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Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease.

Identifieur interne : 000625 ( PubMed/Curation ); précédent : 000624; suivant : 000626

Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease.

Auteurs : Gang Ye [République populaire de Chine] ; Feng Deng [République populaire de Chine] ; Zhou Shen [République populaire de Chine] ; Rui Luo [République populaire de Chine] ; Ling Zhao [République populaire de Chine] ; Shaobo Xiao [République populaire de Chine] ; Zhen F. Fu [États-Unis] ; Guiqing Peng [République populaire de Chine]

Source :

RBID : pubmed:27128350

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English descriptors

Abstract

Porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus, has caused significant damage to the Asian and American pork industries. Coronavirus 3C-like protease (3CL(pro)), which is involved in the processing of viral polyproteins for viral replication, is an appealing antiviral drug target. Here, we present the crystal structures of PEDV 3CL(pro) and a molecular complex between an inactive PEDV 3CL(pro) variant C144A bound to a peptide substrate. Structural characterization, mutagenesis and biochemical analysis reveal the substrate-binding pockets and the residues that comprise the active site of PEDV 3CL(pro). The dimerization of PEDV 3CL(pro) is similar to that of other Alphacoronavirus 3CL(pro)s but has several differences from that of SARS-CoV 3CL(pro) from the genus Betacoronavirus. Furthermore, the non-conserved motifs in the pockets cause different cleavage of substrate between PEDV and SARS-CoV 3CL(pro)s, which may provide new insights into the recognition of substrates by 3CL(pro)s in various coronavirus genera.

DOI: 10.1016/j.virol.2016.04.018
PubMed: 27128350

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<div type="abstract" xml:lang="en">Porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus, has caused significant damage to the Asian and American pork industries. Coronavirus 3C-like protease (3CL(pro)), which is involved in the processing of viral polyproteins for viral replication, is an appealing antiviral drug target. Here, we present the crystal structures of PEDV 3CL(pro) and a molecular complex between an inactive PEDV 3CL(pro) variant C144A bound to a peptide substrate. Structural characterization, mutagenesis and biochemical analysis reveal the substrate-binding pockets and the residues that comprise the active site of PEDV 3CL(pro). The dimerization of PEDV 3CL(pro) is similar to that of other Alphacoronavirus 3CL(pro)s but has several differences from that of SARS-CoV 3CL(pro) from the genus Betacoronavirus. Furthermore, the non-conserved motifs in the pockets cause different cleavage of substrate between PEDV and SARS-CoV 3CL(pro)s, which may provide new insights into the recognition of substrates by 3CL(pro)s in various coronavirus genera.</div>
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<MedlineTA>Virology</MedlineTA>
<NlmUniqueID>0110674</NlmUniqueID>
<ISSNLinking>0042-6822</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D014764">Viral Proteins</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>EC 3.4.-</RegistryNumber>
<NameOfSubstance UI="D010447">Peptide Hydrolases</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D020816" MajorTopicYN="N">Amino Acid Motifs</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName>
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<MeshHeading>
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</MeshHeading>
<MeshHeading>
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<MeshHeading>
<DescriptorName UI="D008958" MajorTopicYN="Y">Models, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D010447" MajorTopicYN="N">Peptide Hydrolases</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D053485" MajorTopicYN="N">Porcine epidemic diarrhea virus</DescriptorName>
<QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D011485" MajorTopicYN="N">Protein Binding</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D011487" MajorTopicYN="N">Protein Conformation</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D054730" MajorTopicYN="N">Protein Interaction Domains and Motifs</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D055503" MajorTopicYN="Y">Protein Multimerization</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D013329" MajorTopicYN="N">Structure-Activity Relationship</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D013379" MajorTopicYN="N">Substrate Specificity</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D013552" MajorTopicYN="N">Swine</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D014764" MajorTopicYN="N">Viral Proteins</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM">
<Keyword MajorTopicYN="Y">Corona virus</Keyword>
<Keyword MajorTopicYN="Y">Crystal structure</Keyword>
<Keyword MajorTopicYN="Y">Dimerization</Keyword>
<Keyword MajorTopicYN="Y">PEDV 3CL(pro)</Keyword>
<Keyword MajorTopicYN="Y">Substrate specificity</Keyword>
</KeywordList>
</MedlineCitation>
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<Year>2015</Year>
<Month>10</Month>
<Day>19</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised">
<Year>2016</Year>
<Month>04</Month>
<Day>14</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted">
<Year>2016</Year>
<Month>04</Month>
<Day>15</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez">
<Year>2016</Year>
<Month>4</Month>
<Day>30</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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<PubMedPubDate PubStatus="pubmed">
<Year>2016</Year>
<Month>4</Month>
<Day>30</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2017</Year>
<Month>5</Month>
<Day>5</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">27128350</ArticleId>
<ArticleId IdType="pii">S0042-6822(16)30076-9</ArticleId>
<ArticleId IdType="doi">10.1016/j.virol.2016.04.018</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
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