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New page: left|200px<br /><applet load="1irx" size="450" color="white" frame="true" align="right" spinBox="true" caption="1irx, resolution 2.6Å" /> '''Crystal structure of ...
 
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[[Image:1irx.gif|left|200px]]<br /><applet load="1irx" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1irx, resolution 2.6&Aring;" />
'''Crystal structure of class I lysyl-tRNA synthetase'''<br />


==Overview==
==Crystal structure of class I lysyl-tRNA synthetase==
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.
<StructureSection load='1irx' size='340' side='right'caption='[[1irx]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SYK_PYRHO SYK_PYRHO]
== 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/ir/1irx_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1irx ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==About this Structure==
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>
1IRX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1IRX OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=11887185 11887185]
</div>
[[Category: Lysine--tRNA ligase]]
<div class="pdbe-citations 1irx" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
[[Category: Single protein]]
[[Category: Ambrogelly A]]
[[Category: Ambrogelly, A.]]
[[Category: Ibba M]]
[[Category: Ibba, M.]]
[[Category: Ishitani R]]
[[Category: Ishitani, R.]]
[[Category: Nureki O]]
[[Category: Nureki, O.]]
[[Category: Soll D]]
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
[[Category: Terada T]]
[[Category: Soll, D.]]
[[Category: Yokoyama S]]
[[Category: Terada, T.]]
[[Category: Yokoyama, S.]]
[[Category: ZN]]
[[Category: alpha-helix cage]]
[[Category: beta sandwitch]]
[[Category: riken structural genomics/proteomics initiative]]
[[Category: rossmann fold]]
[[Category: rsgi]]
[[Category: structural genomics]]
[[Category: zinc-binding structure]]
 
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