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2cya

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(New page: 200px<br /><applet load="2cya" size="450" color="white" frame="true" align="right" spinBox="true" caption="2cya, resolution 2.20&Aring;" /> '''Crystal structure of...)
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[[Image:2cya.gif|left|200px]]<br /><applet load="2cya" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2cya, resolution 2.20&Aring;" />
 
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'''Crystal structure of tyrosyl-tRNA synthetase from Aeropyrum pernix'''<br />
 
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==Overview==
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==Crystal structure of tyrosyl-tRNA synthetase from Aeropyrum pernix==
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Tyrosyl-tRNA synthetase (TyrRS) catalyzes the tyrosylation of tRNA(Tyr) in, a two-step reaction. TyrRS has the "HIGH" and "KMSKS" motifs, which play, essential roles in the formation of the tyrosyl-adenylate from tyrosine, and ATP. Here, we determined the crystal structures of Archaeoglobus, fulgidus and Pyrococcus horikoshii TyrRSs in the l-tyrosine-bound form at, 1.8A and 2.2A resolutions, respectively, and that of Aeropyrum pernix, TyrRS in the substrate-free form at 2.2 A. The conformation of the KMSKS, motif differs among the three TyrRSs. In the A.pernix TyrRS, the KMSKS, loop conformation corresponds to the ATP-bound "closed" form. In contrast, the KMSKS loop of the P.horikoshii TyrRS forms a novel 3(10) helix, which, appears to correspond to the "semi-closed" form. This conformation, enlarges the entrance to the tyrosine-binding pocket, which facilitates, the pyrophosphate ion release after the tyrosyl-adenylate formation, and, probably is involved in the initial tRNA binding. The KMSSS loop of the, A.fulgidus TyrRS is somewhat farther from the active site and is, stabilized by hydrogen bonds. Based on the three structures, possible, structural changes of the KMSKS motif during the tyrosine activation, reaction are discussed. We suggest that the insertion sequence just before, the KMSKS motif, which exists in some archaeal species, enhances the, binding affinity of the TyrRS for its cognate tRNA. In addition, a, non-proline cis peptide bond, which is involved in the tRNA binding, is, conserved among the archaeal TyrRSs.
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<StructureSection load='2cya' size='340' side='right'caption='[[2cya]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2cya]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CYA 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]] 2.2&#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=SO4:SULFATE+ION'>SO4</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=2cya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cya OCA], [https://pdbe.org/2cya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cya RCSB], [https://www.ebi.ac.uk/pdbsum/2cya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cya ProSAT], [https://www.topsan.org/Proteins/RSGI/2cya TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SYY_AERPE SYY_AERPE] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).[HAMAP-Rule:MF_02009]
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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/cy/2cya_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=2cya ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2CYA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2CYA OCA].
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structures of tyrosyl-tRNA synthetases from Archaea., Kuratani M, Sakai H, Takahashi M, Yanagisawa T, Kobayashi T, Murayama K, Chen L, Liu ZJ, Wang BC, Kuroishi C, Kuramitsu S, Terada T, Bessho Y, Shirouzu M, Sekine S, Yokoyama S, J Mol Biol. 2006 Jan 20;355(3):395-408. Epub 2005 Nov 14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16325203 16325203]
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[[Category: Aeropyrum pernix]]
[[Category: Aeropyrum pernix]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Tyrosine--tRNA ligase]]
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[[Category: Bessho Y]]
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[[Category: Bessho, Y.]]
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[[Category: Chen L]]
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[[Category: Chen, L.]]
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[[Category: Kobayashi T]]
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[[Category: Kobayashi, T.]]
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[[Category: Kuramitsu S]]
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[[Category: Kuramitsu, S.]]
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[[Category: Kuratani M]]
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[[Category: Kuratani, M.]]
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[[Category: Kuroishi C]]
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[[Category: Kuroishi, C.]]
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[[Category: Liu ZJ]]
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[[Category: Liu, Z.J.]]
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[[Category: Murayama K]]
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[[Category: Murayama, K.]]
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[[Category: Sakai H]]
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[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
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[[Category: Sekine SI]]
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[[Category: Sakai, H.]]
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[[Category: Shirouzu M]]
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[[Category: Sekine, S.I.]]
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[[Category: Takahashi M]]
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[[Category: Shirouzu, M.]]
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[[Category: Terada T]]
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[[Category: Takahashi, M.]]
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[[Category: Wang BC]]
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[[Category: Terada, T.]]
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[[Category: Yanagisawa T]]
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[[Category: Wang, B.C.]]
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[[Category: Yokoyama S]]
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[[Category: Yanagisawa, T.]]
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[[Category: Yokoyama, S.]]
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[[Category: SO4]]
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[[Category: aminoacylation]]
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[[Category: national project on protein structural and functional analyses]]
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[[Category: nppsfa]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rsgi]]
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[[Category: structural genomics]]
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[[Category: tyrrs]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:20:28 2007''
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Current revision

Crystal structure of tyrosyl-tRNA synthetase from Aeropyrum pernix

PDB ID 2cya

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