2cyb

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[[Image:2cyb.gif|left|200px]]
 
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==Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Archaeoglobus fulgidus==
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The line below this paragraph, containing "STRUCTURE_2cyb", creates the "Structure Box" on the page.
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<StructureSection load='2cyb' size='340' side='right'caption='[[2cyb]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2cyb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CYB FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.8&#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=TYR:TYROSINE'>TYR</scene></td></tr>
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{{STRUCTURE_2cyb| PDB=2cyb | SCENE= }}
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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=2cyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cyb OCA], [https://pdbe.org/2cyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cyb RCSB], [https://www.ebi.ac.uk/pdbsum/2cyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cyb ProSAT], [https://www.topsan.org/Proteins/RSGI/2cyb TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SYY_ARCFU SYY_ARCFU] 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) (By similarity).[HAMAP-Rule:MF_02008]
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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/2cyb_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=2cyb ConSurf].
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<div style="clear:both"></div>
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'''Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Archaeoglobus fulgidus'''
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==See Also==
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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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==About this Structure==
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2CYB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYB OCA].
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/16325203 16325203]
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[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
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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: Kobayashi T]]
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[[Category: Kobayashi, T.]]
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[[Category: Kuratani M]]
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[[Category: Kuratani, M.]]
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[[Category: Sakai H]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Shirouzu M]]
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[[Category: Sakai, H.]]
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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: Yanagisawa T]]
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[[Category: Terada, T.]]
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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: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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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 genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 23:20:30 2008''
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Current revision

Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Archaeoglobus fulgidus

PDB ID 2cyb

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