteria. Curr Opin Struct Biol 2018; 51:61-72. [DOI: 10.1016/j.sbi.2018.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/28/2018] [Indexed: 01/19/2023]
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15
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Zeytuni N, Flanagan KA, Worrall LJ, Massoni SC, Camp AH, Strynadka NCJ. Structural characterization of SpoIIIAB sporulation-essential protein in Bacillus subtilis. J Struct Biol 2017; 202:105-112. [PMID: 29288127 DOI: 10.1016/j.jsb.2017.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 11/28/2022]
Abstract
Endospore formation in the Gram-positive bacterium Bacillus subtilis initiates in response to nutrient depletion and involves a series of morphological changes that result in the creation of a dormant spore. Early in this developmental process, the cell undergoes an asymmetric cell division that produces the larger mother cell and smaller forespore, the latter destined to become the mature spore. The mother cell septal membrane then engulfs the forespore, at which time an essential channel, the so-called feeding-tube apparatus, is thought to cross both membranes to create a direct conduit between the cells. At least nine proteins are required to form this channel including SpoIIQ under forespore control and SpoIIIAA-AH under the mother cell control. Several of these proteins share similarity to components of Type-II, -III and -IV secretion systems as well as the flagellum from Gram-negative bacteria. Here we report the X-ray crystallographic structure of the cytosolic domain of SpoIIIAB to 2.3 Å resolution. This domain adopts a conserved, secretion-system related fold of a six membered anti-parallel helical bundle with a positively charged membrane-interaction face at one end and a small groove at the other end that may serve as a binding site for partner proteins in the assembled apparatus. We analyzed and identified potential interaction interfaces by structure-guided mutagenesis in vivo. Furthermore, we were able to identify a remarkable structural homology to the C-subunit of a bacterial V-ATPase. Collectively, our data provides new insight into the possible roles of SpoIIIAB protein within the secretion-like apparatus essential to bacterial sporulation.
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Affiliation(s)
- N Zeytuni
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - K A Flanagan
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | - L J Worrall
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - S C Massoni
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | - A H Camp
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA.
| | - N C J Strynadka
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada.
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16
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Deng W, Marshall NC, Rowland JL, McCoy JM, Worrall LJ, Santos AS, Strynadka NCJ, Finlay BB. Erratum: Assembly, structure, function and regulation of type III secretion systems. Nat Rev Microbiol 2017; 15:379. [DOI: 10.1038/nrmicro.2017.54] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Sobhanifar S, Worrall LJ, King DT, Wasney GA, Baumann L, Gale RT, Nosella M, Brown ED, Withers SG, Strynadka NCJ. Structure and Mechanism of Staphylococcus aureus TarS, the Wall Teichoic Acid β-glycosyltransferase Involved in Methicillin Resistance. PLoS Pathog 2016; 12:e1006067. [PMID: 27973583 PMCID: PMC5156392 DOI: 10.1371/journal.ppat.1006067] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/15/2016] [Indexed: 01/05/2023] Open
Abstract
In recent years, there has been a growing interest in teichoic acids as targets for antibiotic drug design against major clinical pathogens such as Staphylococcus aureus, reflecting the disquieting increase in antibiotic resistance and the historical success of bacterial cell wall components as drug targets. It is now becoming clear that β-O-GlcNAcylation of S. aureus wall teichoic acids plays a major role in both pathogenicity and antibiotic resistance. Here we present the first structure of S. aureus TarS, the enzyme responsible for polyribitol phosphate β-O-GlcNAcylation. Using a divide and conquer strategy, we obtained crystal structures of various TarS constructs, mapping high resolution overlapping N-terminal and C-terminal structures onto a lower resolution full-length structure that resulted in a high resolution view of the entire enzyme. Using the N-terminal structure that encapsulates the catalytic domain, we furthermore captured several snapshots of TarS, including the native structure, the UDP-GlcNAc donor complex, and the UDP product complex. These structures along with structure-guided mutants allowed us to elucidate various catalytic features and identify key active site residues and catalytic loop rearrangements that provide a valuable platform for anti-MRSA drug design. We furthermore observed for the first time the presence of a trimerization domain composed of stacked carbohydrate binding modules, commonly observed in starch active enzymes, but adapted here for a poly sugar-phosphate glycosyltransferase. Historically, β-lactam class antibiotics such as methicillin have been very successful in the treatment of bacterial infections, effectively destroying bacteria by rupturing their cell walls while posing little harm to the human organism. In recent years, however, the alarming emergence of Methicillin Resistant S. aureus or MRSA has resulted in a world-wide health crisis, calling on new strategies to combat pathogenesis and antibiotic resistance. As such, understanding the pathways and players that orchestrate resistance is important for overcoming these mechanisms and restoring our powerful β-lactam antibiotic arsenal. In this article we describe the crystal structure of TarS, an enzyme responsible for the glycosylation of wall teichoic acid polymers of the S. aureus cell wall, a process that has been shown to be specifically responsible for methicillin resistance in MRSA. TarS is therefore a promising drug target whose inhibition in combinational therapies would result in MRSA re-sensitization to β-lactam antibiotics. Here we present the first structure of TarS together with several snap-shots of its substrate/product complexes, and elucidate important catalytic features that are valuable for rational drug design efforts to combat resistance in MRSA.
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Affiliation(s)
- Solmaz Sobhanifar
- Department of Biochemistry and Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dustin T. King
- Department of Biochemistry and Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gregory A. Wasney
- Department of Biochemistry and Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lars Baumann
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert T. Gale
- Department of Chemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Michael Nosella
- Department of Biochemistry and Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric D. Brown
- Department of Chemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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18
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Volkers G, Worrall LJ, Kwan DH, Yu CC, Baumann L, Lameignere E, Wasney GA, Scott NE, Wakarchuk W, Foster LJ, Withers SG, Strynadka NCJ. Structure of human ST8SiaIII sialyltransferase provides insight into cell-surface polysialylation. Nat Struct Mol Biol 2015; 22:627-35. [DOI: 10.1038/nsmb.3060] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 06/19/2015] [Indexed: 11/09/2022]
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19
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Burkinshaw BJ, Deng W, Lameignère E, Wasney GA, Zhu H, Worrall LJ, Finlay BB, Strynadka NCJ. Structural analysis of a specialized type III secretion system peptidoglycan-cleaving enzyme. J Biol Chem 2015; 290:10406-17. [PMID: 25678709 DOI: 10.1074/jbc.m115.639013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Indexed: 01/20/2023] Open
Abstract
The Gram-negative bacterium enteropathogenic Escherichia coli uses a syringe-like type III secretion system (T3SS) to inject virulence or "effector" proteins into the cytoplasm of host intestinal epithelial cells. To assemble, the T3SS must traverse both bacterial membranes, as well as the peptidoglycan layer. Peptidoglycan is made of repeating N-acetylmuramic acid and N-acetylglucosamine disaccharides cross-linked by pentapeptides to form a tight mesh barrier. Assembly of many macromolecular machines requires a dedicated peptidoglycan lytic enzyme (PG-lytic enzyme) to locally clear peptidoglycan. Here we have solved the first structure of a T3SS-associated PG-lytic enzyme, EtgA from enteropathogenic E. coli. Unexpectedly, the active site of EtgA has features in common with both lytic transglycosylases and hen egg white lysozyme. Most notably, the β-hairpin region resembles that of lysozyme and contains an aspartate that aligns with lysozyme Asp-52 (a residue critical for catalysis), a conservation not observed in other previously characterized lytic transglycosylase families to which the conserved T3SS enzymes had been presumed to belong. Mutation of the EtgA catalytic glutamate, Glu-42, conserved across lytic transglycosylases and hen egg white lysozyme, and this differentiating aspartate diminishes type III secretion in vivo, supporting its essential role in clearing the peptidoglycan for T3SS assembly. Finally, we show that EtgA forms a 1:1 complex with the building block of the polymerized T3SS inner rod component, EscI, and that this interaction enhances PG-lytic activity of EtgA in vitro, collectively providing the necessary strict localization and regulation of the lytic activity to prevent overall cell lysis.
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Affiliation(s)
- Brianne J Burkinshaw
- From the Department of Biochemistry and Molecular Biology and the Center for Blood Research
| | | | - Emilie Lameignère
- From the Department of Biochemistry and Molecular Biology and the Center for Blood Research
| | - Gregory A Wasney
- From the Department of Biochemistry and Molecular Biology and the Center for Blood Research
| | - Haizhong Zhu
- From the Department of Biochemistry and Molecular Biology and the Center for Blood Research
| | - Liam J Worrall
- From the Department of Biochemistry and Molecular Biology and the Center for Blood Research
| | - B Brett Finlay
- From the Department of Biochemistry and Molecular Biology and the Center for Blood Research, the Michael Smith Laboratories, and the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Natalie C J Strynadka
- From the Department of Biochemistry and Molecular Biology and the Center for Blood Research,
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20
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Bergeron JRC, Worrall LJ, De S, Sgourakis NG, Cheung AH, Lameignere E, Okon M, Wasney GA, Baker D, McIntosh LP, Strynadka NCJ. The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body. Structure 2014; 23:161-172. [PMID: 25533490 DOI: 10.1016/j.str.2014.10.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 10/13/2014] [Accepted: 10/17/2014] [Indexed: 10/24/2022]
Abstract
The type III secretion system (T3SS) is a large macromolecular assembly found at the surface of many pathogenic Gram-negative bacteria. Its role is to inject toxic "effector" proteins into the cells of infected organisms. The molecular details of the assembly of this large, multimembrane-spanning complex remain poorly understood. Here, we report structural, biochemical, and functional analyses of PrgK, an inner-membrane component of the prototypical Salmonella typhimurium T3SS. We have obtained the atomic structures of the two ring building globular domains and show that the C-terminal transmembrane helix is not essential for assembly and secretion. We also demonstrate that structural rearrangement of the two PrgK globular domains, driven by an interconnecting linker region, may promote oligomerization into ring structures. Finally, we used electron microscopy-guided symmetry modeling to propose a structural model for the intimately associated PrgH-PrgK ring interaction within the assembled basal body.
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Affiliation(s)
- Julien R C Bergeron
- Department of Biochemistry and Molecular Biology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Soumya De
- Department of Biochemistry and Molecular Biology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Nikolaos G Sgourakis
- National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Adrienne H Cheung
- Department of Biochemistry and Molecular Biology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Emilie Lameignere
- Department of Biochemistry and Molecular Biology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Gregory A Wasney
- Department of Biochemistry and Molecular Biology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - David Baker
- Department of Biochemistry, Department of Genome Sciences, and Howard Hughes Medical Institute, University of Washington, 4000 15th Avenue NE, Seattle, WA 98195, USA
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada; Department of Chemistry, University of British Columbia, 2350 Health Sciences Mall, Vancouver BC, V6T 1Z3, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
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21
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Penfield JS, Worrall LJ, Strynadka NC, Eltis LD. Substrate specificities and conformational flexibility of 3-ketosteroid 9α-hydroxylases. J Biol Chem 2014; 289:25523-36. [PMID: 25049233 DOI: 10.1074/jbc.m114.575886] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
KshA is the oxygenase component of 3-ketosteroid 9α-hydroxylase, a Rieske oxygenase involved in the bacterial degradation of steroids. Consistent with its role in bile acid catabolism, KshA1 from Rhodococcus rhodochrous DSM43269 had the highest apparent specificity (kcat/Km) for steroids with an isopropyl side chain at C17, such as 3-oxo-23,24-bisnorcholesta-1,4-diene-22-oate (1,4-BNC). By contrast, the KshA5 homolog had the highest apparent specificity for substrates with no C17 side chain (kcat/Km >10(5) s(-1) M(-1) for 4-estrendione, 5α-androstandione, and testosterone). Unexpectedly, substrates such as 4-androstene-3,17-dione (ADD) and 4-BNC displayed strong substrate inhibition (Ki S ∼100 μM). By comparison, the cholesterol-degrading KshAMtb from Mycobacterium tuberculosis had the highest specificity for CoA-thioesterified substrates. These specificities are consistent with differences in the catabolism of cholesterol and bile acids, respectively, in actinobacteria. X-ray crystallographic structures of the KshAMtb·ADD, KshA1·1,4-BNC-CoA, KshA5·ADD, and KshA5·1,4-BNC-CoA complexes revealed that the enzymes have very similar steroid-binding pockets with the substrate's C17 oriented toward the active site opening. Comparisons suggest Tyr-245 and Phe-297 are determinants of KshA1 specificity. All enzymes have a flexible 16-residue "mouth loop," which in some structures completely occluded the substrate-binding pocket from the bulk solvent. Remarkably, the catalytic iron and α-helices harboring its ligands were displaced up to 4.4 Å in the KshA5·substrate complexes as compared with substrate-free KshA, suggesting that Rieske oxygenases may have a dynamic nature similar to cytochrome P450.
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Affiliation(s)
| | - Liam J Worrall
- From the Departments of Biochemistry and Molecular Biology and
| | | | - Lindsay D Eltis
- From the Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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22
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Bergeron JRC, Worrall LJ, Sgourakis NG, DiMaio F, Pfuetzner RA, Felise HB, Vuckovic M, Yu AC, Miller SI, Baker D, Strynadka NCJ. A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly. PLoS Pathog 2013; 9:e1003307. [PMID: 23633951 PMCID: PMC3635987 DOI: 10.1371/journal.ppat.1003307] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 03/02/2013] [Indexed: 12/22/2022] Open
Abstract
The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed of a “basal body”, a lock-nut structure spanning both bacterial membranes, and a “needle” that protrudes away from the bacterial surface. A hollow channel spans throughout the apparatus, permitting the translocation of effector proteins from the bacterial cytosol to the host plasma membrane. The basal body is composed largely of three membrane-embedded proteins that form oligomerized concentric rings. Here, we report the crystal structures of three domains of the prototypical Salmonella SPI-1 basal body, and use a new approach incorporating symmetric flexible backbone docking and EM data to produce a model for their oligomeric assembly. The obtained models, validated by biochemical and in vivo assays, reveal the molecular details of the interactions driving basal body assembly, and notably demonstrate a conserved oligomerization mechanism. Gram-negative bacteria such as E. coli, Salmonella, Shigella, Pseudomonas aeruginosa, and Yersinia pestis are responsible for a wide range of diseases, from pneumonia to lethal diarrhea and plague. A common trait shared by these bacteria is their capacity to inject toxins directly inside the cells of infected individuals, thanks to a syringe-shaped “nano-machine” called the Type III Secretion System injectisome. These toxins lead to modifications of the host cell, allowing the bacteria to replicate efficiently and/or to evade the immune system, and are necessary to establish an infection. As a consequence, the injectisome is an important potential target for the development of novel therapeutics against bacterial infection. In this study, we focus on the basal body, an essential region of the injectisome that forms the continuous hollow channel across both membranes of the bacteria. We have used an array of biophysical methods to obtain an atomic model of the basal body. This model provides new insights as to how the basal body assembles at the surface of bacteria, and could be used for the design of novel antibiotics.
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Affiliation(s)
- Julien R. C. Bergeron
- Department of Biochemistry and Molecular Biology, and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology, and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nikolaos G. Sgourakis
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Richard A. Pfuetzner
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Heather B. Felise
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology, and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angel C. Yu
- Department of Biochemistry and Molecular Biology, and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel I. Miller
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
- * E-mail: (DB); (NCJS)
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology, and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail: (DB); (NCJS)
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23
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King DT, Worrall LJ, Gruninger R, Strynadka NCJ. New Delhi metallo-β-lactamase: structural insights into β-lactam recognition and inhibition. J Am Chem Soc 2012; 134:11362-5. [PMID: 22713171 DOI: 10.1021/ja303579d] [Citation(s) in RCA: 228] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The β-lactam antibiotics have long been a cornerstone for the treatment of bacterial disease. Recently, a readily transferable antibiotic resistance factor called the New Delhi metallo-β-lactamase-1 (NDM-1) has been found to confer enteric bacteria resistance to nearly all β-lactams, including the heralded carbapenems, posing a serious threat to human health. The crystal structure of NDM-1 bound to meropenem shows for the first time the molecular details of how carbapenem antibiotics are recognized by dizinc-containing metallo-β-lactamases. Additionally, product complex structures of hydrolyzed benzylpenicillin-, methicillin-, and oxacillin-bound NDM-1 have been solved to 1.8, 1.2, and 1.2 Å, respectively, and represent the highest-resolution structural data for any metallo-β-lactamase reported to date. Finally, we present the crystal structure of NDM-1 bound to the potent competitive inhibitor l-captopril, which reveals a unique binding mechanism. An analysis of the NDM-1 active site in these structures reveals key features important for the informed design of novel inhibitors of NDM-1 and other metallo-β-lactamases.
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Affiliation(s)
- Dustin T King
- Department of Biochemistry and Molecular Biology and Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
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24
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Yu ACY, Worrall LJ, Strynadka NCJ. Structural insight into the bacterial mucinase StcE essential to adhesion and immune evasion during enterohemorrhagic E. coli infection. Structure 2012; 20:707-17. [PMID: 22483117 DOI: 10.1016/j.str.2012.02.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 02/11/2012] [Accepted: 02/16/2012] [Indexed: 01/19/2023]
Abstract
Mucin glycoproteins with large numbers of O-linked glycosylations comprise the mucosal barrier lining the mammalian gastrointestinal tract from mouth to gut. A critical biological function of mucins is to protect the underlying epithelium from infection. Enterohemorrhagic Escherichia coli (EHEC), the mediator of severe food- and water-borne disease, can breach this barrier and adhere to intestinal cells. StcE, a ∼100 kDa metalloprotease secreted by EHEC, plays a pivotal role in remodeling the mucosal lining during infection. To obtain mechanistic insight into its function, we have determined the structure of StcE. Our data reveal a dynamic, multidomain architecture featuring an unusually large substrate-binding cleft and a prominent polarized surface charge distribution highly suggestive of an electrostatic role in substrate targeting. The observation of key conserved motifs in the active site allows us to propose the structural basis for the specific recognition of α-O-glycan-containing substrates. Complementary biochemical analysis provides further insight into its distinct substrate specificity and binding stoichiometry.
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Affiliation(s)
- Angel C Y Yu
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, Life Sciences Center, 2350 Health Sciences Mall, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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25
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Burkinshaw BJ, Prehna G, Worrall LJ, Strynadka NCJ. Structure of Salmonella effector protein SopB N-terminal domain in complex with host Rho GTPase Cdc42. J Biol Chem 2012; 287:13348-55. [PMID: 22362774 DOI: 10.1074/jbc.m111.331330] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
SopB is a type III secreted Salmonella effector protein with phosphoinositide phosphatase activity and a distinct GTPase binding domain. The latter interacts with host Cdc42, an essential Rho GTPase that regulates critical events in eukaryotic cytoskeleton organization and membrane trafficking. Structural and biochemical analysis of the SopB GTPase binding domain in complex with Cdc42 shows for the first time that SopB structurally and functionally mimics a host guanine nucleotide dissociation inhibitor (GDI) by contacting key residues in the regulatory switch regions of Cdc42 and slowing Cdc42 nucleotide exchange.
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Affiliation(s)
- Brianne J Burkinshaw
- Department of Biochemistry and Molecular Biology and Center for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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26
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Worrall LJ, Lameignere E, Strynadka NCJ. Structural overview of the bacterial injectisome. Curr Opin Microbiol 2010; 14:3-8. [PMID: 21112241 DOI: 10.1016/j.mib.2010.10.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 10/27/2010] [Accepted: 10/29/2010] [Indexed: 12/30/2022]
Abstract
The bacterial injectisome is a specialized protein-export system utilized by many pathogenic Gram-negative bacteria for the delivery of virulence proteins into the hosts they infect. This needle-like molecular nanomachine comprises >20 proteins creating a continuous passage from bacterial to host cytoplasm. The last few years have witnessed significant progress in our understanding of the structure of the injectisome with important contributions from X-ray crystallography, NMR and EM. This review will present the current state of the structure of the injectisome with particular focus on the molecular structures of individual components and how these assemble together in a functioning T3SS.
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Affiliation(s)
- Liam J Worrall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall Vancouver, British Columbia, Canada
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27
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Worrall LJ, Vuckovic M, Strynadka NCJ. Crystal structure of the C-terminal domain of the Salmonella type III secretion system export apparatus protein InvA. Protein Sci 2010; 19:1091-6. [PMID: 20306492 DOI: 10.1002/pro.382] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
InvA is a prominent inner-membrane component of the Salmonella type III secretion system (T3SS) apparatus, which is responsible for regulating virulence protein export in pathogenic bacteria. InvA is made up of an N-terminal integral membrane domain and a C-terminal cytoplasmic domain that is proposed to form part of a docking platform for the soluble export apparatus proteins notably the T3SS ATPase InvC. Here, we report the novel crystal structure of the C-terminal domain of Salmonella InvA which shows a compact structure composed of four subdomains. The overall structure is unique although the first and second subdomains exhibit structural similarity to the peripheral stalk of the A/V-type ATPase and a ring building motif found in other T3SS proteins respectively.
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Affiliation(s)
- Liam J Worrall
- Centre for Blood Research, Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, British Columbia, Canada V6T 1Z3
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28
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Worrall LJ, Wear MA, Page AP, Walkinshaw MD. Cloning, purification and characterization of the Caenorhabditis elegans small glutamine-rich tetratricopeptide repeat-containing protein. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2008; 1784:496-503. [DOI: 10.1016/j.bbapap.2007.12.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 11/27/2007] [Accepted: 12/10/2007] [Indexed: 11/15/2022]
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Worrall LJ, Walkinshaw MD. Crystal structure of the C-terminal three-helix bundle subdomain of C. elegans Hsp70. Biochem Biophys Res Commun 2007; 357:105-10. [PMID: 17407764 DOI: 10.1016/j.bbrc.2007.03.107] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 03/16/2007] [Indexed: 01/21/2023]
Abstract
Hsp70 chaperones are composed of two domains; the 40 kDa N-terminal nucleotide-binding domain (NDB) and the 30 kDa C-terminal substrate-binding domain (SBD). Structures of the SBD from Escherichia coli homologues DnaK and HscA show it can be further divided into an 18 kDa beta-sandwich subdomain, which forms the hydrophobic binding pocket, and a 10 kDa C-terminal three-helix bundle that forms a lid over the binding pocket. Across prokaryotes and eukaryotes, the NBD and beta-sandwich subdomain are well conserved in both sequence and structure. The C-terminal subdomain is, however, more evolutionary variable and the only eukaryotic structure from rat Hsc70 revealed a diverged helix-loop-helix fold. We have solved the crystal structure of the C-terminal 10 kDa subdomain from Caenorhabditis elegans Hsp70 which forms a helical-bundle similar to the prokaryotic homologues. This provides the first confirmation of the structural conservation of this subdomain in eukaryotes. Comparison with the rat structure reveals a domain-swap dimerisation mechanism; however, the C. elegans subdomain exists exclusively as a monomer in solution in agreement with the hypothesis that regions out with the C-terminal subdomain are necessary for Hsp70 self-association.
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Affiliation(s)
- Liam J Worrall
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK
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