The first position of a codon placed in the A site of the human 80S ribosome contacts nucleotide C1696 of the 18S rRNA as well as proteins S2, S3, S3a, S30, and S15.
Identifieur interne : 002349 ( PubMed/Corpus ); précédent : 002348; suivant : 002350The first position of a codon placed in the A site of the human 80S ribosome contacts nucleotide C1696 of the 18S rRNA as well as proteins S2, S3, S3a, S30, and S15.
Auteurs : Konstantin Bulygin ; Laurent Chavatte ; Ludmila Frolova ; Galina Karpova ; Alain FavreSource :
- Biochemistry [ 0006-2960 ] ; 2005.
English descriptors
- KwdEn :
- Base Sequence, Binding Sites (genetics), Codon (chemistry), Codon (genetics), Cross-Linking Reagents (chemistry), Cytosine (chemistry), Humans, Molecular Sequence Data, Nucleic Acid Conformation, Peptide Fragments (chemistry), Peptide Fragments (genetics), RNA, Messenger (chemistry), RNA, Ribosomal, 18S (chemistry), RNA, Ribosomal, 18S (genetics), RNA, Transfer, Asp (chemistry), RNA, Transfer, Asp (genetics), Ribosomal Proteins (chemistry), Ribosomal Proteins (genetics), Ribosomes (chemistry), Ribosomes (genetics), Templates, Genetic, Thiouridine (chemistry).
- MESH :
- chemical , chemistry : Codon, Cross-Linking Reagents, Cytosine, Peptide Fragments, RNA, Messenger, RNA, Ribosomal, 18S, RNA, Transfer, Asp, Ribosomal Proteins, Thiouridine.
- chemistry : Ribosomes.
- genetics : Binding Sites, Codon, Peptide Fragments, RNA, Ribosomal, 18S, RNA, Transfer, Asp, Ribosomal Proteins, Ribosomes.
- Base Sequence, Humans, Molecular Sequence Data, Nucleic Acid Conformation, Templates, Genetic.
Abstract
Messenger RNA analogues (42-mers) containing a GAC codon (aspartic acid) in the middle of their sequence followed by a s(4)UGA stop codon were used to identify the components of the human ribosomal A site in direct contact with the photoactivatable 4-thiouridine (s(4)U) residue. We compared the behavior of the nonphased ribosome-mRNA complex, (-)tRNA(Asp), to the one of the phased complex, (+)tRNA(Asp), in the absence and in the presence of eRF1, the eukaryotic class 1 translation termination factor of human origin. The patterns of cross-links obtained for the three complexes were similar to those previously reported for rabbit ribosomes [Chavatte, L., et al. (2001) Eur. J. Biochem. 268, 2896-2904]. Cross-links involving proteins S2, S3, S3a, and S30 were poorly dependent on the presence of tRNA(Asp) and eRF1. Cross-linking to nucleotide C1696 of 18S rRNA occurred in all complexes, but its yield was at least two times higher in the phased complex with an empty A site than in the nonphased complex or when the A site was occupied by eRF1. In contrast, protein S15 cross-linked only in the phased complex in the absence of eRF1. The data obtained point to notable differences in organization of the decoding site between mammalian and prokaryotic ribosomes and to large internal mobility of the components of the tRNA (eRF1)-free A site.
DOI: 10.1021/bi0487802
PubMed: 15697241
Links to Exploration step
pubmed:15697241Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The first position of a codon placed in the A site of the human 80S ribosome contacts nucleotide C1696 of the 18S rRNA as well as proteins S2, S3, S3a, S30, and S15.</title><author><name sortKey="Bulygin, Konstantin" sort="Bulygin, Konstantin" uniqKey="Bulygin K" first="Konstantin" last="Bulygin">Konstantin Bulygin</name><affiliation><nlm:affiliation>Institut Jacques Monod, UMR 7592 CNRS-Universites Paris 7-Paris 6, 2 place Jussieu Tour 43, 75251 Paris Cedex 05, France.</nlm:affiliation></affiliation></author><author><name sortKey="Chavatte, Laurent" sort="Chavatte, Laurent" uniqKey="Chavatte L" first="Laurent" last="Chavatte">Laurent Chavatte</name></author><author><name sortKey="Frolova, Ludmila" sort="Frolova, Ludmila" uniqKey="Frolova L" first="Ludmila" last="Frolova">Ludmila Frolova</name></author><author><name sortKey="Karpova, Galina" sort="Karpova, Galina" uniqKey="Karpova G" first="Galina" last="Karpova">Galina Karpova</name></author><author><name sortKey="Favre, Alain" sort="Favre, Alain" uniqKey="Favre A" first="Alain" last="Favre">Alain Favre</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="RBID">pubmed:15697241</idno><idno type="pmid">15697241</idno><idno type="doi">10.1021/bi0487802</idno><idno type="wicri:Area/PubMed/Corpus">002349</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002349</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The first position of a codon placed in the A site of the human 80S ribosome contacts nucleotide C1696 of the 18S rRNA as well as proteins S2, S3, S3a, S30, and S15.</title><author><name sortKey="Bulygin, Konstantin" sort="Bulygin, Konstantin" uniqKey="Bulygin K" first="Konstantin" last="Bulygin">Konstantin Bulygin</name><affiliation><nlm:affiliation>Institut Jacques Monod, UMR 7592 CNRS-Universites Paris 7-Paris 6, 2 place Jussieu Tour 43, 75251 Paris Cedex 05, France.</nlm:affiliation></affiliation></author><author><name sortKey="Chavatte, Laurent" sort="Chavatte, Laurent" uniqKey="Chavatte L" first="Laurent" last="Chavatte">Laurent Chavatte</name></author><author><name sortKey="Frolova, Ludmila" sort="Frolova, Ludmila" uniqKey="Frolova L" first="Ludmila" last="Frolova">Ludmila Frolova</name></author><author><name sortKey="Karpova, Galina" sort="Karpova, Galina" uniqKey="Karpova G" first="Galina" last="Karpova">Galina Karpova</name></author><author><name sortKey="Favre, Alain" sort="Favre, Alain" uniqKey="Favre A" first="Alain" last="Favre">Alain Favre</name></author></analytic><series><title level="j">Biochemistry</title><idno type="ISSN">0006-2960</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Binding Sites (genetics)</term><term>Codon (chemistry)</term><term>Codon (genetics)</term><term>Cross-Linking Reagents (chemistry)</term><term>Cytosine (chemistry)</term><term>Humans</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>Peptide Fragments (chemistry)</term><term>Peptide Fragments (genetics)</term><term>RNA, Messenger (chemistry)</term><term>RNA, Ribosomal, 18S (chemistry)</term><term>RNA, Ribosomal, 18S (genetics)</term><term>RNA, Transfer, Asp (chemistry)</term><term>RNA, Transfer, Asp (genetics)</term><term>Ribosomal Proteins (chemistry)</term><term>Ribosomal Proteins (genetics)</term><term>Ribosomes (chemistry)</term><term>Ribosomes (genetics)</term><term>Templates, Genetic</term><term>Thiouridine (chemistry)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Codon</term><term>Cross-Linking Reagents</term><term>Cytosine</term><term>Peptide Fragments</term><term>RNA, Messenger</term><term>RNA, Ribosomal, 18S</term><term>RNA, Transfer, Asp</term><term>Ribosomal Proteins</term><term>Thiouridine</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Ribosomes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Binding Sites</term><term>Codon</term><term>Peptide Fragments</term><term>RNA, Ribosomal, 18S</term><term>RNA, Transfer, Asp</term><term>Ribosomal Proteins</term><term>Ribosomes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Humans</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>Templates, Genetic</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Messenger RNA analogues (42-mers) containing a GAC codon (aspartic acid) in the middle of their sequence followed by a s(4)UGA stop codon were used to identify the components of the human ribosomal A site in direct contact with the photoactivatable 4-thiouridine (s(4)U) residue. We compared the behavior of the nonphased ribosome-mRNA complex, (-)tRNA(Asp), to the one of the phased complex, (+)tRNA(Asp), in the absence and in the presence of eRF1, the eukaryotic class 1 translation termination factor of human origin. The patterns of cross-links obtained for the three complexes were similar to those previously reported for rabbit ribosomes [Chavatte, L., et al. (2001) Eur. J. Biochem. 268, 2896-2904]. Cross-links involving proteins S2, S3, S3a, and S30 were poorly dependent on the presence of tRNA(Asp) and eRF1. Cross-linking to nucleotide C1696 of 18S rRNA occurred in all complexes, but its yield was at least two times higher in the phased complex with an empty A site than in the nonphased complex or when the A site was occupied by eRF1. In contrast, protein S15 cross-linked only in the phased complex in the absence of eRF1. The data obtained point to notable differences in organization of the decoding site between mammalian and prokaryotic ribosomes and to large internal mobility of the components of the tRNA (eRF1)-free A site.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15697241</PMID><DateCompleted><Year>2005</Year><Month>04</Month><Day>08</Day></DateCompleted><DateRevised><Year>2013</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0006-2960</ISSN><JournalIssue CitedMedium="Print"><Volume>44</Volume><Issue>6</Issue><PubDate><Year>2005</Year><Month>Feb</Month><Day>15</Day></PubDate></JournalIssue><Title>Biochemistry</Title><ISOAbbreviation>Biochemistry</ISOAbbreviation></Journal><ArticleTitle>The first position of a codon placed in the A site of the human 80S ribosome contacts nucleotide C1696 of the 18S rRNA as well as proteins S2, S3, S3a, S30, and S15.</ArticleTitle><Pagination><MedlinePgn>2153-62</MedlinePgn></Pagination><Abstract><AbstractText>Messenger RNA analogues (42-mers) containing a GAC codon (aspartic acid) in the middle of their sequence followed by a s(4)UGA stop codon were used to identify the components of the human ribosomal A site in direct contact with the photoactivatable 4-thiouridine (s(4)U) residue. We compared the behavior of the nonphased ribosome-mRNA complex, (-)tRNA(Asp), to the one of the phased complex, (+)tRNA(Asp), in the absence and in the presence of eRF1, the eukaryotic class 1 translation termination factor of human origin. The patterns of cross-links obtained for the three complexes were similar to those previously reported for rabbit ribosomes [Chavatte, L., et al. (2001) Eur. J. Biochem. 268, 2896-2904]. Cross-links involving proteins S2, S3, S3a, and S30 were poorly dependent on the presence of tRNA(Asp) and eRF1. Cross-linking to nucleotide C1696 of 18S rRNA occurred in all complexes, but its yield was at least two times higher in the phased complex with an empty A site than in the nonphased complex or when the A site was occupied by eRF1. In contrast, protein S15 cross-linked only in the phased complex in the absence of eRF1. The data obtained point to notable differences in organization of the decoding site between mammalian and prokaryotic ribosomes and to large internal mobility of the components of the tRNA (eRF1)-free A site.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bulygin</LastName><ForeName>Konstantin</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Institut Jacques Monod, UMR 7592 CNRS-Universites Paris 7-Paris 6, 2 place Jussieu Tour 43, 75251 Paris Cedex 05, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chavatte</LastName><ForeName>Laurent</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Frolova</LastName><ForeName>Ludmila</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Karpova</LastName><ForeName>Galina</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Favre</LastName><ForeName>Alain</ForeName><Initials>A</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><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>Biochemistry</MedlineTA><NlmUniqueID>0370623</NlmUniqueID><ISSNLinking>0006-2960</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D003062">Codon</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D003432">Cross-Linking Reagents</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010446">Peptide Fragments</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, 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S30</NameOfSubstance></Chemical><Chemical><RegistryNumber>13957-31-8</RegistryNumber><NameOfSubstance UI="D013891">Thiouridine</NameOfSubstance></Chemical><Chemical><RegistryNumber>8J337D1HZY</RegistryNumber><NameOfSubstance UI="D003596">Cytosine</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003062" MajorTopicYN="N">Codon</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003432" MajorTopicYN="N">Cross-Linking Reagents</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003596" MajorTopicYN="N">Cytosine</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010446" MajorTopicYN="N">Peptide Fragments</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName 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