1gax
From Proteopedia
(Difference between revisions)
| (12 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:1gax.png|left|200px]] | ||
| - | + | ==CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE== | |
| + | <StructureSection load='1gax' size='340' side='right'caption='[[1gax]], [[Resolution|resolution]] 2.90Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <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> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></tr> | ||
| + | <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> | ||
| + | <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> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [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] | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ga/1gax_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </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]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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. | ||
| - | + | 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> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 1gax" style="background-color:#fffaf0;"></div> | |
| - | + | ||
==See Also== | ==See Also== | ||
| - | *[[Aminoacyl tRNA | + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] |
| - | *[[ | + | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] |
| - | + | == References == | |
| - | == | + | <references/> |
| - | < | + | __TOC__ |
| + | </StructureSection> | ||
[[Category: Aminoacyl-tRNA Synthetases]] | [[Category: Aminoacyl-tRNA Synthetases]] | ||
| + | [[Category: Large Structures]] | ||
[[Category: RCSB PDB Molecule of the Month]] | [[Category: RCSB PDB Molecule of the Month]] | ||
[[Category: Thermus thermophilus]] | [[Category: Thermus thermophilus]] | ||
| - | + | [[Category: Fukai S]] | |
| - | [[Category: Fukai | + | [[Category: Nureki O]] |
| - | [[Category: Nureki | + | [[Category: Sekine S]] |
| - | + | [[Category: Shimada A]] | |
| - | [[Category: Sekine | + | [[Category: Tao J]] |
| - | [[Category: Shimada | + | [[Category: Vassylyev DG]] |
| - | [[Category: Tao | + | [[Category: Yokoyama S]] |
| - | [[Category: Vassylyev | + | |
| - | [[Category: Yokoyama | + | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE
| |||||||||||
