2byt

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[[Image:2byt.gif|left|200px]]<br /><applet load="2byt" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2byt, resolution 3.30&Aring;" />
 
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'''THERMUS THERMOPHILUS LEUCYL-TRNA SYNTHETASE COMPLEXED WITH A TRNALEU TRANSCRIPT IN THE POST-EDITING CONFORMATION'''<br />
 
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==Overview==
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==Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation==
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Leucyl-tRNA synthetase (LeuRS) has a specific post-transfer editing, activity directed against mischarged isoleucine and similar noncognate, amino acids. We describe the post-transfer-editing and product complexes, of Thermus thermophilus LeuRS (LeuRSTT) with tRNA(Leu) at 2.9- to 3.3-A, resolution. In the post-transfer-editing configuration, A76 binds in the, editing active site exactly as previously found for the adenosine moiety, of a small-molecule editing-substrate analog. The 60 C-terminal residues, of LeuRSTT, unseen in previous structures, fold into a compact domain, flexibly linked to the rest of the molecule and interacting with the, G19-C56 tertiary base pair of tRNA(Leu). LeuRS recognition of tRNA(Leu), depends essentially on tRNA shape rather than base-specific interactions., The structures show that considerable domain rotations, notably of the, editing domain, accompany the tRNA-3' end dynamics associated successively, with aminoacylation, post-transfer editing and product release.
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<StructureSection load='2byt' size='340' side='right'caption='[[2byt]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2byt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BYT FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2byt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2byt OCA], [https://pdbe.org/2byt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2byt RCSB], [https://www.ebi.ac.uk/pdbsum/2byt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2byt ProSAT], [https://www.topsan.org/Proteins/RSGI/2byt TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q7SIE4_THETH Q7SIE4_THETH]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/by/2byt_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2byt ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Leucyl-tRNA synthetase (LeuRS) has a specific post-transfer editing activity directed against mischarged isoleucine and similar noncognate amino acids. We describe the post-transfer-editing and product complexes of Thermus thermophilus LeuRS (LeuRSTT) with tRNA(Leu) at 2.9- to 3.3-A resolution. In the post-transfer-editing configuration, A76 binds in the editing active site exactly as previously found for the adenosine moiety of a small-molecule editing-substrate analog. The 60 C-terminal residues of LeuRSTT, unseen in previous structures, fold into a compact domain flexibly linked to the rest of the molecule and interacting with the G19-C56 tertiary base pair of tRNA(Leu). LeuRS recognition of tRNA(Leu) depends essentially on tRNA shape rather than base-specific interactions. The structures show that considerable domain rotations, notably of the editing domain, accompany the tRNA-3' end dynamics associated successively with aminoacylation, post-transfer editing and product release.
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==About this Structure==
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The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation.,Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S Nat Struct Mol Biol. 2005 Oct;12(10):923-30. Epub 2005 Sep 11. PMID:16155583<ref>PMID:16155583</ref>
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2BYT is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=HG:'>HG</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=LEU:'>LEU</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=AC1:Hg+Binding+Site+For+Chain+D'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BYT OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation., Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S, Nat Struct Mol Biol. 2005 Oct;12(10):923-30. Epub 2005 Sep 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16155583 16155583]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 2byt" style="background-color:#fffaf0;"></div>
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[[Category: Thermus thermophilus]]
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[[Category: Cusack, S.]]
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[[Category: Fukunaga, R.]]
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[[Category: Tukalo, M.]]
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[[Category: Yaremchuk, A.]]
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[[Category: Yokoyama, S.]]
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[[Category: HG]]
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[[Category: LEU]]
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[[Category: SO4]]
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[[Category: ZN]]
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[[Category: aminoacyl-trna synthetase]]
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[[Category: atp + l-leucine + trna (leu) gives amp + ppi l-leucyl-trna(leu)]]
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[[Category: class i aminoacyl-trna synthetase]]
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[[Category: editing]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:29:29 2008''
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==See Also==
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Thermus thermophilus]]
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[[Category: Cusack S]]
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[[Category: Fukunaga R]]
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[[Category: Tukalo M]]
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[[Category: Yaremchuk A]]
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[[Category: Yokoyama S]]

Current revision

Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation

PDB ID 2byt

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