1irx

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[[Image:1irx.gif|left|200px]]
 
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{{Structure
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==Crystal structure of class I lysyl-tRNA synthetase==
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|PDB= 1irx |SIZE=350|CAPTION= <scene name='initialview01'>1irx</scene>, resolution 2.6&Aring;
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<StructureSection load='1irx' size='340' side='right'caption='[[1irx]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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<table><tr><td colspan='2'>[[1irx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IRX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IRX FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysine--tRNA_ligase Lysine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.6 6.1.1.6] </span>
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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]] 2.6&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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|DOMAIN=
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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=1irx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1irx OCA], [https://pdbe.org/1irx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1irx RCSB], [https://www.ebi.ac.uk/pdbsum/1irx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1irx ProSAT], [https://www.topsan.org/Proteins/RSGI/1irx TOPSAN]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1irx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1irx OCA], [http://www.ebi.ac.uk/pdbsum/1irx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1irx RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/SYK_PYRHO SYK_PYRHO]
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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/ir/1irx_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=1irx 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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Lysyl-tRNA can be synthesized by both a class I (LysRS-I) and a class II (LysRS-II) lysyl-tRNA synthetase. The crystal structure of LysRS-I from Pyrococcus horikoshii at 2.6 A resolution reveals extensive similarity with glutamyl-tRNA synthetase (GluRS). A comparison of the structures of LysRS-I and LysRS-II in complex with lysine shows that both enzymes use similar strategies for substrate recognition within unrelated active site topologies. A docking model based upon the GluRS-tRNA complex suggests how LysRS-I and LysRS-II can recognize the same molecular determinants in tRNALys, as shown by biochemical results, while approaching the acceptor helix of the tRNA from opposite sides.
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'''Crystal structure of class I lysyl-tRNA synthetase'''
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Functional convergence of two lysyl-tRNA synthetases with unrelated topologies.,Terada T, Nureki O, Ishitani R, Ambrogelly A, Ibba M, Soll D, Yokoyama S Nat Struct Biol. 2002 Apr;9(4):257-62. PMID:11887185<ref>PMID:11887185</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1irx" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Lysyl-tRNA can be synthesized by both a class I (LysRS-I) and a class II (LysRS-II) lysyl-tRNA synthetase. The crystal structure of LysRS-I from Pyrococcus horikoshii at 2.6 A resolution reveals extensive similarity with glutamyl-tRNA synthetase (GluRS). A comparison of the structures of LysRS-I and LysRS-II in complex with lysine shows that both enzymes use similar strategies for substrate recognition within unrelated active site topologies. A docking model based upon the GluRS-tRNA complex suggests how LysRS-I and LysRS-II can recognize the same molecular determinants in tRNALys, as shown by biochemical results, while approaching the acceptor helix of the tRNA from opposite sides.
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1IRX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IRX OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Functional convergence of two lysyl-tRNA synthetases with unrelated topologies., Terada T, Nureki O, Ishitani R, Ambrogelly A, Ibba M, Soll D, Yokoyama S, Nat Struct Biol. 2002 Apr;9(4):257-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11887185 11887185]
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[[Category: Lysine--tRNA ligase]]
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[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
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[[Category: Single protein]]
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[[Category: Ambrogelly A]]
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[[Category: Ambrogelly, A.]]
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[[Category: Ibba M]]
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[[Category: Ibba, M.]]
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[[Category: Ishitani R]]
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[[Category: Ishitani, R.]]
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[[Category: Nureki O]]
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[[Category: Nureki, O.]]
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[[Category: Soll D]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Terada T]]
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[[Category: Soll, D.]]
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[[Category: Yokoyama S]]
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[[Category: Terada, T.]]
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[[Category: Yokoyama, S.]]
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[[Category: alpha-helix cage]]
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[[Category: beta sandwitch]]
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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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[[Category: zinc-binding structure]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:23:47 2008''
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Current revision

Crystal structure of class I lysyl-tRNA synthetase

PDB ID 1irx

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