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Singh A, Chakraborty J, Pal S, Das D. Site-selective peptide bond hydrolysis and ligation in water by short peptide-based assemblies. Proc Natl Acad Sci U S A 2024; 121:e2321396121. [PMID: 39042686 PMCID: PMC11295027 DOI: 10.1073/pnas.2321396121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 06/20/2024] [Indexed: 07/25/2024] Open
Abstract
The evolution of complex chemical inventory from Darwin's nutrient-rich warm pond necessitated rudimentary yet efficient catalytic folds. Short peptides and their self-organized microstructures, ranging from spherical colloids to amyloidogenic aggregates might have played a crucial role in the emergence of contemporary catalytic entities. However, the question of how short peptide fragments had functions akin to contemporary complex enzymes to catalyze cleavage and formation of highly stable peptide bonds that constitute the backbone of all proteins remains an unresolved yet fundamentally important question in terms of the origins of enzymes. We report short-peptide-based spherical assemblies that demonstrated residue-specific cleavage and formation of peptide bonds of diverse peptide-based substrates under aqueous environment. Despite the short sequence length, the assemblies utilized the synergistic collaboration of four residues which included the catalytic triad of extant serine proteases with a nonproteinogenic amino acid (quinone moiety), to facilitate proteolysis, ligation, and a three-step (hydrolysis-ligation-hydrolysis) cascade. Such short-peptide-based catalytic assemblies argue for their candidacy as the earliest protein folds and open up avenues for biotechnological applications.
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Affiliation(s)
- Abhishek Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
| | - Janardan Chakraborty
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
| | - Sumit Pal
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
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2
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Miura T, Malla TR, Owen CD, Tumber A, Brewitz L, McDonough MA, Salah E, Terasaka N, Katoh T, Lukacik P, Strain-Damerell C, Mikolajek H, Walsh MA, Kawamura A, Schofield CJ, Suga H. In vitro selection of macrocyclic peptide inhibitors containing cyclic γ 2,4-amino acids targeting the SARS-CoV-2 main protease. Nat Chem 2023:10.1038/s41557-023-01205-1. [PMID: 37217786 DOI: 10.1038/s41557-023-01205-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/14/2023] [Indexed: 05/24/2023]
Abstract
γ-Amino acids can play important roles in the biological activities of natural products; however, the ribosomal incorporation of γ-amino acids into peptides is challenging. Here we report how a selection campaign employing a non-canonical peptide library containing cyclic γ2,4-amino acids resulted in the discovery of very potent inhibitors of the SARS-CoV-2 main protease (Mpro). Two kinds of cyclic γ2,4-amino acids, cis-3-aminocyclobutane carboxylic acid (γ1) and (1R,3S)-3-aminocyclopentane carboxylic acid (γ2), were ribosomally introduced into a library of thioether-macrocyclic peptides. One resultant potent Mpro inhibitor (half-maximal inhibitory concentration = 50 nM), GM4, comprising 13 residues with γ1 at the fourth position, manifests a 5.2 nM dissociation constant. An Mpro:GM4 complex crystal structure reveals the intact inhibitor spans the substrate binding cleft. The γ1 interacts with the S1' catalytic subsite and contributes to a 12-fold increase in proteolytic stability compared to its alanine-substituted variant. Knowledge of interactions between GM4 and Mpro enabled production of a variant with a 5-fold increase in potency.
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Affiliation(s)
- Takashi Miura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tika R Malla
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - C David Owen
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Anthony Tumber
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Lennart Brewitz
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Michael A McDonough
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Eidarus Salah
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Petra Lukacik
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Claire Strain-Damerell
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Halina Mikolajek
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Martin A Walsh
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Akane Kawamura
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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3
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Chan HTH, Moesser MA, Walters RK, Malla TR, Twidale RM, John T, Deeks HM, Johnston-Wood T, Mikhailov V, Sessions RB, Dawson W, Salah E, Lukacik P, Strain-Damerell C, Owen CD, Nakajima T, Świderek K, Lodola A, Moliner V, Glowacki DR, Spencer J, Walsh MA, Schofield CJ, Genovese L, Shoemark DK, Mulholland AJ, Duarte F, Morris GM. Discovery of SARS-CoV-2 M pro peptide inhibitors from modelling substrate and ligand binding. Chem Sci 2021; 12:13686-13703. [PMID: 34760153 PMCID: PMC8549791 DOI: 10.1039/d1sc03628a] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/05/2021] [Indexed: 12/22/2022] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target, but little is known about structural aspects of how it binds to its 11 natural cleavage sites. We used biophysical and crystallographic data and an array of biomolecular simulation techniques, including automated docking, molecular dynamics (MD) and interactive MD in virtual reality, QM/MM, and linear-scaling DFT, to investigate the molecular features underlying recognition of the natural Mpro substrates. We extensively analysed the subsite interactions of modelled 11-residue cleavage site peptides, crystallographic ligands, and docked COVID Moonshot-designed covalent inhibitors. Our modelling studies reveal remarkable consistency in the hydrogen bonding patterns of the natural Mpro substrates, particularly on the N-terminal side of the scissile bond. They highlight the critical role of interactions beyond the immediate active site in recognition and catalysis, in particular plasticity at the S2 site. Building on our initial Mpro-substrate models, we used predictive saturation variation scanning (PreSaVS) to design peptides with improved affinity. Non-denaturing mass spectrometry and other biophysical analyses confirm these new and effective 'peptibitors' inhibit Mpro competitively. Our combined results provide new insights and highlight opportunities for the development of Mpro inhibitors as anti-COVID-19 drugs.
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Affiliation(s)
- H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Marc A Moesser
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
| | - Rebecca K Walters
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tika R Malla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Helen M Deeks
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tristan Johnston-Wood
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Victor Mikhailov
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - William Dawson
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Petra Lukacik
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - C David Owen
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Takahito Nakajima
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Katarzyna Świderek
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - Alessio Lodola
- Food and Drug Department, University of Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Vicent Moliner
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - David R Glowacki
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - James Spencer
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Martin A Walsh
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Luigi Genovese
- Univ. Grenoble Alpes, CEA, IRIG-MEM-L_Sim 38000 Grenoble France
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Garrett M Morris
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
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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: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [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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5
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He Y, Lei J, Pan X, Huang X, Zhao Y. The hydrolytic water molecule of Class A β-lactamase relies on the acyl-enzyme intermediate ES* for proper coordination and catalysis. Sci Rep 2020; 10:10205. [PMID: 32576842 PMCID: PMC7311446 DOI: 10.1038/s41598-020-66431-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/06/2020] [Indexed: 11/16/2022] Open
Abstract
Serine-based β-lactamases of Class A, C and D all rely on a key water molecule to hydrolyze and inactivate β-lactam antibiotics. This process involves two conserved catalytic steps. In the first acylation step, the β-lactam antibiotic forms an acyl-enzyme intermediate (ES*) with the catalytic serine residue. In the second deacylation step, an activated water molecule serves as nucleophile (WAT_Nu) to attack ES* and release the inactivated β-lactam. The coordination and activation of WAT_Nu is not fully understood. Using time-resolved x-ray crystallography and QM/MM simulations, we analyzed three intermediate structures of Class A β-lactamase PenP as it slowly hydrolyzed cephaloridine. WAT_Nu is centrally located in the apo structure but becomes slightly displaced away by ES* in the post-acylation structure. In the deacylation structure, WAT_Nu moves back and is positioned along the Bürgi–Dunitz trajectory with favorable energetic profile to attack ES*. Unexpectedly, WAT_Nu is also found to adopt a catalytically incompetent conformation in the deacylation structure forming a hydrogen bond with ES*. Our results reveal that ES* plays a significant role in coordinating and activating WAT_Nu through subtle yet distinct interactions at different stages of the catalytic process. These interactions may serve as potential targets to circumvent β-lactamase-mediated antibiotic resistance.
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Affiliation(s)
- Yunjiao He
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, P. R. China.,Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Jinping Lei
- Department of Chemistry, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China.,School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Xuehua Pan
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, P. R. China.,Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Xuhui Huang
- Department of Chemistry, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China.
| | - Yanxiang Zhao
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, P. R. China. .,Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China.
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6
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Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes. Sci Rep 2016; 6:27808. [PMID: 27298067 PMCID: PMC4906287 DOI: 10.1038/srep27808] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/19/2016] [Indexed: 11/10/2022] Open
Abstract
Enzyme activity (often quantified by kcat/Km) is the main function of enzyme when it is active against the specific substrate. Higher or lower activities are highly desired for the design of novel enzyme and drug resistance. However, it is difficult to measure the activities of all possible variants and find the “hot-spot” within the limit of experimental time. In this study, we explore the underlying energy landscape of enzyme-substrate interactions and introduce the intrinsic specificity ratio (ISR), which reflects the landscape topography. By studying two concrete systems, we uncover the statistical correlation between the intrinsic specificity and the enzyme activity kcat/Km. This physics-based concept and method show that the energy landscape topography is valuable for understanding the relationship between enzyme specificity and activity. In addition, it can reveal the underlying mechanism of enzyme-substrate actions and has potential applications on enzyme design.
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7
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Choi H, Paton RS, Park H, Schofield CJ. Investigations on recyclisation and hydrolysis in avibactam mediated serine β-lactamase inhibition. Org Biomol Chem 2016; 14:4116-28. [PMID: 27072755 PMCID: PMC4847122 DOI: 10.1039/c6ob00353b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/04/2016] [Indexed: 01/13/2023]
Abstract
β-Lactams inhibit penicillin-binding proteins (PBPs) and serine β-lactamases by acylation of a nucleophilic active site serine. Avibactam is approved for clinical use in combination with ceftazidime, and is a breakthrough non β-lactam β-lactamase inhibitor also reacting via serine acylation. Molecular dynamics (MD) and quantum chemical calculations on avibactam-mediated inhibition of a clinically relevant cephalosporinase reveal that recyclisation of the avibactam derived carbamoyl complex is favoured over hydrolysis. In contrast, we show that analogous recyclisation in β-lactam mediated inhibition is disfavoured. Avibactam recyclisation is promoted by a proton shuttle, a 'structural' water protonating the nucleophilic serine, and stabilization of the negative charge developed on aminocarbonyl oxygen. The results imply the potential of calculations for distinguishing between bifurcating pathways during inhibition and in generating hypotheses for predicting resistance. The inability of β-lactams to undergo recyclisation may be an Achilles heel, but one that can be addressed by suitably functionalized reversibly binding inhibitors.
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Affiliation(s)
- Hwanho Choi
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 143-747, Korea. and Chemical Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Robert S Paton
- Chemical Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 143-747, Korea.
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8
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Shoda SI, Uyama H, Kadokawa JI, Kimura S, Kobayashi S. Enzymes as Green Catalysts for Precision Macromolecular Synthesis. Chem Rev 2016; 116:2307-413. [PMID: 26791937 DOI: 10.1021/acs.chemrev.5b00472] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The present article comprehensively reviews the macromolecular synthesis using enzymes as catalysts. Among the six main classes of enzymes, the three classes, oxidoreductases, transferases, and hydrolases, have been employed as catalysts for the in vitro macromolecular synthesis and modification reactions. Appropriate design of reaction including monomer and enzyme catalyst produces macromolecules with precisely controlled structure, similarly as in vivo enzymatic reactions. The reaction controls the product structure with respect to substrate selectivity, chemo-selectivity, regio-selectivity, stereoselectivity, and choro-selectivity. Oxidoreductases catalyze various oxidation polymerizations of aromatic compounds as well as vinyl polymerizations. Transferases are effective catalysts for producing polysaccharide having a variety of structure and polyesters. Hydrolases catalyzing the bond-cleaving of macromolecules in vivo, catalyze the reverse reaction for bond forming in vitro to give various polysaccharides and functionalized polyesters. The enzymatic polymerizations allowed the first in vitro synthesis of natural polysaccharides having complicated structures like cellulose, amylose, xylan, chitin, hyaluronan, and chondroitin. These polymerizations are "green" with several respects; nontoxicity of enzyme, high catalyst efficiency, selective reactions under mild conditions using green solvents and renewable starting materials, and producing minimal byproducts. Thus, the enzymatic polymerization is desirable for the environment and contributes to "green polymer chemistry" for maintaining sustainable society.
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Affiliation(s)
- Shin-ichiro Shoda
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University , Aoba-ku, Sendai 980-8579, Japan
| | - Hiroshi Uyama
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Jun-ichi Kadokawa
- Department of Chemistry, Biotechnology, and Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University , Korimoto, Kagoshima 890-0065, Japan
| | - Shunsaku Kimura
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University , Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shiro Kobayashi
- Center for Fiber & Textile Science, Kyoto Institute of Technology , Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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9
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Hofbauer S, Brito JA, Mulchande J, Nogly P, Pessanha M, Moreira R, Archer M. Stabilization of porcine pancreatic elastase crystals by glutaraldehyde cross-linking. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:1346-51. [PMID: 26457529 DOI: 10.1107/s2053230x15017045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/11/2015] [Indexed: 11/10/2022]
Abstract
Elastase is a serine protease from the chymotrypsin family of enzymes with the ability to degrade elastin, an important component of connective tissues. Excessive elastin proteolysis leads to a number of pathological diseases. Porcine pancreatic elastase (PPE) is often used for drug development as a model for human leukocyte elastase (HLE), with which it shares high sequence identity. Crystals of PPE were grown overnight using sodium sulfate and sodium acetate at acidic pH. Cross-linking the crystals with glutaraldehyde was needed to resist the soaking procedure with a diethyl N-(methyl)pyridinyl-substituted oxo-β-lactam inhibitor. Crystals of PPE bound to the inhibitor belonged to the orthorhombic space group P2₁2₁2₁, with unit-cell parameters a = 51.0, b = 58.3, c = 74.9 Å, and diffracted to 1.8 Å resolution using an in-house X-ray source.
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Affiliation(s)
- Stefan Hofbauer
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, 2780-157 Oeiras, Portugal
| | - José A Brito
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, 2780-157 Oeiras, Portugal
| | - Jalmira Mulchande
- Research Institute for Medicines (i-Med.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Avenida Professor Gama Pinto, 1649-003 Lisboa, Portugal
| | - Przemyslaw Nogly
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, 2780-157 Oeiras, Portugal
| | - Miguel Pessanha
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, 2780-157 Oeiras, Portugal
| | - Rui Moreira
- Research Institute for Medicines (i-Med.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Avenida Professor Gama Pinto, 1649-003 Lisboa, Portugal
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, 2780-157 Oeiras, Portugal
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10
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Fako VE, Zhang JT, Liu JY. Mechanism of Orlistat Hydrolysis by the Thioesterase of Human Fatty Acid Synthase. ACS Catal 2014; 4:3444-3453. [PMID: 25309810 PMCID: PMC4188697 DOI: 10.1021/cs500956m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 08/15/2014] [Indexed: 01/25/2023]
Abstract
Fatty acid synthase (FASN), the sole protein capable of de novo synthesis of free fatty acids, is overexpressed in a wide variety of human cancers and is associated with poor prognosis and aggressiveness of these cancers. Orlistat, an FDA-approved drug for obesity treatment that inhibits pancreatic lipases in the GI tract, also inhibits the thioesterase (TE) of human FASN. The cocrystal structure of TE with orlistat shows a pseudo TE dimer containing two different forms of orlistat in the active site, an intermediate that is covalently bound to a serine residue (Ser2308) and a hydrolyzed and inactivated product. In this study, we attempted to understand the mechanism of TE-catalyzed orlistat hydrolysis by examining the role of the hexyl tail of the covalently bound orlistat in water activation for hydrolysis using molecular dynamics simulations. We found that the hexyl tail of the covalently bound orlistat undergoes a conformational transition, which is accompanied by destabilization of a hydrogen bond between a hydroxyl moiety of orlistat and the catalytic His2481 of TE that in turn leads to an increased hydrogen bonding between water molecules and His2481 and increased chance for water activation to hydrolyze the covalent bond between orlistat and Ser2308. Thus, the conformation of the hexyl tail of orlistat plays an important role in orlistat hydrolysis. Strategies that stabilize the hexyl tail may lead to the design of more potent irreversible inhibitors that target FASN and block TE activity with greater endurance.
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Affiliation(s)
| | | | - Jing-Yuan Liu
- Department
of Computer and Information Science, Indiana University-Purdue University, 635 Barnhill Drive, Indianapolis, Indiana 46202, United States
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11
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Kobayashi S. Green Polymer Chemistry: Recent Developments. ADVANCES IN POLYMER SCIENCE 2013. [DOI: 10.1007/12_2013_236] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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12
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Schiebel J, Kapilashrami K, Fekete A, Bommineni GR, Schaefer CM, Mueller MJ, Tonge PJ, Kisker C. Structural basis for the recognition of mycolic acid precursors by KasA, a condensing enzyme and drug target from Mycobacterium tuberculosis. J Biol Chem 2013; 288:34190-34204. [PMID: 24108128 DOI: 10.1074/jbc.m113.511436] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The survival of Mycobacterium tuberculosis depends on mycolic acids, very long α-alkyl-β-hydroxy fatty acids comprising 60-90 carbon atoms. However, despite considerable efforts, little is known about how enzymes involved in mycolic acid biosynthesis recognize and bind their hydrophobic fatty acyl substrates. The condensing enzyme KasA is pivotal for the synthesis of very long (C38-42) fatty acids, the precursors of mycolic acids. To probe the mechanism of substrate and inhibitor recognition by KasA, we determined the structure of this protein in complex with a mycobacterial phospholipid and with several thiolactomycin derivatives that were designed as substrate analogs. Our structures provide consecutive snapshots along the reaction coordinate for the enzyme-catalyzed reaction and support an induced fit mechanism in which a wide cavity is established through the concerted opening of three gatekeeping residues and several α-helices. The stepwise characterization of the binding process provides mechanistic insights into the induced fit recognition in this system and serves as an excellent foundation for the development of high affinity KasA inhibitors.
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Affiliation(s)
- Johannes Schiebel
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany; Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
| | - Kanishk Kapilashrami
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Agnes Fekete
- Julius-von-Sachs Institute of Biosciences, Biocenter, Department of Pharmaceutical Biology, University of Wuerzburg, D-97082 Wuerzburg, Germany
| | - Gopal R Bommineni
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Christin M Schaefer
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany
| | - Martin J Mueller
- Julius-von-Sachs Institute of Biosciences, Biocenter, Department of Pharmaceutical Biology, University of Wuerzburg, D-97082 Wuerzburg, Germany
| | - Peter J Tonge
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany.
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13
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Jenkins CM, Yang J, Gross RW. Mechanism-based inhibition of iPLA2β demonstrates a highly reactive cysteine residue (C651) that interacts with the active site: mass spectrometric elucidation of the mechanisms underlying inhibition. Biochemistry 2013; 52:4250-63. [PMID: 23701211 DOI: 10.1021/bi4004233] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The multifaceted roles of calcium-independent phospholipase A2β (iPLA2β) in numerous cellular processes have been extensively examined through utilization of the iPLA2-selective inhibitor (E)-6-(bromomethylene)-3-(1-naphthalenyl)-2H-tetrahydropyran-2-one (BEL). Herein, we employed accurate mass/high resolution mass spectrometry to demonstrate that the active site serine (S465) and C651 of iPLA2β are covalently cross-linked during incubations with BEL demonstrating their close spatial proximity. This cross-link results in macroscopic alterations in enzyme molecular geometry evidenced by anomalous migration of the cross-linked enzyme by SDS-PAGE. Molecular models of iPLA2β constructed from the crystal structure of iPLA2α (patatin) indicate that the distance between S465 and C651 is approximately 10 Å within the active site of iPLA2β. Kinetic analysis of the formation of the 75 kDa iPLA2β-BEL species with the (R) and (S) enantiomers of BEL demonstrated that the reaction of (S)-BEL with iPLA2β was more rapid than for (R)-BEL paralleling the enantioselectivity for the inhibition of catalysis by each inhibitor with iPLA2β. Moreover, we demonstrate that the previously identified selective acylation of iPLA2β by oleoyl-CoA occurs at C651 thereby indicating the importance of active site architecture for acylation of this enzyme. Collectively, these results identify C651 as a highly reactive nucleophilic residue within the active site of iPLA2β which is thioesterified by BEL, acylated by oleoyl-CoA, and located in close spatial proximity to the catalytic serine thereby providing important chemical insights on the mechanisms through which BEL inhibits iPLA2β and the topology of the active site.
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Affiliation(s)
- Christopher M Jenkins
- Division of Bioorganic Chemistry and Molecular Pharmacology, Washington University School of Medicine , St. Louis, Missouri 63110, USA
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14
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Goepfert A, Stanger FV, Dehio C, Schirmer T. Conserved inhibitory mechanism and competent ATP binding mode for adenylyltransferases with Fic fold. PLoS One 2013; 8:e64901. [PMID: 23738009 PMCID: PMC3667792 DOI: 10.1371/journal.pone.0064901] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 04/19/2013] [Indexed: 11/19/2022] Open
Abstract
The ubiquitous FIC domain is evolutionarily conserved from bacteria to human and has been shown to catalyze AMP transfer onto protein side-chain hydroxyl groups. Recently, it was predicted that most catalytically competent Fic proteins are inhibited by the presence of an inhibitory helix αinh that is provided by a cognate anti-toxin (class I), or is part of the N- or C-terminal part of the Fic protein itself (classes II and III). In vitro, inhibition is relieved by mutation of a conserved glutamate of αinh to glycine. For the class III bacterial Fic protein NmFic from Neisseria meningitidis, the inhibitory mechanism has been elucidated. Here, we extend above study by including bacterial class I and II Fic proteins VbhT from Bartonella schoenbuchensis and SoFic from Shewanella oneidensis, respectively, and the respective E->G mutants. Comparative enzymatic and crystallographic analyses show that, in all three classes, the ATP substrate binds to the wild-type FIC domains, but with the α-phosphate in disparate and non-competent orientations. In the E->G mutants, however, the tri-phosphate moiety is found reorganized to the same tightly bound structure through a unique set of hydrogen bonds with Fic signature motif residues. The γ-phosphate adopts the location that is taken by the inhibitory glutamate in wild-type resulting in an α-phosphate orientation that can be attacked in-line by a target side-chain hydroxyl group. The latter is properly registered to the Fic active center by main-chain β-interactions with the β-hairpin flap. These data indicate that the active site motif and the exposed edge of the flap are both required to form an adenylylation-competent Fic protein.
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Affiliation(s)
- Arnaud Goepfert
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
| | - Frédéric V. Stanger
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
- * E-mail: (TS); (CD)
| | - Tilman Schirmer
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
- * E-mail: (TS); (CD)
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15
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Ohara H, Nishioka E, Yamaguchi S, Kawai F, Kobayashi S. Protease-Catalyzed Oligomerization and Hydrolysis of Alkyl Lactates Involving l-Enantioselective Deacylation Step. Biomacromolecules 2011; 12:3833-7. [DOI: 10.1021/bm201004g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hitomi Ohara
- Department of Biobased Materials Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku,
Kyoto 606-8585, Japan
| | - Emiko Nishioka
- Department of Biobased Materials Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku,
Kyoto 606-8585, Japan
| | - Syuhei Yamaguchi
- Department of Biobased Materials Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku,
Kyoto 606-8585, Japan
| | - Fusako Kawai
- Center
for Nanomaterials and Devices, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Shiro Kobayashi
- Center
for Nanomaterials and Devices, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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16
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Iqbal A, Clifton IJ, Chowdhury R, Ivison D, Domene C, Schofield CJ. Structural and biochemical analyses reveal how ornithine acetyl transferase binds acidic and basic amino acid substrates. Org Biomol Chem 2011; 9:6219-25. [PMID: 21796301 DOI: 10.1039/c1ob05554b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural and biochemical analyses reveal how ornithine acetyl-transferases catalyse the reversible transfer of an acetyl-group from a basic (ornithine) to an acidic (glutamate) amino acid by employing a common mechanism involving an acetyl-enzyme intermediate but using different side chain binding modes.
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Affiliation(s)
- Aman Iqbal
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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17
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Chung IYW, Paetzel M. Crystal structure of a viral protease intramolecular acyl-enzyme complex: insights into cis-cleavage at the VP4/VP3 junction of Tellina birnavirus. J Biol Chem 2011; 286:12475-82. [PMID: 21288899 PMCID: PMC3069450 DOI: 10.1074/jbc.m110.198812] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/10/2011] [Indexed: 11/06/2022] Open
Abstract
Viruses of the Birnaviridae family are characterized by their bisegmented double-stranded RNA genome that resides within a single-shelled non-enveloped icosahedral particle. They infect birds, aquatic organisms, and insects. Tellina virus 1 (TV-1) is an Aquabirnavirus isolated from the mollusk Tellina tenuis. It encodes a polyprotein (NH2-pVP2-X-VP4-VP3-COOH) that is cleaved by the self-encoded protease VP4 to yield capsid precursor protein pVP2, peptide X, and ribonucleoprotein VP3. Here we report the crystal structure of an intramolecular (cis) acyl-enzyme complex of TV-1 VP4 at 2.1-Å resolution. The structure reveals how the enzyme can recognize its own carboxyl terminus during the VP4/VP3 cleavage event. The methyl side chains of Ala830(P1) and Ala828(P3) at the VP4/VP3 junction point into complementary shallow and hydrophobic S1 and S3 binding pockets adjacent to the VP4 catalytic residues: nucleophile Ser738 and general base Lys777. The electron density clearly shows that the carbonyl carbon of Ala830 is covalently attached via an ester bond to the Oγ of Ser738. A highly ordered water molecule in the active site is coordinated in the proper position to act as the deacylating water. A comparative analysis of this intramolecular (cis) acyl-enzyme structure with the previously solved intermolecular (trans) acyl-enzyme structure of infectious pancreatic necrosis virus VP4 explains the narrower specificity observed in the cleavage sites of TV-1 VP4.
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Affiliation(s)
- Ivy Yeuk Wah Chung
- From the Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Mark Paetzel
- From the Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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18
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Jiang Y, Morley KL, Schrag JD, Kazlauskas RJ. Different active-site loop orientation in serine hydrolases versus acyltransferases. Chembiochem 2011; 12:768-76. [PMID: 21351219 DOI: 10.1002/cbic.201000693] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Indexed: 11/07/2022]
Abstract
Acyl transfer is a key reaction in biosynthesis, including synthesis of antibiotics and polyesters. Although researchers have long recognized the similar protein fold and catalytic machinery in acyltransferases and hydrolases, the molecular basis for the different reactivity has been a long-standing mystery. By comparison of X-ray structures, we identified a different oxyanion-loop orientation in the active site. In esterases/lipases a carbonyl oxygen points toward the active site, whereas in acyltransferases a NH of the main-chain amide points toward the active site. Amino acid sequence comparisons alone cannot identify such a difference in the main-chain orientation. To identify how this difference might change the reaction mechanism, we solved the X-ray crystal structure of Pseudomonas fluorescens esterase containing a sulfonate transition-state analogue bound to the active-site serine. This structure mimics the transition state for the attack of water on the acyl-enzyme and shows a bridging water molecule between the carbonyl oxygen mentioned above and the sulfonyl oxygen that mimics the attacking water. A possible mechanistic role for this bridging water molecule is to position and activate the attacking water molecule in hydrolases, but to deactivate the attacking water molecule in acyl transferases.
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Affiliation(s)
- Yun Jiang
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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19
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Palanivelu DV, Goepfert A, Meury M, Guye P, Dehio C, Schirmer T. Fic domain-catalyzed adenylylation: insight provided by the structural analysis of the type IV secretion system effector BepA. Protein Sci 2011; 20:492-9. [PMID: 21213248 DOI: 10.1002/pro.581] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 12/02/2010] [Accepted: 12/03/2010] [Indexed: 11/09/2022]
Abstract
Numerous bacterial pathogens subvert cellular functions of eukaryotic host cells by the injection of effector proteins via dedicated secretion systems. The type IV secretion system (T4SS) effector protein BepA from Bartonella henselae is composed of an N-terminal Fic domain and a C-terminal Bartonella intracellular delivery domain, the latter being responsible for T4SS-mediated translocation into host cells. A proteolysis resistant fragment (residues 10-302) that includes the Fic domain shows autoadenylylation activity and adenylyl transfer onto Hela cell extract proteins as demonstrated by autoradiography on incubation with α-[(32)P]-ATP. Its crystal structure, determined to 2.9-Å resolution by the SeMet-SAD method, exhibits the canonical Fic fold including the HPFxxGNGRxxR signature motif with several elaborations in loop regions and an additional β-rich domain at the C-terminus. On crystal soaking with ATP/Mg(2+), additional electron density indicated the presence of a PP(i) /Mg(2+) moiety, the side product of the adenylylation reaction, in the anion binding nest of the signature motif. On the basis of this information and that of the recent structure of IbpA(Fic2) in complex with the eukaryotic target protein Cdc42, we present a detailed model for the ternary complex of Fic with the two substrates, ATP/Mg(2+) and target tyrosine. The model is consistent with an in-line nucleophilic attack of the deprotonated side-chain hydroxyl group onto the α-phosphorus of the nucleotide to accomplish AMP transfer. Furthermore, a general, sequence-independent mechanism of target positioning through antiparallel β-strand interactions between enzyme and target is suggested.
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Affiliation(s)
- Dinesh V Palanivelu
- Core program of Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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20
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Brown T, Charlier P, Herman R, Schofield CJ, Sauvage E. Structural basis for the interaction of lactivicins with serine beta-lactamases. J Med Chem 2010; 53:5890-4. [PMID: 20593835 DOI: 10.1021/jm100437u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lactivicin (LTV) is a natural non-beta-lactam antibiotic that inhibits penicillin-binding proteins and serine beta-lactamases. A crystal structure of a BS3-LTV complex reveals that, as for its reaction with PBPs, LTV reacts with the nucleophilic serine and that cycloserine and lactone rings of LTV are opened. This structure, together with reported structures of PBP1b with lactivicins, provides a basis for developing improved lactivicin-based gamma-lactam antibiotics.
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Affiliation(s)
- Tom Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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21
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Mileni M, Kamtekar S, Wood DC, Benson TE, Cravatt BF, Stevens RC. Crystal structure of fatty acid amide hydrolase bound to the carbamate inhibitor URB597: discovery of a deacylating water molecule and insight into enzyme inactivation. J Mol Biol 2010; 400:743-54. [PMID: 20493882 DOI: 10.1016/j.jmb.2010.05.034] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 05/13/2010] [Accepted: 05/14/2010] [Indexed: 12/22/2022]
Abstract
The endocannabinoid system regulates a wide range of physiological processes including pain, inflammation, and cognitive/emotional states. URB597 is one of the best characterized covalent inhibitors of the endocannabinoid-degrading enzyme fatty acid amide hydrolase (FAAH). Here, we report the structure of the FAAH-URB597 complex at 2.3 A resolution. The structure provides insights into mechanistic details of enzyme inactivation and experimental evidence of a previously uncharacterized active site water molecule that likely is involved in substrate deacylation. This water molecule is part of an extensive hydrogen-bonding network and is coordinated indirectly to residues lining the cytosolic port of the enzyme. In order to corroborate our hypothesis concerning the role of this water molecule in FAAH's catalytic mechanism, we determined the structure of FAAH conjugated to a urea-based inhibitor, PF-3845, to a higher resolution (2.4 A) than previously reported. The higher-resolution structure confirms the presence of the water molecule in a virtually identical location in the active site. Examination of the structures of serine hydrolases that are non-homologous to FAAH, such as elastase, trypsin, or chymotrypsin, shows a similarly positioned hydrolytic water molecule and suggests a functional convergence between the amidase signature enzymes and serine proteases.
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Affiliation(s)
- Mauro Mileni
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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22
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Yin DLT, Bernhardt P, Morley KL, Jiang Y, Cheeseman JD, Purpero V, Schrag JD, Kazlauskas RJ. Switching catalysis from hydrolysis to perhydrolysis in Pseudomonas fluorescens esterase. Biochemistry 2010; 49:1931-42. [PMID: 20112920 DOI: 10.1021/bi9021268] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many serine hydrolases catalyze perhydrolysis, the reversible formation of peracids from carboxylic acids and hydrogen peroxide. Recently, we showed that a single amino acid substitution in the alcohol binding pocket, L29P, in Pseudomonas fluorescens (SIK WI) aryl esterase (PFE) increased the specificity constant of PFE for peracetic acid formation >100-fold [Bernhardt et al. (2005) Angew. Chem., Int. Ed. 44, 2742]. In this paper, we extend this work to address the three following questions. First, what is the molecular basis of the increase in perhydrolysis activity? We previously proposed that the L29P substitution creates a hydrogen bond between the enzyme and hydrogen peroxide in the transition state. Here we report two X-ray structures of L29P PFE that support this proposal. Both structures show a main chain carbonyl oxygen closer to the active site serine as expected. One structure further shows acetate in the active site in an orientation consistent with reaction by an acyl-enzyme mechanism. We also detected an acyl-enzyme intermediate in the hydrolysis of epsilon-caprolactone by mass spectrometry. Second, can we further increase perhydrolysis activity? We discovered that the reverse reaction, hydrolysis of peracetic acid to acetic acid and hydrogen peroxide, occurs at nearly the diffusion limited rate. Since the reverse reaction cannot increase further, neither can the forward reaction. Consistent with this prediction, two variants with additional amino acid substitutions showed 2-fold higher k(cat), but K(m) also increased so the specificity constant, k(cat)/K(m), remained similar. Third, how does the L29P substitution change the esterase activity? Ester hydrolysis decreased for most esters (75-fold for ethyl acetate) but not for methyl esters. In contrast, L29P PFE catalyzed hydrolysis of epsilon-caprolactone five times more efficiently than wild-type PFE. Molecular modeling suggests that moving the carbonyl group closer to the active site blocks access for larger alcohol moieties but binds epsilon-caprolactone more tightly. These results are consistent with the natural function of perhydrolases being either hydrolysis of peroxycarboxylic acids or hydrolysis of lactones.
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Affiliation(s)
- De Lu Tyler Yin
- Department of Biochemistry, Molecular Biology, and Biophysics and The Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, USA
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23
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Structure of a serine protease poised to resynthesize a peptide bond. Proc Natl Acad Sci U S A 2009; 106:11034-9. [PMID: 19549826 DOI: 10.1073/pnas.0902463106] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The serine proteases are among the most thoroughly studied enzymes, and numerous crystal structures representing the enzyme-substrate complex and intermediates in the hydrolysis reactions have been reported. Some aspects of the catalytic mechanism remain controversial, however, especially the role of conformational changes in the reaction. We describe here a high-resolution (1.46 A) crystal structure of a complex formed between a cleaved form of bovine pancreatic trypsin inhibitor (BPTI) and a catalytically inactive trypsin variant with the BPTI cleavage site ideally positioned in the active site for resynthesis of the peptide bond. This structure defines the positions of the newly generated amino and carboxyl groups following the 2 steps in the hydrolytic reaction. Comparison of this structure with those representing other intermediates in the reaction demonstrates that the residues of the catalytic triad are positioned to promote each step of both the forward and reverse reaction with remarkably little motion and with conservation of hydrogen-bonding interactions. The results also provide insights into the mechanism by which inhibitors like BPTI normally resist hydrolysis when bound to their target proteases.
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24
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Iqbal A, Clifton IJ, Bagonis M, Kershaw NJ, Domene C, Claridge TDW, Wharton CW, Schofield CJ. Anatomy of a Simple Acyl Intermediate in Enzyme Catalysis: Combined Biophysical and Modeling Studies on Ornithine Acetyl Transferase. J Am Chem Soc 2008; 131:749-57. [DOI: 10.1021/ja807215u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aman Iqbal
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Ian J. Clifton
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Maria Bagonis
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Nadia J. Kershaw
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Carmen Domene
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Christopher W. Wharton
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Christopher J. Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
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25
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Sanggaard KW, Sonne-Schmidt CS, Krogager TP, Kristensen T, Wisniewski HG, Thøgersen IB, Enghild JJ. TSG-6 transfers proteins between glycosaminoglycans via a Ser28-mediated covalent catalytic mechanism. J Biol Chem 2008; 283:33919-26. [PMID: 18820257 DOI: 10.1074/jbc.m804240200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Studies of the interaction between Bikunin proteins, tumor necrosis factor-stimulated gene-6 protein (TSG-6), and glycosaminoglycans have revealed a unique catalytic activity where TSG-6/heavy chain 2 transfer heavy chain subunits between glycosaminoglycan chains. The activity is mediated by TSG-6/heavy chain 2 and involves a transient SDS stable interaction between TSG-6 and the heavy chain to be transferred. The focus of this study was to characterize the molecular structure of this cross-link to gain further insight into the catalytic mechanism. The result showed that the C-terminal Asp residue of the heavy chains forms an ester bond to Ser(28) beta-carbon of TSG-6 suggesting that this residue plays a role during catalysis.
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Affiliation(s)
- Kristian W Sanggaard
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, University of Aarhus, 8000 Aarhus C, Denmark
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26
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Lee J, Feldman AR, Delmas B, Paetzel M. Crystal Structure of the VP4 Protease from Infectious Pancreatic Necrosis Virus Reveals the Acyl-Enzyme Complex for an Intermolecular Self-cleavage Reaction. J Biol Chem 2007; 282:24928-37. [PMID: 17553791 DOI: 10.1074/jbc.m701551200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Infectious pancreatic necrosis virus (IPNV), an aquatic birnavirus that infects salmonid fish, encodes a large polyprotein (NH(2)-pVP2-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease, VP4, to release the proteins pVP2 and VP3. pVP2 is further processed to give rise to the capsid protein VP2 and three peptides that are incorporated into the virion. Reported here are two crystal structures of the IPNV VP4 protease solved from two different crystal symmetries. The electron density at the active site in the triclinic crystal form, refined to 2.2-A resolution, reveals the acyl-enzyme complex formed with an internal VP4 cleavage site. The complex was generated using a truncated enzyme in which the general base lysine was substituted. Inside the complex, the nucleophilic Ser(633)Ogamma forms an ester bond with the main-chain carbonyl of the C-terminal residue, Ala(716), of a neighboring VP4. The structure of this substrate-VP4 complex allows us to identify the S1, S3, S5, and S6 substrate binding pockets as well as other substrate-VP4 interactions and therefore provides structural insights into the substrate specificity of this enzyme. The structure from the hexagonal crystal form, refined to 2.3-A resolution, reveals the free-binding site of the protease. Three-dimensional alignment with the VP4 of blotched snakehead virus, another birnavirus, shows that the overall structure of VP4 is conserved despite a low level of sequence identity ( approximately 19%). The structure determinations of IPNV VP4, the first of an acyl-enzyme complex for a Ser/Lys dyad protease, provide insights into the catalytic mechanism and substrate recognition of this type of protease.
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Affiliation(s)
- Jaeyong Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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27
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Liu B, Schofield CJ, Wilmouth RC. Structural analyses on intermediates in serine protease catalysis. J Biol Chem 2006; 281:24024-35. [PMID: 16754679 DOI: 10.1074/jbc.m600495200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the subject of many studies, detailed structural information on aspects of the catalytic cycle of serine proteases is lacking. Crystallographic analyses were performed in which an acyl-enzyme complex, formed from elastase and a peptide, was reacted with a series of nucleophilic dipeptides. Multiple analyses led to electron density maps consistent with the formation of a tetrahedral species. In certain cases, apparent peptide bond formation at the active site was observed, and the electron density maps suggested production of a cis-amide rather than a trans-amide. Evidence for a cis-amide configuration was also observed in the noncovalent complex between elastase and an alpha1-antitrypsin-derived tetrapeptide. Although there are caveats on the relevance of the crystallographic data to solution catalysis, the results enable detailed proposals for the pathway of the acylation step to be made. At least in some cases, it is proposed that the alcohol of Ser-195 may preferentially attack the carbonyl of the cis-amide form of the substrate, in a stereoelectronically favored manner, to give a tetrahedral oxyanion intermediate, which undergoes N-inversion and/or C-N bond rotation to enable protonation of the leaving group nitrogen. The mechanistic proposals may have consequences for protease inhibition, in particular for the design of high energy intermediate analogues.
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Affiliation(s)
- Bin Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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28
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Radisky ES, Lee JM, Lu CJK, Koshland DE. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates. Proc Natl Acad Sci U S A 2006; 103:6835-40. [PMID: 16636277 PMCID: PMC1458980 DOI: 10.1073/pnas.0601910103] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Atomic resolution structures of trypsin acyl-enzymes and a tetrahedral intermediate analog, along with previously solved structures representing the Michaelis complex, are used to reconstruct events in the catalytic cycle of this classic serine protease. Structural comparisons provide insight into active site adjustments involved in catalysis. Subtle motions of the catalytic serine and histidine residues coordinated with translation of the substrate reaction center are seen to favor the forward progress of the acylation reaction. The structures also clarify the attack trajectory of the hydrolytic water in the deacylation reaction.
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Affiliation(s)
- Evette S. Radisky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Justin M. Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Chia-Jung Karen Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Daniel E. Koshland
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
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29
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Vivares D, Arnoux P, Pignol D. A papain-like enzyme at work: native and acyl-enzyme intermediate structures in phytochelatin synthesis. Proc Natl Acad Sci U S A 2005; 102:18848-53. [PMID: 16339904 PMCID: PMC1310510 DOI: 10.1073/pnas.0505833102] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Indexed: 11/18/2022] Open
Abstract
Phytochelatin synthase (PCS) is a key enzyme for heavy-metal detoxification in plants. PCS catalyzes the production of glutathione (GSH)-derived peptides (called phytochelatins or PCs) that bind heavy-metal ions before vacuolar sequestration. The enzyme can also hydrolyze GSH and GS-conjugated xenobiotics. In the cyanobacterium Nostoc, the enzyme (NsPCS) contains only the catalytic domain of the eukaryotic synthase and can act as a GSH hydrolase and weakly as a peptide ligase. The crystal structure of NsPCS in its native form solved at a 2.0-A resolution shows that NsPCS is a dimer that belongs to the papain superfamily of cysteine proteases, with a conserved catalytic machinery. Moreover, the structure of the protein solved as a complex with GSH at a 1.4-A resolution reveals a gamma-glutamyl cysteine acyl-enzyme intermediate stabilized in a cavity of the protein adjacent to a second putative GSH binding site. GSH hydrolase and PCS activities of the enzyme are discussed in the light of both structures.
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Affiliation(s)
- Denis Vivares
- Département d'Ecophysiologie Végétale et de Microbiologie, Direction des Sciences du Vivant, Laboratoire de Bioénergétique Cellulaire, Commissariat á l'Energie Atomique/Cadarache, 13108 St Paul lez Durance Cedex, France
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30
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Vrielink A, Sampson N. Sub-Angstrom resolution enzyme X-ray structures: is seeing believing? Curr Opin Struct Biol 2004; 13:709-15. [PMID: 14675549 DOI: 10.1016/j.sbi.2003.10.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Recent technical advances in crystallographic analysis, particularly highly focused and high brilliance synchrotron beam lines, have significantly improved the resolutions that are attainable for many macromolecular crystal structures. The Protein Data Bank (http://www.rcsb.org/pdb/) contains an increasing number of atomic resolution structures, which are providing a wealth of structural information that was not previously visible in lower resolution electron density maps. Here, we review the importance of visualizing hydrogen atoms and multiple sidechain conformations or anisotropy, as well as substrate strain, at sub-Angstrom resolution. The additional structural features that are visible in the electron density maps as a result of atomic resolution data provide a better understanding of the catalytic mechanisms of cholesterol oxidase, ribonuclease A, beta-lactamase, serine proteases, triosephosphate isomerase and endoglucanase.
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Affiliation(s)
- Alice Vrielink
- Department of Molecular, Cellular and Developmental Biology, University of California, 1156 High Street, Santa Cruz, CA 95064, USA.
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31
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Matern U, Schleberger C, Jelakovic S, Weckesser J, Schulz GE. Binding structure of elastase inhibitor scyptolin A. ACTA ACUST UNITED AC 2004; 10:997-1001. [PMID: 14583266 DOI: 10.1016/j.chembiol.2003.10.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Natural bioactive compounds are of general interest to pharmaceutical research because they may be used as leads in drug development campaigns. Among them, scyptolin A and B from Scytonema hofmanni PCC 7110 are known to inhibit porcine pancreatic elastase, which in turn resembles the attractive drug target neutrophil elastase. The crystal structure of scyptolin A as bound to pancreatic elastase was solved at 2.8 A resolution. The inhibitor occupies the most prominent subsites S1 through S4 of the elastase and prevents a hydrolytic attack by covering the active center with its rigid ring structure. The observed binding structure may help to design potent elastase inhibitors.
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Affiliation(s)
- Ute Matern
- Institut für Biologie II, Mikrobiologie, Albert-Ludwigs-Universität, Schänzlestrasse 1, D-79104 Freiburg im Breisgau, Germany
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32
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McDonough MA, Schofield CJ. New structural insights into the inhibition of serine proteases by cyclic peptides from bacteria. ACTA ACUST UNITED AC 2004; 10:898-900. [PMID: 14583255 DOI: 10.1016/j.chembiol.2003.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Michael A McDonough
- The Dyson Perrins Laboratory and The Oxford Centre for Molecular Sciences, South Parks Road, Oxford OX1 3QY, United Kingdom
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33
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Pochet L, Dieu M, Frédérick R, Murray AM, Kempen I, Pirotte B, Masereel B. Investigation of the inhibition mechanism of coumarins on chymotrypsin by mass spectrometry. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00660-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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34
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Antony J, Gresh N, Olsen L, Hemmingsen L, Schofield CJ, Bauer R. Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem 2002; 23:1281-96. [PMID: 12210153 DOI: 10.1002/jcc.10111] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The bacterial Zn2+ metallo-beta-lactamase from B. fragilis is a zinc-enzyme with two potential metal ion binding sites. It cleaves the lactam ring of antibiotics, thus contributing to the acquired resistance of bacteria against antibiotics. The present study bears on the binuclear form of the enzyme. We compare several possible binding modes of captopril, a mercaptocarboxamide inhibitor of several zinc-metalloenzymes. Two diastereoisomers of captopril were considered, with either a D- or an L-proline residue. We have used the polarizable molecular mechanics procedure SIBFA (Sum of Interactions Between Fragments ab initio computed). Two beta-lactamase models were considered, encompassing 104 and 188 residues, respectively. The energy balances included the inter and intramolecular interaction energies as well as the contribution from solvation computed using a continuum reaction field procedure. The thiolate ion of the inhibitor is binding to both metal ions, expelling the bridging solvent molecule from the uncomplexed enzyme. Different competing binding modes of captopril were considered, either where the inhibitor binds in a monodentate mode to the zinc cations only with its thiolate ion, or in bidentate modes involving additional zinc binding by its carboxylate or ketone carbonyl groups. The additional coordination by the inhibitor's carboxylate or carbonyl group always occurs at the zinc ion, which is bound by a histidine, a cysteine, and an aspartate side chain. For both diastereomers, the energy balances favor monodentate binding of captopril via S-. The preference over bidentate binding is small. The interaction energies were recomputed in model sites restricted to captopril, the Zn2+ cations, and their coordinating end side chains from beta-lactamase (98 atoms). The interaction energies and their ranking among competing arrangements were consistent with those computed by ab initio HF and DFT procedures.
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Affiliation(s)
- Jens Antony
- Department of Mathematics and Physics, The Royal Veterinary and Agricultural University, DK-1871 Frederiksberg C, Denmark
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35
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Katona G, Wilmouth RC, Wright PA, Berglund GI, Hajdu J, Neutze R, Schofield CJ. X-ray structure of a serine protease acyl-enzyme complex at 0.95-A resolution. J Biol Chem 2002; 277:21962-70. [PMID: 11896054 DOI: 10.1074/jbc.m200676200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinetic analyses led to the discovery that N-acetylated tripeptides with polar residues at P3 are inhibitors of porcine pancreatic elastase (PPE) that form unusually stable acyl-enzyme complexes. Peptides terminating in a C-terminal carboxylate were more potent than those terminating in a C-terminal amide, suggesting recognition by the oxy-anion hole is important in binding. X-ray diffraction data were recorded to 0.95-A resolution for an acyl-enzyme complex formed between PPE and N-acetyl-Asn-Pro-Ile-CO2H at approximately pH 5. The accuracy of the crystallographic coordinates allows structural issues concerning the mechanism of serine proteases to be addressed. Significantly, the ester bond of the acyl-enzyme showed a high level of planarity, suggesting geometric strain of the ester link is not important during catalysis. Several hydrogen atoms could be clearly identified and were included within the model. In keeping with a recent x-ray structure of subtilisin at 0.78 A (1), limited electron density is visible consistent with the putative location of a hydrogen atom approximately equidistant between the histidine and aspartate residues of the catalytic triad. Comparison of this high resolution crystal structure of the acyl-enzyme complex with that of native elastase at 1.1 A (2) showed that binding of the N-terminal part of the substrate can be accommodated with negligible structural rearrangements. In contrast, comparison with structures obtained as part of "time-resolved" studies on the reacting acyl-enzyme complex at >pH 7 (3) indicate small but significant structural differences, consistent with the proposed synchronization of ester hydrolysis and substrate release.
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Affiliation(s)
- Gergely Katona
- Department of Molecular Biotechnology, Chalmers University of Technology, Box 462, 40530 Gothenburg, Sweden
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36
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Topf M, Várnai P, Schofield CJ, Richards WG. Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases. Proteins 2002; 47:357-69. [PMID: 11948789 DOI: 10.1002/prot.10097] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Despite the availability of many experimental data and some modeling studies, questions remain as to the precise mechanism of the serine proteases. Here we report molecular dynamics simulations on the acyl-enzyme complex and the tetrahedral intermediate during the deacylation step in elastase catalyzed hydrolysis of a simple peptide. The models are based on recent crystallographic data for an acyl-enzyme intermediate at pH 5 and a time-resolved study on the deacylation step. Simulations were carried out on the acyl enzyme complex with His-57 in protonated (as for the pH 5 crystallographic work) and deprotonated forms. In both cases, a water molecule that could provide the nucleophilic hydroxide ion to attack the ester carbonyl was located between the imidazole ring of His-57 and the carbonyl carbon, close to the hydrolytic position assigned in the crystal structure. In the "neutral pH" simulations of the acyl-enzyme complex, the hydrolytic water oxygen was hydrogen bonded to the imidazole ring and the side chain of Arg-61. Alternative stable locations for water in the active site were also observed. Movement of the His-57 side-chain from that observed in the crystal structure allowed more solvent waters to enter the active site, suggesting that an alternative hydrolytic process directly involving two water molecules may be possible. At the acyl-enzyme stage, the ester carbonyl was found to flip easily in and out of the oxyanion hole. In contrast, simulations on the tetrahedral intermediate showed no significant movement of His-57 and the ester carbonyl was constantly located in the oxyanion hole. A comparison between the simulated tetrahedral intermediate and a time-resolved crystallographic structure assigned as predominantly reflecting the tetrahedral intermediate suggests that the experimental structure may not precisely represent an optimal arrangement for catalysis in solution. Movement of loop residues 216-223 and P3 residue, seen both in the tetrahedral simulation and the experimental analysis, could be related to product release. Furthermore, an analysis of the geometric data obtained from the simulations and the pH 5 crystal structure of the acyl-enzyme suggests that since His-57 is protonated, in some aspects, this crystal structure resembles the tetrahedral intermediate.
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Affiliation(s)
- Maya Topf
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom.
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37
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Paetzel M, Dalbey RE, Strynadka NCJ. Crystal structure of a bacterial signal peptidase apoenzyme: implications for signal peptide binding and the Ser-Lys dyad mechanism. J Biol Chem 2002; 277:9512-9. [PMID: 11741964 DOI: 10.1074/jbc.m110983200] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report here the x-ray crystal structure of a soluble catalytically active fragment of the Escherichia coli type I signal peptidase (SPase-(Delta2-75)) in the absence of inhibitor or substrate (apoenzyme). The structure was solved by molecular replacement and refined to 2.4 A resolution in a different space group (P4(1)2(1)2) from that of the previously published acyl-enzyme inhibitor-bound structure (P2(1)2(1)2) (Paetzel, M., Dalbey, R.E., and Strynadka, N.C.J. (1998) Nature 396, 186-190). A comparison with the acyl-enzyme structure shows significant side-chain and main-chain differences in the binding site and active site regions, which result in a smaller S1 binding pocket in the apoenzyme. The apoenzyme structure is consistent with SPase utilizing an unusual oxyanion hole containing one side-chain hydroxyl hydrogen (Ser-88 OgammaH) and one main-chain amide hydrogen (Ser-90 NH). Analysis of the apoenzyme active site reveals a potential deacylating water that was displaced by the inhibitor. It has been proposed that SPase utilizes a Ser-Lys dyad mechanism in the cleavage reaction. A similar mechanism has been proposed for the LexA family of proteases. A structural comparison of SPase and members of the LexA family of proteases reveals a difference in the side-chain orientation for the general base lysine, both of which are stabilized by an adjacent hydroxyl group. To gain insight into how signal peptidase recognizes its substrates, we have modeled a signal peptide into the binding site of SPase. The model is built based on the recently solved crystal structure of the analogous enzyme LexA (Luo, Y., Pfuetzner, R. A., Mosimann, S., Paetzel, M., Frey, E. A., Cherney, M., Kim, B., Little, J. W., and Strynadka, N. C. J. (2001) Cell 106, 1-10) with its bound cleavage site region.
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Affiliation(s)
- Mark Paetzel
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3 Canada
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38
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Wright PA, Wilmouth RC, Clifton IJ, Schofield CJ. Kinetic and crystallographic analysis of complexes formed between elastase and peptides from β-casein. ACTA ACUST UNITED AC 2001; 268:2969-74. [PMID: 11358514 DOI: 10.1046/j.1432-1327.2001.02186.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Human beta-casomorphin-7 (NH2-Tyr-Pro-Phe-Val-Glu-Pro-Ile-CO2H) is a naturally occurring peptide inhibitor of elastase that has been shown to form an acyl-enzyme complex stable enough for X-ray crystallographic analysis at pH 5. To investigate the importance of the N-terminal residues of the beta-casomorphin-7 peptide for the inhibition of elastase, kinetic and crystallographic analyses were undertaken to identify the minimum number of residues required for effective formation of a stable complex between truncated beta-casomorphin-7 peptides and porcine pancreatic elastase (PPE). The results clearly demonstrate that significant inhibition of PPE can be effected by simple tri-, tetra-and pentapeptides terminating in a carboxylic acid. These results also suggest that in vivo regulation of protease activity could be mediated via short peptides as well as by proteins. Crystallographic analysis of the complex formed between N-acetyl-Val-Glu-Pro-Ile-CO2H and PPE at pH 5 (to 1.67 A resolution) revealed an active site water molecule in an analogous position to that observed in the PPE/beta-casomorphin-7 structure supportive of its assignment as the 'hydrolytic water' in the deacylation step of serine protease catalysis.
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Affiliation(s)
- P A Wright
- The Dyson Perrins Laboratory and The Oxford Centre for Molecular Sciences, Oxford, UK
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39
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Rockwell NC, Fuller RS. Differential utilization of enzyme-substrate interactions for acylation but not deacylation during the catalytic cycle of Kex2 protease. J Biol Chem 2001; 276:38394-9. [PMID: 11514565 DOI: 10.1074/jbc.m105782200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kex2 protease from Saccharomyces cerevisiae is the prototype for a family of eukaryotic proprotein processing proteases belonging to the subtilase superfamily of serine proteases. Kex2 can be distinguished from degradative subtilisins on the basis of stringent substrate specificity and distinct pre-steady-state behavior. To better understand these mechanistic differences, we have examined the effects of substrate residues at P(1) and P(4) on individual steps in the Kex2 catalytic cycle with a systematic series of isosteric peptidyl amide and ester substrates. The results demonstrate that substrates based on known, physiological cleavage sites exhibit high acylation rates (> or =550 s(-1)) with Kex2. Substitution of Lys for the physiologically correct Arg at P(1) resulted in a > or =200-fold drop in acylation rate with almost no apparent effect on binding or deacylation. In contrast, substitution of the physiologically incorrect Ala for Nle at P(4) resulted in a much smaller defect in acylation and a modest but significant effect on binding with Lys at P(1). This substitution also had no effect on deacylation. These results demonstrate that Kex2 utilizes enzyme-substrate interactions in different ways at different steps in the catalytic cycle, with the S(1)-P(1) contact providing a key specificity determinant at the acylation step.
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Affiliation(s)
- N C Rockwell
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
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40
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Skordalakes E, Dodson GG, Green DS, Goodwin CA, Scully MF, Hudson HR, Kakkar VV, Deadman JJ. Inhibition of human alpha-thrombin by a phosphonate tripeptide proceeds via a metastable pentacoordinated phosphorus intermediate. J Mol Biol 2001; 311:549-55. [PMID: 11493008 DOI: 10.1006/jmbi.2001.4872] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
X-ray crystallographic studies of human alpha-thrombin with a novel synthetic inhibitor, an acyl (alpha-aminoalkyl)phosphonate, reveal the existence of a pentacovalent phosphorus intermediate state. Crystal structures of the complex of alpha-thrombin with the phosphonate compound were determined independently using crystals of different ages. The first structure, solved from a crystal less than seven days old, showed a pentacoordinated phosphorus moiety. The second structure, determined from a crystal that was 12 weeks old, showed a tetracoordinated phosphorus moiety. In the first structure, a water molecule, made nucleophilic by coordination to His57 of alpha-thrombin, is bonded to the pentacoordinated phosphorus atom. Its position is approximately equivalent to that occupied by the water molecule responsible for hydrolytic deacylation during normal hydrolysis. The pentacoordinated phosphorus adduct collapses to give the expected pseudo tetrahedral complex, where the phosphorus atom is covalently bonded to Ser195 O(gamma). The crystallographic data presented here therefore suggest that the covalent bond formed between the inhibitor's phosphorus atom and O(gamma) of Ser195 proceeds via an addition-elimination mechanism, which involves the formation of a pentacoordinate intermediate.
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Affiliation(s)
- E Skordalakes
- Chemistry Department and Biochemistry Department, Thrombosis Research Institute, Emmanuel Kaye Building, London, SW3 6LR, UK
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41
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42
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Wright PA, Rostom AA, Robinson CV, Schofield CJ. Mass spectrometry reveals elastase inhibitors from the reactive centre loop of alpha1-antitrypsin. Bioorg Med Chem Lett 2000; 10:1219-21. [PMID: 10866385 DOI: 10.1016/s0960-894x(00)00194-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Peptides derived from the reactive centre loop of alpha1-antitrypsin, a serpin, were screened as potential elastase inhibitors by mass spectrometry. An octapeptide, MFLEAIPM, formed a 'stable' ternary complex with porcine elastase: one MFLEAIPM molecule reacted covalently with loss of water, whilst an additional peptide was bound non-covalently. Kinetic analyses suggested that MFLEAIPM may act as an uncompetitive inhibitor and that the activity was associated with the four N-terminal residues.
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Affiliation(s)
- P A Wright
- The Oxford Centre for Molecular Sciences, UK
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43
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Taylor P, Anderson V, Dowden J, Flitsch SL, Turner NJ, Loughran K, Walkinshaw MD. Novel mechanism of inhibition of elastase by beta-lactams is defined by two inhibitor crystal complexes. J Biol Chem 1999; 274:24901-5. [PMID: 10455164 DOI: 10.1074/jbc.274.35.24901] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two structurally related beta-lactams form different covalent complexes upon reaction with porcine elastase. The high resolution x-ray structures of these two complexes provide a clear insight into the mechanism of the reaction and suggest the design of a new class of serine protease inhibitors that resist enzyme reactivation by hydrolysis of the acyl intermediate. The presence of a hydroxyethyl substituent on the beta-lactam ring provides a new reaction pathway resulting in the elimination of the hydroxyethyl group and the formation of a stabilizing conjugated double bond system. In contrast, the presence of a diethyl substituent on the beta-lactam ring leads to addition of water. The two enzyme complexes show very different binding modes in the enzyme active site.
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Affiliation(s)
- P Taylor
- Structural Biochemistry Group, The Edinburgh Centre for Protein Technology, Institute of Cell and Molecular Biology, The University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
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Wu C, Robertson DH, Hubbard SJ, Gaskell SJ, Beynon RJ. Proteolysis of native proteins. Trapping of a reaction intermediate. J Biol Chem 1999; 274:1108-15. [PMID: 9873058 DOI: 10.1074/jbc.274.2.1108] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
When limited proteolysis of the mouse major urinary proteins by trypsin was stopped by rapid denaturation of the proteinase, a covalent adduct of the two proteins was observed. The formation of this complex required active trypsin, was favored at low pH, and could be reversed by the addition of covalent or non-covalent trypsin inhibitors. Electrospray mass spectrometry of the complex demonstrated that it was an acyl-enzyme complex, formed after an unusual exopeptidase attack on the C-terminal-Arg-Glu-OH sequence by trypsin. The complex could sequester over 50% of the trypsin in a digestion mixture, and as anticipated, the protein was an effective trypsin inhibitor.
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Affiliation(s)
- C Wu
- Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, Manchester M60 1QD, United Kingdom
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