1gax

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(New page: 200px<br /> <applet load="1gax" size="450" color="white" frame="true" align="right" spinBox="true" caption="1gax, resolution 2.9&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:1gax.gif|left|200px]]<br />
 
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<applet load="1gax" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1gax, resolution 2.9&Aring;" />
 
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'''CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE==
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Valyl-tRNA synthetase (ValRS) strictly discriminates the cognate L-valine, from the larger L-isoleucine and the isosteric L-threonine by the, tRNA-dependent "double sieve" mechanism. In this study, we determined the, 2.9 A crystal structure of a complex of Thermus thermophilus ValRS, tRNA(Val), and an analog of the Val-adenylate intermediate. The analog is, bound in a pocket, where Pro(41) allows accommodation of the Val and Thr, moieties but precludes the Ile moiety (the first sieve), on the, aminoacylation domain. The editing domain, which hydrolyzes incorrectly, synthesized Thr-tRNA(Val), is bound to the 3' adenosine of tRNA(Val). A, contiguous pocket was found to accommodate the Thr moiety, but not the Val, moiety (the second sieve). Furthermore, another Thr binding pocket for, Thr-adenylate hydrolysis was suggested on the editing domain.
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<StructureSection load='1gax' size='340' side='right'caption='[[1gax]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1gax]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GAX 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]] 2.9&#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=VAA:N-[VALINYL]-N-[ADENOSYL]-DIAMINOSUFONE'>VAA</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=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [https://pdbe.org/1gax PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB], [https://www.ebi.ac.uk/pdbsum/1gax PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gax ProSAT], [https://www.topsan.org/Proteins/RSGI/1gax TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SYV_THETH SYV_THETH] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]
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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/ga/1gax_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1gax 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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Valyl-tRNA synthetase (ValRS) strictly discriminates the cognate L-valine from the larger L-isoleucine and the isosteric L-threonine by the tRNA-dependent "double sieve" mechanism. In this study, we determined the 2.9 A crystal structure of a complex of Thermus thermophilus ValRS, tRNA(Val), and an analog of the Val-adenylate intermediate. The analog is bound in a pocket, where Pro(41) allows accommodation of the Val and Thr moieties but precludes the Ile moiety (the first sieve), on the aminoacylation domain. The editing domain, which hydrolyzes incorrectly synthesized Thr-tRNA(Val), is bound to the 3' adenosine of tRNA(Val). A contiguous pocket was found to accommodate the Thr moiety, but not the Val moiety (the second sieve). Furthermore, another Thr binding pocket for Thr-adenylate hydrolysis was suggested on the editing domain.
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==About this Structure==
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Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase.,Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S Cell. 2000 Nov 22;103(5):793-803. PMID:11114335<ref>PMID:11114335</ref>
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1GAX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with ZN and VAA as [http://en.wikipedia.org/wiki/ligands ligands]. The following page contains interesting information on the relation of 1GAX with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb16_1.html Aminoacyl-tRNA Synthetases]]. Active as [http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1GAX 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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Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase., Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S, Cell. 2000 Nov 22;103(5):793-803. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11114335 11114335]
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</div>
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<div class="pdbe-citations 1gax" style="background-color:#fffaf0;"></div>
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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>
[[Category: Aminoacyl-tRNA Synthetases]]
[[Category: Aminoacyl-tRNA Synthetases]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: RCSB PDB Molecule of the Month]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
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[[Category: Valine--tRNA ligase]]
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[[Category: Fukai S]]
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[[Category: Fukai, S.]]
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[[Category: Nureki O]]
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[[Category: Nureki, O.]]
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[[Category: Sekine S]]
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[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
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[[Category: Shimada A]]
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[[Category: Sekine, S.]]
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[[Category: Tao J]]
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[[Category: Shimada, A.]]
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[[Category: Vassylyev DG]]
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[[Category: Tao, J.]]
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[[Category: Yokoyama S]]
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[[Category: Vassylyev, D.G.]]
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[[Category: Yokoyama, S.]]
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[[Category: VAA]]
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[[Category: ZN]]
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[[Category: coiled coil]]
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[[Category: protein-rna complex]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rossmann fold]]
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[[Category: rsgi]]
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[[Category: structural genomics]]
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[[Category: trna]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:00:40 2007''
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Current revision

CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE

PDB ID 1gax

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