Structure and dynamics in solution of the stop codon decoding N‐terminal domain of the human polypeptide chain release factor eRF1
The high‐resolution NMR structure of the N‐domain of human eRF1, responsible for stop codon recognition, has been determined in solution. The overall fold of the protein is the same as that found in the crystal structure. However, the structures of several loops, including those participating in sto...
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| Veröffentlicht in: | Protein science 2012-06, Vol.21 (6), p.896-903 |
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| creator | Polshakov, Vladimir I. Eliseev, Boris D. Birdsall, Berry Frolova, Ludmila Yu |
| description | The high‐resolution NMR structure of the N‐domain of human eRF1, responsible for stop codon recognition, has been determined in solution. The overall fold of the protein is the same as that found in the crystal structure. However, the structures of several loops, including those participating in stop codon decoding, are different. Analysis of the NMR relaxation data reveals that most of the regions with the highest structural discrepancy between the solution and solid states undergo internal motions on the ps–ns and ms time scales. The NMR data show that the N‐domain of human eRF1 exists in two conformational states. The distribution of the residues having the largest chemical shift differences between the two forms indicates that helices α2 and α3, with the NIKS loop between them, can switch their orientation relative to the β‐core of the protein. Such structural plasticity may be essential for stop codon recognition by human eRF1.
PDB Code(s): 2LLX |
| doi_str_mv | 10.1002/pro.2067 |
| format | Article |
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PDB Code(s): 2LLX</description><identifier>ISSN: 0961-8368</identifier><identifier>EISSN: 1469-896X</identifier><identifier>DOI: 10.1002/pro.2067</identifier><identifier>PMID: 22517631</identifier><identifier>CODEN: PRCIEI</identifier><language>eng</language><publisher>Hoboken: Wiley Subscription Services, Inc., A Wiley Company</publisher><subject>Codon, Terminator ; Crystal structure ; Eukaryotes ; human polypeptide release factor eRF1 ; Humans ; Models, Molecular ; NMR ; NMR structure and dynamics ; Nuclear magnetic resonance ; Nuclear Magnetic Resonance, Biomolecular ; N‐domain ; Peptide Termination Factors - chemistry ; Protein Structure, Secondary ; Protein Structure, Tertiary ; stop codon recognition ; termination of protein synthesis</subject><ispartof>Protein science, 2012-06, Vol.21 (6), p.896-903</ispartof><rights>Copyright © 2012 The Protein Society</rights><rights>Copyright © 2012 The Protein Society.</rights><rights>Copyright © 2012 The Protein Society 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4387-2807b02315baf3bed5800c3ac8010d0469589b02d317d07f2983199d2625a4a43</citedby><cites>FETCH-LOGICAL-c4387-2807b02315baf3bed5800c3ac8010d0469589b02d317d07f2983199d2625a4a43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3403424/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3403424/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,1411,1427,27901,27902,45550,45551,46384,46808,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22517631$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Polshakov, Vladimir I.</creatorcontrib><creatorcontrib>Eliseev, Boris D.</creatorcontrib><creatorcontrib>Birdsall, Berry</creatorcontrib><creatorcontrib>Frolova, Ludmila Yu</creatorcontrib><title>Structure and dynamics in solution of the stop codon decoding N‐terminal domain of the human polypeptide chain release factor eRF1</title><title>Protein science</title><addtitle>Protein Sci</addtitle><description>The high‐resolution NMR structure of the N‐domain of human eRF1, responsible for stop codon recognition, has been determined in solution. The overall fold of the protein is the same as that found in the crystal structure. However, the structures of several loops, including those participating in stop codon decoding, are different. Analysis of the NMR relaxation data reveals that most of the regions with the highest structural discrepancy between the solution and solid states undergo internal motions on the ps–ns and ms time scales. The NMR data show that the N‐domain of human eRF1 exists in two conformational states. The distribution of the residues having the largest chemical shift differences between the two forms indicates that helices α2 and α3, with the NIKS loop between them, can switch their orientation relative to the β‐core of the protein. Such structural plasticity may be essential for stop codon recognition by human eRF1.
PDB Code(s): 2LLX</description><subject>Codon, Terminator</subject><subject>Crystal structure</subject><subject>Eukaryotes</subject><subject>human polypeptide release factor eRF1</subject><subject>Humans</subject><subject>Models, Molecular</subject><subject>NMR</subject><subject>NMR structure and dynamics</subject><subject>Nuclear magnetic resonance</subject><subject>Nuclear Magnetic Resonance, Biomolecular</subject><subject>N‐domain</subject><subject>Peptide Termination Factors - chemistry</subject><subject>Protein Structure, Secondary</subject><subject>Protein Structure, Tertiary</subject><subject>stop codon recognition</subject><subject>termination of protein synthesis</subject><issn>0961-8368</issn><issn>1469-896X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kc9qFTEUh4Mo9loFn0ACbtxMPUlmMslGkNKqUKxUBXchN8n0pswkY5JR7s6FD-Az-iTm2nr9A64O55yPj5P8EHpI4IgA0KdzikcUeH8LrUjLZSMk_3AbrUBy0gjGxQG6l_MVALSEsrvogNKO9JyRFfr6tqTFlCU5rIPFdhv05E3GPuAcx6X4GHAccNk4nEucsYm2Tqyr1YdL_Pr7l2_FpckHPWIbJ-33-GaZdMBzHLezm4u3DpvNbp3c6HR2eNCmxITdxSm5j-4MeszuwU09RO9PT94dv2zOzl-8On5-1piWib6hAvo1UEa6tR7Y2tlOABimjQACFurDOyErYBnpLfQDlYIRKS3ltNOtbtkhenbtnZf15KxxoSQ9qjn5SaetitqrvzfBb9Rl_KRYC6ylO8GTG0GKHxeXi5p8Nm4cdXBxyYoA6UCKnvCKPv4HvYpLqt9UqZ5z0VIiyW-hSTHn5Ib9MQTULtraR7WLtqKP_jx-D_7KsgLNNfDZj277X5F6c3H-U_gDMTmvMA</recordid><startdate>201206</startdate><enddate>201206</enddate><creator>Polshakov, Vladimir I.</creator><creator>Eliseev, Boris D.</creator><creator>Birdsall, Berry</creator><creator>Frolova, Ludmila Yu</creator><general>Wiley Subscription Services, Inc., A Wiley Company</general><general>Wiley Subscription Services, Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7T5</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>201206</creationdate><title>Structure and dynamics in solution of the stop codon decoding N‐terminal domain of the human polypeptide chain release factor eRF1</title><author>Polshakov, Vladimir I. ; Eliseev, Boris D. ; Birdsall, Berry ; Frolova, Ludmila Yu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4387-2807b02315baf3bed5800c3ac8010d0469589b02d317d07f2983199d2625a4a43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Codon, Terminator</topic><topic>Crystal structure</topic><topic>Eukaryotes</topic><topic>human polypeptide release factor eRF1</topic><topic>Humans</topic><topic>Models, Molecular</topic><topic>NMR</topic><topic>NMR structure and dynamics</topic><topic>Nuclear magnetic resonance</topic><topic>Nuclear Magnetic Resonance, Biomolecular</topic><topic>N‐domain</topic><topic>Peptide Termination Factors - chemistry</topic><topic>Protein Structure, Secondary</topic><topic>Protein Structure, Tertiary</topic><topic>stop codon recognition</topic><topic>termination of protein synthesis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Polshakov, Vladimir I.</creatorcontrib><creatorcontrib>Eliseev, Boris D.</creatorcontrib><creatorcontrib>Birdsall, Berry</creatorcontrib><creatorcontrib>Frolova, Ludmila Yu</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Immunology Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Protein science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Polshakov, Vladimir I.</au><au>Eliseev, Boris D.</au><au>Birdsall, Berry</au><au>Frolova, Ludmila Yu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structure and dynamics in solution of the stop codon decoding N‐terminal domain of the human polypeptide chain release factor eRF1</atitle><jtitle>Protein science</jtitle><addtitle>Protein Sci</addtitle><date>2012-06</date><risdate>2012</risdate><volume>21</volume><issue>6</issue><spage>896</spage><epage>903</epage><pages>896-903</pages><issn>0961-8368</issn><eissn>1469-896X</eissn><coden>PRCIEI</coden><abstract>The high‐resolution NMR structure of the N‐domain of human eRF1, responsible for stop codon recognition, has been determined in solution. The overall fold of the protein is the same as that found in the crystal structure. However, the structures of several loops, including those participating in stop codon decoding, are different. Analysis of the NMR relaxation data reveals that most of the regions with the highest structural discrepancy between the solution and solid states undergo internal motions on the ps–ns and ms time scales. The NMR data show that the N‐domain of human eRF1 exists in two conformational states. The distribution of the residues having the largest chemical shift differences between the two forms indicates that helices α2 and α3, with the NIKS loop between them, can switch their orientation relative to the β‐core of the protein. Such structural plasticity may be essential for stop codon recognition by human eRF1.
PDB Code(s): 2LLX</abstract><cop>Hoboken</cop><pub>Wiley Subscription Services, Inc., A Wiley Company</pub><pmid>22517631</pmid><doi>10.1002/pro.2067</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Codon, Terminator Crystal structure Eukaryotes human polypeptide release factor eRF1 Humans Models, Molecular NMR NMR structure and dynamics Nuclear magnetic resonance Nuclear Magnetic Resonance, Biomolecular N‐domain Peptide Termination Factors - chemistry Protein Structure, Secondary Protein Structure, Tertiary stop codon recognition termination of protein synthesis |
| title | Structure and dynamics in solution of the stop codon decoding N‐terminal domain of the human polypeptide chain release factor eRF1 |
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