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GTPase activation of elongation factor EF-Tu by the ribosome during decoding
We have used single‐particle reconstruction in cryo‐electron microscopy to determine a structure of the Thermus thermophilus ribosome in which the ternary complex of elongation factor Tu (EF‐Tu), tRNA and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. This repre...
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| Published in: | The EMBO journal 2009-03, Vol.28 (6), p.755-765 |
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| creator | Schuette, Jan-Christian Murphy IV, Frank V Kelley, Ann C Weir, John R Giesebrecht, Jan Connell, Sean R Loerke, Justus Mielke, Thorsten Zhang, Wei Penczek, Pawel A Ramakrishnan, V Spahn, Christian M T |
| description | We have used single‐particle reconstruction in cryo‐electron microscopy to determine a structure of the
Thermus thermophilus
ribosome in which the ternary complex of elongation factor Tu (EF‐Tu), tRNA and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. This represents the state in the decoding process just after codon recognition by tRNA and the resulting GTP hydrolysis by EF‐Tu, but before the release of EF‐Tu from the ribosome. Progress in sample purification and image processing made it possible to reach a resolution of 6.4 Å. Secondary structure elements in tRNA, EF‐Tu and the ribosome, and even GDP and kirromycin, could all be visualized directly. The structure reveals a complex conformational rearrangement of the tRNA in the A/T state and the interactions with the functionally important switch regions of EF‐Tu crucial to GTP hydrolysis. Thus, the structure provides insights into the molecular mechanism of signalling codon recognition from the decoding centre of the 30S subunit to the GTPase centre of EF‐Tu. |
| doi_str_mv | 10.1038/emboj.2009.26 |
| format | article |
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Thermus thermophilus
ribosome in which the ternary complex of elongation factor Tu (EF‐Tu), tRNA and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. This represents the state in the decoding process just after codon recognition by tRNA and the resulting GTP hydrolysis by EF‐Tu, but before the release of EF‐Tu from the ribosome. Progress in sample purification and image processing made it possible to reach a resolution of 6.4 Å. Secondary structure elements in tRNA, EF‐Tu and the ribosome, and even GDP and kirromycin, could all be visualized directly. The structure reveals a complex conformational rearrangement of the tRNA in the A/T state and the interactions with the functionally important switch regions of EF‐Tu crucial to GTP hydrolysis. Thus, the structure provides insights into the molecular mechanism of signalling codon recognition from the decoding centre of the 30S subunit to the GTPase centre of EF‐Tu.</description><identifier>ISSN: 0261-4189</identifier><identifier>EISSN: 1460-2075</identifier><identifier>DOI: 10.1038/emboj.2009.26</identifier><identifier>PMID: 19229291</identifier><identifier>CODEN: EMJODG</identifier><language>eng</language><publisher>Chichester, UK: John Wiley & Sons, Ltd</publisher><subject>Cellular biology ; cryo-electron microscopy ; Cryoelectron Microscopy ; Electron microscopy ; elongation factor ; EMBO31 ; EMBO40 ; Enzyme Activation ; GTPase ; Guanosine Diphosphate - chemistry ; Hydrolysis ; Models, Molecular ; Molecular biology ; Peptide Elongation Factor Tu - chemistry ; Peptide Elongation Factor Tu - metabolism ; Peptide Elongation Factor Tu - ultrastructure ; Protein Structure, Secondary ; Proteins ; Pyridones - chemistry ; Ribonucleic acid ; ribosome ; Ribosomes - chemistry ; Ribosomes - enzymology ; Ribosomes - ultrastructure ; RNA ; RNA, Transfer - chemistry ; RNA, Transfer - ultrastructure ; Signal transduction ; Static Electricity ; Thermus thermophilus - enzymology ; translation</subject><ispartof>The EMBO journal, 2009-03, Vol.28 (6), p.755-765</ispartof><rights>European Molecular Biology Organization 2009</rights><rights>Copyright © 2009 European Molecular Biology Organization</rights><rights>Copyright Nature Publishing Group Mar 18, 2009</rights><rights>Copyright © 2009, European Molecular Biology Organization 2009</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c6276-8da817b9663fb3729435a5a5ebc74478e0d64202428876b23c3162f60693ac0f3</citedby><cites>FETCH-LOGICAL-c6276-8da817b9663fb3729435a5a5ebc74478e0d64202428876b23c3162f60693ac0f3</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/PMC2666022/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666022/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19229291$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Schuette, Jan-Christian</creatorcontrib><creatorcontrib>Murphy IV, Frank V</creatorcontrib><creatorcontrib>Kelley, Ann C</creatorcontrib><creatorcontrib>Weir, John R</creatorcontrib><creatorcontrib>Giesebrecht, Jan</creatorcontrib><creatorcontrib>Connell, Sean R</creatorcontrib><creatorcontrib>Loerke, Justus</creatorcontrib><creatorcontrib>Mielke, Thorsten</creatorcontrib><creatorcontrib>Zhang, Wei</creatorcontrib><creatorcontrib>Penczek, Pawel A</creatorcontrib><creatorcontrib>Ramakrishnan, V</creatorcontrib><creatorcontrib>Spahn, Christian M T</creatorcontrib><title>GTPase activation of elongation factor EF-Tu by the ribosome during decoding</title><title>The EMBO journal</title><addtitle>EMBO J</addtitle><addtitle>EMBO J</addtitle><description>We have used single‐particle reconstruction in cryo‐electron microscopy to determine a structure of the
Thermus thermophilus
ribosome in which the ternary complex of elongation factor Tu (EF‐Tu), tRNA and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. This represents the state in the decoding process just after codon recognition by tRNA and the resulting GTP hydrolysis by EF‐Tu, but before the release of EF‐Tu from the ribosome. Progress in sample purification and image processing made it possible to reach a resolution of 6.4 Å. Secondary structure elements in tRNA, EF‐Tu and the ribosome, and even GDP and kirromycin, could all be visualized directly. The structure reveals a complex conformational rearrangement of the tRNA in the A/T state and the interactions with the functionally important switch regions of EF‐Tu crucial to GTP hydrolysis. Thus, the structure provides insights into the molecular mechanism of signalling codon recognition from the decoding centre of the 30S subunit to the GTPase centre of EF‐Tu.</description><subject>Cellular biology</subject><subject>cryo-electron microscopy</subject><subject>Cryoelectron Microscopy</subject><subject>Electron microscopy</subject><subject>elongation factor</subject><subject>EMBO31</subject><subject>EMBO40</subject><subject>Enzyme Activation</subject><subject>GTPase</subject><subject>Guanosine Diphosphate - chemistry</subject><subject>Hydrolysis</subject><subject>Models, Molecular</subject><subject>Molecular biology</subject><subject>Peptide Elongation Factor Tu - chemistry</subject><subject>Peptide Elongation Factor Tu - metabolism</subject><subject>Peptide Elongation Factor Tu - ultrastructure</subject><subject>Protein Structure, Secondary</subject><subject>Proteins</subject><subject>Pyridones - chemistry</subject><subject>Ribonucleic acid</subject><subject>ribosome</subject><subject>Ribosomes - chemistry</subject><subject>Ribosomes - enzymology</subject><subject>Ribosomes - ultrastructure</subject><subject>RNA</subject><subject>RNA, Transfer - chemistry</subject><subject>RNA, Transfer - ultrastructure</subject><subject>Signal transduction</subject><subject>Static Electricity</subject><subject>Thermus thermophilus - enzymology</subject><subject>translation</subject><issn>0261-4189</issn><issn>1460-2075</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><recordid>eNp9kd1v0zAUxS0EYt3gkVcUeOAtxR-JP16QxtQWpgJDKhrixXKSm84ljYudbPS_x22qMpBAfvC17s_H5_og9IzgMcFMvoZ14VZjirEaU_4AjUjGcUqxyB-iEaacpBmR6gSdhrDCGOdSkMfohChKFVVkhOazxZUJkJiys7ems65NXJ1A49rlcKpjx_lkMk0XfVJsk-4GEm8LF9wakqr3tl0mFZSuisUT9Kg2TYCnh_0MfZlOFhfv0vmn2fuL83lacip4KisjiSgU56wumKAqY7mJC4pSZJmQgCueUUwzKqXgBWUlI5zWHHPFTIlrdobeDLqbvlhDVULbedPojbdr47faGav_7LT2Ri_draacc0xpFHh1EPDuRw-h02sbSmga04Lrg-YC51jmKoIv_wJXrvdtHE4TlVMejbEIpQNUeheCh_rohGC9C0nvQ9K7kKKFyD-_b_83fUglAvkA3NkGtv9X05MPby939V54PNwLm10u4O-5_YeTF8OF1nS9h-NLe-ooepjOhg5-HhHjv8dvYiLX1x9nmn-9vL76NpX6M_sF6BrH1A</recordid><startdate>20090318</startdate><enddate>20090318</enddate><creator>Schuette, Jan-Christian</creator><creator>Murphy IV, Frank V</creator><creator>Kelley, Ann C</creator><creator>Weir, John R</creator><creator>Giesebrecht, Jan</creator><creator>Connell, Sean R</creator><creator>Loerke, Justus</creator><creator>Mielke, Thorsten</creator><creator>Zhang, Wei</creator><creator>Penczek, Pawel A</creator><creator>Ramakrishnan, V</creator><creator>Spahn, Christian M T</creator><general>John Wiley & Sons, Ltd</general><general>Nature Publishing Group UK</general><general>Blackwell Publishing Ltd</general><general>Nature Publishing Group</general><scope>BSCLL</scope><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>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M7N</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PCBAR</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20090318</creationdate><title>GTPase activation of elongation factor EF-Tu by the ribosome during decoding</title><author>Schuette, Jan-Christian ; Murphy IV, Frank V ; Kelley, Ann C ; Weir, John R ; Giesebrecht, Jan ; Connell, Sean R ; Loerke, Justus ; Mielke, Thorsten ; Zhang, Wei ; Penczek, Pawel A ; Ramakrishnan, V ; Spahn, Christian M T</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c6276-8da817b9663fb3729435a5a5ebc74478e0d64202428876b23c3162f60693ac0f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Cellular biology</topic><topic>cryo-electron microscopy</topic><topic>Cryoelectron Microscopy</topic><topic>Electron microscopy</topic><topic>elongation factor</topic><topic>EMBO31</topic><topic>EMBO40</topic><topic>Enzyme Activation</topic><topic>GTPase</topic><topic>Guanosine Diphosphate - chemistry</topic><topic>Hydrolysis</topic><topic>Models, Molecular</topic><topic>Molecular biology</topic><topic>Peptide Elongation Factor Tu - chemistry</topic><topic>Peptide Elongation Factor Tu - metabolism</topic><topic>Peptide Elongation Factor Tu - ultrastructure</topic><topic>Protein Structure, Secondary</topic><topic>Proteins</topic><topic>Pyridones - chemistry</topic><topic>Ribonucleic acid</topic><topic>ribosome</topic><topic>Ribosomes - chemistry</topic><topic>Ribosomes - enzymology</topic><topic>Ribosomes - ultrastructure</topic><topic>RNA</topic><topic>RNA, Transfer - chemistry</topic><topic>RNA, Transfer - ultrastructure</topic><topic>Signal transduction</topic><topic>Static Electricity</topic><topic>Thermus thermophilus - enzymology</topic><topic>translation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Schuette, Jan-Christian</creatorcontrib><creatorcontrib>Murphy IV, Frank V</creatorcontrib><creatorcontrib>Kelley, Ann C</creatorcontrib><creatorcontrib>Weir, John R</creatorcontrib><creatorcontrib>Giesebrecht, Jan</creatorcontrib><creatorcontrib>Connell, Sean R</creatorcontrib><creatorcontrib>Loerke, Justus</creatorcontrib><creatorcontrib>Mielke, Thorsten</creatorcontrib><creatorcontrib>Zhang, Wei</creatorcontrib><creatorcontrib>Penczek, Pawel A</creatorcontrib><creatorcontrib>Ramakrishnan, V</creatorcontrib><creatorcontrib>Spahn, Christian M T</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Immunology Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection (Proquest)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database (Proquest)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection (Proquest) (PQ_SDU_P3)</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>ProQuest Biological Science Journals</collection><collection>Research Library (Corporate)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The EMBO journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Schuette, Jan-Christian</au><au>Murphy IV, Frank V</au><au>Kelley, Ann C</au><au>Weir, John R</au><au>Giesebrecht, Jan</au><au>Connell, Sean R</au><au>Loerke, Justus</au><au>Mielke, Thorsten</au><au>Zhang, Wei</au><au>Penczek, Pawel A</au><au>Ramakrishnan, V</au><au>Spahn, Christian M T</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>GTPase activation of elongation factor EF-Tu by the ribosome during decoding</atitle><jtitle>The EMBO journal</jtitle><stitle>EMBO J</stitle><addtitle>EMBO J</addtitle><date>2009-03-18</date><risdate>2009</risdate><volume>28</volume><issue>6</issue><spage>755</spage><epage>765</epage><pages>755-765</pages><issn>0261-4189</issn><eissn>1460-2075</eissn><coden>EMJODG</coden><abstract>We have used single‐particle reconstruction in cryo‐electron microscopy to determine a structure of the
Thermus thermophilus
ribosome in which the ternary complex of elongation factor Tu (EF‐Tu), tRNA and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. This represents the state in the decoding process just after codon recognition by tRNA and the resulting GTP hydrolysis by EF‐Tu, but before the release of EF‐Tu from the ribosome. Progress in sample purification and image processing made it possible to reach a resolution of 6.4 Å. Secondary structure elements in tRNA, EF‐Tu and the ribosome, and even GDP and kirromycin, could all be visualized directly. The structure reveals a complex conformational rearrangement of the tRNA in the A/T state and the interactions with the functionally important switch regions of EF‐Tu crucial to GTP hydrolysis. Thus, the structure provides insights into the molecular mechanism of signalling codon recognition from the decoding centre of the 30S subunit to the GTPase centre of EF‐Tu.</abstract><cop>Chichester, UK</cop><pub>John Wiley & Sons, Ltd</pub><pmid>19229291</pmid><doi>10.1038/emboj.2009.26</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | The EMBO journal, 2009-03, Vol.28 (6), p.755-765 |
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| subjects | Cellular biology cryo-electron microscopy Cryoelectron Microscopy Electron microscopy elongation factor EMBO31 EMBO40 Enzyme Activation GTPase Guanosine Diphosphate - chemistry Hydrolysis Models, Molecular Molecular biology Peptide Elongation Factor Tu - chemistry Peptide Elongation Factor Tu - metabolism Peptide Elongation Factor Tu - ultrastructure Protein Structure, Secondary Proteins Pyridones - chemistry Ribonucleic acid ribosome Ribosomes - chemistry Ribosomes - enzymology Ribosomes - ultrastructure RNA RNA, Transfer - chemistry RNA, Transfer - ultrastructure Signal transduction Static Electricity Thermus thermophilus - enzymology translation |
| title | GTPase activation of elongation factor EF-Tu by the ribosome during decoding |
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