Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating activity of SARS-CoV papain-like protease.
Identifieur interne : 000F89 ( PubMed/Corpus ); précédent : 000F88; suivant : 000F90Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating activity of SARS-CoV papain-like protease.
Auteurs : Kiira Ratia ; Andrew Kilianski ; Yahira M. Baez-Santos ; Susan C. Baker ; Andrew MesecarSource :
- PLoS pathogens [ 1553-7374 ] ; 2014.
English descriptors
- KwdEn :
- Amino Acid Sequence, Catalytic Domain, Coronavirus Infections (metabolism), Coronavirus Infections (virology), Crystallography, X-Ray, Cysteine Endopeptidases (chemistry), Cysteine Endopeptidases (genetics), Cysteine Endopeptidases (metabolism), Cytokines (metabolism), HEK293 Cells, Humans, Models, Molecular, Protein Conformation, Protein Processing, Post-Translational, SARS Virus (enzymology), SARS Virus (genetics), SARS Virus (metabolism), Substrate Specificity, Ubiquitin (metabolism), Ubiquitination (genetics), Ubiquitins (metabolism), Viral Proteins (chemistry), Viral Proteins (genetics), Viral Proteins (metabolism).
- MESH :
- chemical , chemistry : Cysteine Endopeptidases, Viral Proteins.
- chemical , genetics : Cysteine Endopeptidases, Viral Proteins.
- enzymology : SARS Virus.
- genetics : SARS Virus, Ubiquitination.
- metabolism : Coronavirus Infections, Cysteine Endopeptidases, Cytokines, SARS Virus, Ubiquitin, Ubiquitins, Viral Proteins.
- virology : Coronavirus Infections.
- Amino Acid Sequence, Catalytic Domain, Crystallography, X-Ray, HEK293 Cells, Humans, Models, Molecular, Protein Conformation, Protein Processing, Post-Translational, Substrate Specificity.
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) encodes a papain-like protease (PLpro) with both deubiquitinating (DUB) and deISGylating activities that are proposed to counteract the post-translational modification of signaling molecules that activate the innate immune response. Here we examine the structural basis for PLpro's ubiquitin chain and interferon stimulated gene 15 (ISG15) specificity. We present the X-ray crystal structure of PLpro in complex with ubiquitin-aldehyde and model the interaction of PLpro with other ubiquitin-chain and ISG15 substrates. We show that PLpro greatly prefers K48- to K63-linked ubiquitin chains, and ISG15-based substrates to those that are mono-ubiquitinated. We propose that PLpro's higher affinity for K48-linked ubiquitin chains and ISG15 stems from a bivalent mechanism of binding, where two ubiquitin-like domains prefer to bind in the palm domain of PLpro with the most distal ubiquitin domain interacting with a "ridge" region of the thumb domain. Mutagenesis of residues within this ridge region revealed that these mutants retain viral protease activity and the ability to catalyze hydrolysis of mono-ubiquitin. However, a select number of these mutants have a significantly reduced ability to hydrolyze the substrate ISG15-AMC, or be inhibited by K48-linked diubuiquitin. For these latter residues, we found that PLpro antagonism of the nuclear factor kappa-light-chain-enhancer of activated B-cells (NFκB) signaling pathway is abrogated. This identification of key and unique sites in PLpro required for recognition and processing of diubiquitin and ISG15 versus mono-ubiquitin and protease activity provides new insight into ubiquitin-chain and ISG15 recognition and highlights a role for PLpro DUB and deISGylase activity in antagonism of the innate immune response.
DOI: 10.1371/journal.ppat.1004113
PubMed: 24854014
Links to Exploration step
pubmed:24854014Le document en format XML
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Baez-Santos</name><affiliation><nlm:affiliation>Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Baker, Susan C" sort="Baker, Susan C" uniqKey="Baker S" first="Susan C" last="Baker">Susan C. Baker</name><affiliation><nlm:affiliation>Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Mesecar, Andrew" sort="Mesecar, Andrew" uniqKey="Mesecar A" first="Andrew" last="Mesecar">Andrew Mesecar</name><affiliation><nlm:affiliation>Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.</nlm:affiliation></affiliation></author></analytic><series><title level="j">PLoS pathogens</title><idno type="eISSN">1553-7374</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Catalytic Domain</term><term>Coronavirus Infections (metabolism)</term><term>Coronavirus Infections (virology)</term><term>Crystallography, X-Ray</term><term>Cysteine Endopeptidases (chemistry)</term><term>Cysteine Endopeptidases (genetics)</term><term>Cysteine Endopeptidases (metabolism)</term><term>Cytokines (metabolism)</term><term>HEK293 Cells</term><term>Humans</term><term>Models, Molecular</term><term>Protein Conformation</term><term>Protein Processing, Post-Translational</term><term>SARS Virus (enzymology)</term><term>SARS Virus (genetics)</term><term>SARS Virus (metabolism)</term><term>Substrate Specificity</term><term>Ubiquitin (metabolism)</term><term>Ubiquitination (genetics)</term><term>Ubiquitins (metabolism)</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (genetics)</term><term>Viral Proteins (metabolism)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Cysteine Endopeptidases</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Cysteine Endopeptidases</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>SARS Virus</term><term>Ubiquitination</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Coronavirus Infections</term><term>Cysteine Endopeptidases</term><term>Cytokines</term><term>SARS Virus</term><term>Ubiquitin</term><term>Ubiquitins</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Catalytic Domain</term><term>Crystallography, X-Ray</term><term>HEK293 Cells</term><term>Humans</term><term>Models, Molecular</term><term>Protein Conformation</term><term>Protein Processing, Post-Translational</term><term>Substrate Specificity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Severe acute respiratory syndrome coronavirus (SARS-CoV) encodes a papain-like protease (PLpro) with both deubiquitinating (DUB) and deISGylating activities that are proposed to counteract the post-translational modification of signaling molecules that activate the innate immune response. Here we examine the structural basis for PLpro's ubiquitin chain and interferon stimulated gene 15 (ISG15) specificity. We present the X-ray crystal structure of PLpro in complex with ubiquitin-aldehyde and model the interaction of PLpro with other ubiquitin-chain and ISG15 substrates. We show that PLpro greatly prefers K48- to K63-linked ubiquitin chains, and ISG15-based substrates to those that are mono-ubiquitinated. We propose that PLpro's higher affinity for K48-linked ubiquitin chains and ISG15 stems from a bivalent mechanism of binding, where two ubiquitin-like domains prefer to bind in the palm domain of PLpro with the most distal ubiquitin domain interacting with a "ridge" region of the thumb domain. Mutagenesis of residues within this ridge region revealed that these mutants retain viral protease activity and the ability to catalyze hydrolysis of mono-ubiquitin. However, a select number of these mutants have a significantly reduced ability to hydrolyze the substrate ISG15-AMC, or be inhibited by K48-linked diubuiquitin. For these latter residues, we found that PLpro antagonism of the nuclear factor kappa-light-chain-enhancer of activated B-cells (NFκB) signaling pathway is abrogated. This identification of key and unique sites in PLpro required for recognition and processing of diubiquitin and ISG15 versus mono-ubiquitin and protease activity provides new insight into ubiquitin-chain and ISG15 recognition and highlights a role for PLpro DUB and deISGylase activity in antagonism of the innate immune response. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24854014</PMID><DateCompleted><Year>2015</Year><Month>06</Month><Day>15</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>25</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1553-7374</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>5</Issue><PubDate><Year>2014</Year><Month>May</Month></PubDate></JournalIssue><Title>PLoS pathogens</Title><ISOAbbreviation>PLoS Pathog.</ISOAbbreviation></Journal><ArticleTitle>Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating activity of SARS-CoV papain-like protease.</ArticleTitle><Pagination><MedlinePgn>e1004113</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.ppat.1004113</ELocationID><Abstract><AbstractText>Severe acute respiratory syndrome coronavirus (SARS-CoV) encodes a papain-like protease (PLpro) with both deubiquitinating (DUB) and deISGylating activities that are proposed to counteract the post-translational modification of signaling molecules that activate the innate immune response. Here we examine the structural basis for PLpro's ubiquitin chain and interferon stimulated gene 15 (ISG15) specificity. We present the X-ray crystal structure of PLpro in complex with ubiquitin-aldehyde and model the interaction of PLpro with other ubiquitin-chain and ISG15 substrates. We show that PLpro greatly prefers K48- to K63-linked ubiquitin chains, and ISG15-based substrates to those that are mono-ubiquitinated. We propose that PLpro's higher affinity for K48-linked ubiquitin chains and ISG15 stems from a bivalent mechanism of binding, where two ubiquitin-like domains prefer to bind in the palm domain of PLpro with the most distal ubiquitin domain interacting with a "ridge" region of the thumb domain. Mutagenesis of residues within this ridge region revealed that these mutants retain viral protease activity and the ability to catalyze hydrolysis of mono-ubiquitin. However, a select number of these mutants have a significantly reduced ability to hydrolyze the substrate ISG15-AMC, or be inhibited by K48-linked diubuiquitin. For these latter residues, we found that PLpro antagonism of the nuclear factor kappa-light-chain-enhancer of activated B-cells (NFκB) signaling pathway is abrogated. This identification of key and unique sites in PLpro required for recognition and processing of diubiquitin and ISG15 versus mono-ubiquitin and protease activity provides new insight into ubiquitin-chain and ISG15 recognition and highlights a role for PLpro DUB and deISGylase activity in antagonism of the innate immune response. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ratia</LastName><ForeName>Kiira</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago, Illinois, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kilianski</LastName><ForeName>Andrew</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Baez-Santos</LastName><ForeName>Yahira M</ForeName><Initials>YM</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Baker</LastName><ForeName>Susan C</ForeName><Initials>SC</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mesecar</LastName><ForeName>Andrew</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>AI060915</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH 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