Crystal structures reveal an induced-fit binding of a substrate-like Aza-peptide epoxide to SARS coronavirus main peptidase.
Identifieur interne : 001E38 ( PubMed/Checkpoint ); précédent : 001E37; suivant : 001E39Crystal structures reveal an induced-fit binding of a substrate-like Aza-peptide epoxide to SARS coronavirus main peptidase.
Auteurs : Ting-Wai Lee [Canada] ; Maia M. Cherney ; Jie Liu ; Karen Ellis James ; James C. Powers ; Lindsay D. Eltis ; Michael N G. JamesSource :
- Journal of molecular biology [ 0022-2836 ] ; 2007.
Descripteurs français
- KwdFr :
- Composés époxy (), Composés époxy (métabolisme), Cristallographie aux rayons X, Liaison aux protéines, Modèles moléculaires, Peptides (), Peptides (métabolisme), Protons, Protéines de la matrice virale (), Sites de fixation, Spécificité du substrat, Structure tertiaire des protéines, Virus du SRAS (enzymologie), Électricité statique.
- MESH :
- enzymologie : Virus du SRAS.
- métabolisme : Composés époxy, Peptides.
- Composés époxy, Cristallographie aux rayons X, Liaison aux protéines, Modèles moléculaires, Peptides, Protons, Protéines de la matrice virale, Sites de fixation, Spécificité du substrat, Structure tertiaire des protéines, Électricité statique.
English descriptors
- KwdEn :
- Binding Sites, Crystallography, X-Ray, Epoxy Compounds (chemistry), Epoxy Compounds (metabolism), Models, Molecular, Peptides (chemistry), Peptides (metabolism), Protein Binding, Protein Structure, Tertiary, Protons, SARS Virus (enzymology), Static Electricity, Substrate Specificity, Viral Matrix Proteins (chemistry).
- MESH :
- chemical , chemistry : Epoxy Compounds, Peptides, Viral Matrix Proteins.
- chemical , metabolism : Epoxy Compounds, Peptides.
- enzymology : SARS Virus.
- Binding Sites, Crystallography, X-Ray, Models, Molecular, Protein Binding, Protein Structure, Tertiary, Protons, Static Electricity, Substrate Specificity.
Abstract
The SARS coronavirus main peptidase (SARS-CoV M(pro)) plays an essential role in the life-cycle of the virus and is a primary target for the development of anti-SARS agents. Here, we report the crystal structure of M(pro) at a resolution of 1.82 Angstroms, in space group P2(1) at pH 6.0. In contrast to the previously reported structure of M(pro) in the same space group at the same pH, the active sites and the S1 specificity pockets of both protomers in the structure of M(pro) reported here are in the catalytically competent conformation, suggesting their conformational flexibility. We report two crystal structures of M(pro) having an additional Ala at the N terminus of each protomer (M(+A(-1))(pro)), both at a resolution of 2.00 Angstroms, in space group P4(3)2(1)2: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). In the unbound form, the active sites and the S1 specificity pockets of both protomers of M(+A(-1))(pro) are observed in a collapsed (catalytically incompetent) conformation; whereas they are in an open (catalytically competent) conformation in the APE-bound form. The observed conformational flexibility of the active sites and the S1 specificity pockets suggests that these parts of M(pro) exist in dynamic equilibrium. The structural data further suggest that the binding of APE to M(pro) follows an induced-fit model. The substrate likely also binds in an induced-fit manner in a process that may help drive the catalytic cycle.
DOI: 10.1016/j.jmb.2006.11.078
PubMed: 17196984
Affiliations:
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pubmed:17196984Le document en format XML
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Cherney</name></author><author><name sortKey="Liu, Jie" sort="Liu, Jie" uniqKey="Liu J" first="Jie" last="Liu">Jie Liu</name></author><author><name sortKey="James, Karen Ellis" sort="James, Karen Ellis" uniqKey="James K" first="Karen Ellis" last="James">Karen Ellis James</name></author><author><name sortKey="Powers, James C" sort="Powers, James C" uniqKey="Powers J" first="James C" last="Powers">James C. Powers</name></author><author><name sortKey="Eltis, Lindsay D" sort="Eltis, Lindsay D" uniqKey="Eltis L" first="Lindsay D" last="Eltis">Lindsay D. Eltis</name></author><author><name sortKey="James, Michael N G" sort="James, Michael N G" uniqKey="James M" first="Michael N G" last="James">Michael N G. James</name></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="ISSN">0022-2836</idno><imprint><date when="2007" type="published">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Crystallography, X-Ray</term><term>Epoxy Compounds (chemistry)</term><term>Epoxy Compounds (metabolism)</term><term>Models, Molecular</term><term>Peptides (chemistry)</term><term>Peptides (metabolism)</term><term>Protein Binding</term><term>Protein Structure, Tertiary</term><term>Protons</term><term>SARS Virus (enzymology)</term><term>Static Electricity</term><term>Substrate Specificity</term><term>Viral Matrix Proteins (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Composés époxy ()</term><term>Composés époxy (métabolisme)</term><term>Cristallographie aux rayons X</term><term>Liaison aux protéines</term><term>Modèles moléculaires</term><term>Peptides ()</term><term>Peptides (métabolisme)</term><term>Protons</term><term>Protéines de la matrice virale ()</term><term>Sites de fixation</term><term>Spécificité du substrat</term><term>Structure tertiaire des protéines</term><term>Virus du SRAS (enzymologie)</term><term>Électricité statique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Epoxy Compounds</term><term>Peptides</term><term>Viral Matrix Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Epoxy Compounds</term><term>Peptides</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Composés époxy</term><term>Peptides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Crystallography, X-Ray</term><term>Models, Molecular</term><term>Protein Binding</term><term>Protein Structure, Tertiary</term><term>Protons</term><term>Static Electricity</term><term>Substrate Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Composés époxy</term><term>Cristallographie aux rayons X</term><term>Liaison aux protéines</term><term>Modèles moléculaires</term><term>Peptides</term><term>Protons</term><term>Protéines de la matrice virale</term><term>Sites de fixation</term><term>Spécificité du substrat</term><term>Structure tertiaire des protéines</term><term>Électricité statique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The SARS coronavirus main peptidase (SARS-CoV M(pro)) plays an essential role in the life-cycle of the virus and is a primary target for the development of anti-SARS agents. Here, we report the crystal structure of M(pro) at a resolution of 1.82 Angstroms, in space group P2(1) at pH 6.0. In contrast to the previously reported structure of M(pro) in the same space group at the same pH, the active sites and the S1 specificity pockets of both protomers in the structure of M(pro) reported here are in the catalytically competent conformation, suggesting their conformational flexibility. We report two crystal structures of M(pro) having an additional Ala at the N terminus of each protomer (M(+A(-1))(pro)), both at a resolution of 2.00 Angstroms, in space group P4(3)2(1)2: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). In the unbound form, the active sites and the S1 specificity pockets of both protomers of M(+A(-1))(pro) are observed in a collapsed (catalytically incompetent) conformation; whereas they are in an open (catalytically competent) conformation in the APE-bound form. The observed conformational flexibility of the active sites and the S1 specificity pockets suggests that these parts of M(pro) exist in dynamic equilibrium. The structural data further suggest that the binding of APE to M(pro) follows an induced-fit model. The substrate likely also binds in an induced-fit manner in a process that may help drive the catalytic cycle.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17196984</PMID><DateCompleted><Year>2007</Year><Month>03</Month><Day>29</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>07</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0022-2836</ISSN><JournalIssue CitedMedium="Print"><Volume>366</Volume><Issue>3</Issue><PubDate><Year>2007</Year><Month>Feb</Month><Day>23</Day></PubDate></JournalIssue><Title>Journal of molecular biology</Title><ISOAbbreviation>J. Mol. Biol.</ISOAbbreviation></Journal><ArticleTitle>Crystal structures reveal an induced-fit binding of a substrate-like Aza-peptide epoxide to SARS coronavirus main peptidase.</ArticleTitle><Pagination><MedlinePgn>916-32</MedlinePgn></Pagination><Abstract><AbstractText>The SARS coronavirus main peptidase (SARS-CoV M(pro)) plays an essential role in the life-cycle of the virus and is a primary target for the development of anti-SARS agents. Here, we report the crystal structure of M(pro) at a resolution of 1.82 Angstroms, in space group P2(1) at pH 6.0. In contrast to the previously reported structure of M(pro) in the same space group at the same pH, the active sites and the S1 specificity pockets of both protomers in the structure of M(pro) reported here are in the catalytically competent conformation, suggesting their conformational flexibility. We report two crystal structures of M(pro) having an additional Ala at the N terminus of each protomer (M(+A(-1))(pro)), both at a resolution of 2.00 Angstroms, in space group P4(3)2(1)2: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). In the unbound form, the active sites and the S1 specificity pockets of both protomers of M(+A(-1))(pro) are observed in a collapsed (catalytically incompetent) conformation; whereas they are in an open (catalytically competent) conformation in the APE-bound form. The observed conformational flexibility of the active sites and the S1 specificity pockets suggests that these parts of M(pro) exist in dynamic equilibrium. The structural data further suggest that the binding of APE to M(pro) follows an induced-fit model. The substrate likely also binds in an induced-fit manner in a process that may help drive the catalytic cycle.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Ting-Wai</ForeName><Initials>TW</Initials><AffiliationInfo><Affiliation>Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cherney</LastName><ForeName>Maia M</ForeName><Initials>MM</Initials></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Jie</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>James</LastName><ForeName>Karen Ellis</ForeName><Initials>KE</Initials></Author><Author ValidYN="Y"><LastName>Powers</LastName><ForeName>James C</ForeName><Initials>JC</Initials></Author><Author ValidYN="Y"><LastName>Eltis</LastName><ForeName>Lindsay D</ForeName><Initials>LD</Initials></Author><Author ValidYN="Y"><LastName>James</LastName><ForeName>Michael N G</ForeName><Initials>MN</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>PDB</DataBankName><AccessionNumberList><AccessionNumber>2GT7</AccessionNumber><AccessionNumber>2GT8</AccessionNumber><AccessionNumber>2GTB</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>12</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Mol Biol</MedlineTA><NlmUniqueID>2985088R</NlmUniqueID><ISSNLinking>0022-2836</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004852">Epoxy Compounds</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010455">Peptides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011522">Protons</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014763">Viral Matrix Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>108502-71-2</RegistryNumber><NameOfSubstance UI="C067997">M protein, Coronavirus</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018360" MajorTopicYN="N">Crystallography, X-Ray</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004852" MajorTopicYN="N">Epoxy Compounds</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010455" MajorTopicYN="N">Peptides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011485" MajorTopicYN="N">Protein Binding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017434" MajorTopicYN="N">Protein Structure, Tertiary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011522" MajorTopicYN="N">Protons</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055672" MajorTopicYN="N">Static Electricity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013379" MajorTopicYN="N">Substrate Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014763" MajorTopicYN="N">Viral Matrix Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2006</Year><Month>08</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2006</Year><Month>11</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2006</Year><Month>11</Month><Day>28</Day></PubMedPubDate><PubMedPubDate 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Cherney</name><name sortKey="Eltis, Lindsay D" sort="Eltis, Lindsay D" uniqKey="Eltis L" first="Lindsay D" last="Eltis">Lindsay D. Eltis</name><name sortKey="James, Karen Ellis" sort="James, Karen Ellis" uniqKey="James K" first="Karen Ellis" last="James">Karen Ellis James</name><name sortKey="James, Michael N G" sort="James, Michael N G" uniqKey="James M" first="Michael N G" last="James">Michael N G. James</name><name sortKey="Liu, Jie" sort="Liu, Jie" uniqKey="Liu J" first="Jie" last="Liu">Jie Liu</name><name sortKey="Powers, James C" sort="Powers, James C" uniqKey="Powers J" first="James C" last="Powers">James C. Powers</name></noCountry><country name="Canada"><noRegion><name sortKey="Lee, Ting Wai" sort="Lee, Ting Wai" uniqKey="Lee T" first="Ting-Wai" last="Lee">Ting-Wai Lee</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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