Novel insight into the copper-ligand geometry in the crystal structure of Ulva pertusa plastocyanin at 1.6-A resolution. Structural basis for regulation of the copper site by residue 88.
Identifieur interne : 004873 ( Main/Exploration ); précédent : 004872; suivant : 004874Novel insight into the copper-ligand geometry in the crystal structure of Ulva pertusa plastocyanin at 1.6-A resolution. Structural basis for regulation of the copper site by residue 88.
Auteurs : N. Shibata [Japon] ; T. Inoue ; C. Nagano ; N. Nishio ; T. Kohzuma ; K. Onodera ; F. Yoshizaki ; Y. Sugimura ; Y. KaiSource :
- The Journal of biological chemistry [ 0021-9258 ] ; 1999.
Descripteurs français
- KwdFr :
- MESH :
- composition chimique : Chlorophyta, Plastocyanine.
- métabolisme : Cuivre.
- Cristallographie aux rayons X, Données de séquences moléculaires, Ligands, Relation structure-activité, Séquence d'acides aminés.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Plastocyanin.
- chemical , metabolism : Copper.
- chemistry : Chlorophyta.
- Amino Acid Sequence, Crystallography, X-Ray, Ligands, Molecular Sequence Data, Structure-Activity Relationship.
Abstract
The crystal structure of plastocyanin from a green alga, Ulva pertusa, has been determined at 1.6-A resolution. At its copper site, U. pertusa plastocyanin has a distorted tetrahedral coordination geometry similar to other plastocyanins. In comparison with structures of plastocyanins reported formerly, a Cu(II)-Sdelta(Met92) bond distance (2.69 A) is shorter by about 0.2 A and a Cu(II)-Sgamma(Cys84) distance is longer by less than 0.1 A in U. pertusa plastocyanin. These subtle but significant differences are caused by the structural change at a His-Met loop (His87-Met92) due to an absence of a O(Asp85)-Ogamma(Ser88) hydrogen bond which is found in Enteromorpha prolifera plastocyanin. In addition, poplar and Chlamydomonas reinhardtii plastocyanins with a glutamine at residue 88 have a weak cation-pi interaction with Tyr83. This interaction lengthens the Cu(II)-Sdelta(Met92) bond of poplar and C. reinhardtii plastocyanins by 0.14 and 0.20 A, respectively. As a result of structural differences, U. pertusa plastocyanin has a less distorted geometry than the other plastocyanins. Thus, the cupric geometry is finely tuned by the interactions between residues 85 and 88 and between residues 83 and 88. This result implies that the copper site is more flexible than reported formerly and that the rack mechanism would be preferable to the entatic theory. The His-Met loop may regulate the electron transfer rate within the complex between plastocyanin and cytochrome f.
DOI: 10.1074/jbc.274.7.4225
PubMed: 9933621
Affiliations:
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Nagano</name></author><author><name sortKey="Nishio, N" sort="Nishio, N" uniqKey="Nishio N" first="N" last="Nishio">N. Nishio</name></author><author><name sortKey="Kohzuma, T" sort="Kohzuma, T" uniqKey="Kohzuma T" first="T" last="Kohzuma">T. Kohzuma</name></author><author><name sortKey="Onodera, K" sort="Onodera, K" uniqKey="Onodera K" first="K" last="Onodera">K. Onodera</name></author><author><name sortKey="Yoshizaki, F" sort="Yoshizaki, F" uniqKey="Yoshizaki F" first="F" last="Yoshizaki">F. Yoshizaki</name></author><author><name sortKey="Sugimura, Y" sort="Sugimura, Y" uniqKey="Sugimura Y" first="Y" last="Sugimura">Y. Sugimura</name></author><author><name sortKey="Kai, Y" sort="Kai, Y" uniqKey="Kai Y" first="Y" last="Kai">Y. Kai</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1999">1999</date><idno type="RBID">pubmed:9933621</idno><idno type="pmid">9933621</idno><idno type="doi">10.1074/jbc.274.7.4225</idno><idno type="wicri:Area/Main/Corpus">004934</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">004934</idno><idno type="wicri:Area/Main/Curation">004934</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">004934</idno><idno type="wicri:Area/Main/Exploration">004934</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Novel insight into the copper-ligand geometry in the crystal structure of Ulva pertusa plastocyanin at 1.6-A resolution. Structural basis for regulation of the copper site by residue 88.</title><author><name sortKey="Shibata, N" sort="Shibata, N" uniqKey="Shibata N" first="N" last="Shibata">N. Shibata</name><affiliation wicri:level="1"><nlm:affiliation>Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Osaka 565-0871</wicri:regionArea><wicri:noRegion>Osaka 565-0871</wicri:noRegion></affiliation></author><author><name sortKey="Inoue, T" sort="Inoue, T" uniqKey="Inoue T" first="T" last="Inoue">T. Inoue</name></author><author><name sortKey="Nagano, C" sort="Nagano, C" uniqKey="Nagano C" first="C" last="Nagano">C. Nagano</name></author><author><name sortKey="Nishio, N" sort="Nishio, N" uniqKey="Nishio N" first="N" last="Nishio">N. Nishio</name></author><author><name sortKey="Kohzuma, T" sort="Kohzuma, T" uniqKey="Kohzuma T" first="T" last="Kohzuma">T. Kohzuma</name></author><author><name sortKey="Onodera, K" sort="Onodera, K" uniqKey="Onodera K" first="K" last="Onodera">K. Onodera</name></author><author><name sortKey="Yoshizaki, F" sort="Yoshizaki, F" uniqKey="Yoshizaki F" first="F" last="Yoshizaki">F. Yoshizaki</name></author><author><name sortKey="Sugimura, Y" sort="Sugimura, Y" uniqKey="Sugimura Y" first="Y" last="Sugimura">Y. Sugimura</name></author><author><name sortKey="Kai, Y" sort="Kai, Y" uniqKey="Kai Y" first="Y" last="Kai">Y. Kai</name></author></analytic><series><title level="j">The Journal of biological chemistry</title><idno type="ISSN">0021-9258</idno><imprint><date when="1999" type="published">1999</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (MeSH)</term><term>Chlorophyta (chemistry)</term><term>Copper (metabolism)</term><term>Crystallography, X-Ray (MeSH)</term><term>Ligands (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Plastocyanin (chemistry)</term><term>Structure-Activity Relationship (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Chlorophyta (composition chimique)</term><term>Cristallographie aux rayons X (MeSH)</term><term>Cuivre (métabolisme)</term><term>Données de séquences moléculaires (MeSH)</term><term>Ligands (MeSH)</term><term>Plastocyanine (composition chimique)</term><term>Relation structure-activité (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Plastocyanin</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Copper</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Chlorophyta</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Chlorophyta</term><term>Plastocyanine</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Cuivre</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Crystallography, X-Ray</term><term>Ligands</term><term>Molecular Sequence Data</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cristallographie aux rayons X</term><term>Données de séquences moléculaires</term><term>Ligands</term><term>Relation structure-activité</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The crystal structure of plastocyanin from a green alga, Ulva pertusa, has been determined at 1.6-A resolution. At its copper site, U. pertusa plastocyanin has a distorted tetrahedral coordination geometry similar to other plastocyanins. In comparison with structures of plastocyanins reported formerly, a Cu(II)-Sdelta(Met92) bond distance (2.69 A) is shorter by about 0.2 A and a Cu(II)-Sgamma(Cys84) distance is longer by less than 0.1 A in U. pertusa plastocyanin. These subtle but significant differences are caused by the structural change at a His-Met loop (His87-Met92) due to an absence of a O(Asp85)-Ogamma(Ser88) hydrogen bond which is found in Enteromorpha prolifera plastocyanin. In addition, poplar and Chlamydomonas reinhardtii plastocyanins with a glutamine at residue 88 have a weak cation-pi interaction with Tyr83. This interaction lengthens the Cu(II)-Sdelta(Met92) bond of poplar and C. reinhardtii plastocyanins by 0.14 and 0.20 A, respectively. As a result of structural differences, U. pertusa plastocyanin has a less distorted geometry than the other plastocyanins. Thus, the cupric geometry is finely tuned by the interactions between residues 85 and 88 and between residues 83 and 88. This result implies that the copper site is more flexible than reported formerly and that the rack mechanism would be preferable to the entatic theory. The His-Met loop may regulate the electron transfer rate within the complex between plastocyanin and cytochrome f.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">9933621</PMID><DateCompleted><Year>1999</Year><Month>03</Month><Day>11</Day></DateCompleted><DateRevised><Year>2019</Year><Month>05</Month><Day>08</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0021-9258</ISSN><JournalIssue CitedMedium="Print"><Volume>274</Volume><Issue>7</Issue><PubDate><Year>1999</Year><Month>Feb</Month><Day>12</Day></PubDate></JournalIssue><Title>The Journal of biological chemistry</Title><ISOAbbreviation>J Biol Chem</ISOAbbreviation></Journal><ArticleTitle>Novel insight into the copper-ligand geometry in the crystal structure of Ulva pertusa plastocyanin at 1.6-A resolution. Structural basis for regulation of the copper site by residue 88.</ArticleTitle><Pagination><MedlinePgn>4225-30</MedlinePgn></Pagination><Abstract><AbstractText>The crystal structure of plastocyanin from a green alga, Ulva pertusa, has been determined at 1.6-A resolution. At its copper site, U. pertusa plastocyanin has a distorted tetrahedral coordination geometry similar to other plastocyanins. In comparison with structures of plastocyanins reported formerly, a Cu(II)-Sdelta(Met92) bond distance (2.69 A) is shorter by about 0.2 A and a Cu(II)-Sgamma(Cys84) distance is longer by less than 0.1 A in U. pertusa plastocyanin. These subtle but significant differences are caused by the structural change at a His-Met loop (His87-Met92) due to an absence of a O(Asp85)-Ogamma(Ser88) hydrogen bond which is found in Enteromorpha prolifera plastocyanin. In addition, poplar and Chlamydomonas reinhardtii plastocyanins with a glutamine at residue 88 have a weak cation-pi interaction with Tyr83. This interaction lengthens the Cu(II)-Sdelta(Met92) bond of poplar and C. reinhardtii plastocyanins by 0.14 and 0.20 A, respectively. As a result of structural differences, U. pertusa plastocyanin has a less distorted geometry than the other plastocyanins. Thus, the cupric geometry is finely tuned by the interactions between residues 85 and 88 and between residues 83 and 88. This result implies that the copper site is more flexible than reported formerly and that the rack mechanism would be preferable to the entatic theory. The His-Met loop may regulate the electron transfer rate within the complex between plastocyanin and cytochrome f.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Shibata</LastName><ForeName>N</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Inoue</LastName><ForeName>T</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Nagano</LastName><ForeName>C</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Nishio</LastName><ForeName>N</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Kohzuma</LastName><ForeName>T</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Onodera</LastName><ForeName>K</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Yoshizaki</LastName><ForeName>F</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Sugimura</LastName><ForeName>Y</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Kai</LastName><ForeName>Y</ForeName><Initials>Y</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>PDB</DataBankName><AccessionNumberList><AccessionNumber>1IUZ</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Biol Chem</MedlineTA><NlmUniqueID>2985121R</NlmUniqueID><ISSNLinking>0021-9258</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D008024">Ligands</NameOfSubstance></Chemical><Chemical><RegistryNumber>789U1901C5</RegistryNumber><NameOfSubstance UI="D003300">Copper</NameOfSubstance></Chemical><Chemical><RegistryNumber>9014-09-9</RegistryNumber><NameOfSubstance UI="D010970">Plastocyanin</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000460" MajorTopicYN="N">Chlorophyta</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003300" MajorTopicYN="N">Copper</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018360" MajorTopicYN="N">Crystallography, X-Ray</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008024" MajorTopicYN="N">Ligands</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010970" MajorTopicYN="N">Plastocyanin</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013329" MajorTopicYN="N">Structure-Activity Relationship</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>1999</Year><Month>2</Month><Day>6</Day></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>1999</Year><Month>2</Month><Day>6</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>1999</Year><Month>2</Month><Day>6</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">9933621</ArticleId><ArticleId IdType="doi">10.1074/jbc.274.7.4225</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Japon</li></country></list><tree><noCountry><name sortKey="Inoue, T" sort="Inoue, T" uniqKey="Inoue T" first="T" last="Inoue">T. Inoue</name><name sortKey="Kai, Y" sort="Kai, Y" uniqKey="Kai Y" first="Y" last="Kai">Y. Kai</name><name sortKey="Kohzuma, T" sort="Kohzuma, T" uniqKey="Kohzuma T" first="T" last="Kohzuma">T. Kohzuma</name><name sortKey="Nagano, C" sort="Nagano, C" uniqKey="Nagano C" first="C" last="Nagano">C. Nagano</name><name sortKey="Nishio, N" sort="Nishio, N" uniqKey="Nishio N" first="N" last="Nishio">N. Nishio</name><name sortKey="Onodera, K" sort="Onodera, K" uniqKey="Onodera K" first="K" last="Onodera">K. Onodera</name><name sortKey="Sugimura, Y" sort="Sugimura, Y" uniqKey="Sugimura Y" first="Y" last="Sugimura">Y. Sugimura</name><name sortKey="Yoshizaki, F" sort="Yoshizaki, F" uniqKey="Yoshizaki F" first="F" last="Yoshizaki">F. Yoshizaki</name></noCountry><country name="Japon"><noRegion><name sortKey="Shibata, N" sort="Shibata, N" uniqKey="Shibata N" first="N" last="Shibata">N. Shibata</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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