1irx: Difference between revisions

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{{Seed}}
[[Image:1irx.png|left|200px]]


<!--
==Crystal structure of class I lysyl-tRNA synthetase==
The line below this paragraph, containing "STRUCTURE_1irx", creates the "Structure Box" on the page.
<StructureSection load='1irx' size='340' side='right'caption='[[1irx]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
{{STRUCTURE_1irx|  PDB=1irx  |  SCENE=  }}
<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.


===Crystal structure of class I lysyl-tRNA synthetase===
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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1irx" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_11887185}}, adds the Publication Abstract to the page
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 11887185 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_11887185}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
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].
 
==Reference==
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]
[[Category: Lysine--tRNA ligase]]
[[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: Alpha-helix cage]]
[[Category: Beta sandwitch]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rossmann fold]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Zinc-binding structure]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 13:53:43 2008''

Latest revision as of 02:35, 28 December 2023

Crystal structure of class I lysyl-tRNA synthetaseCrystal structure of class I lysyl-tRNA synthetase

Structural highlights

1irx is a 2 chain structure with sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

SYK_PYRHO

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Terada T, Nureki O, Ishitani R, Ambrogelly A, Ibba M, Soll D, Yokoyama S. Functional convergence of two lysyl-tRNA synthetases with unrelated topologies. Nat Struct Biol. 2002 Apr;9(4):257-62. PMID:11887185 doi:10.1038/nsb777

1irx, resolution 2.60Å

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OCA
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