3a5y: Difference between revisions

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{{STRUCTURE_3a5y|  PDB=3a5y  |  SCENE=  }}
==Crystal structure of GenX from Escherichia coli in complex with lysyladenylate analog==
===Crystal structure of GenX from Escherichia coli in complex with lysyladenylate analog===
<StructureSection load='3a5y' size='340' side='right' caption='[[3a5y]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
{{ABSTRACT_PUBMED_20729861}}
== Structural highlights ==
<table><tr><td colspan='2'>[[3a5y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A5Y FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KAA:5-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE'>KAA</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ECs5136, GenX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3a5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a5y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a5y RCSB], [http://www.ebi.ac.uk/pdbsum/3a5y PDBsum]</span></td></tr>
</table>
== 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/a5/3a5y_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/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Aminoacyl-tRNA synthetase (aaRS) paralogs with unknown functions exist in various species. We now report novel 'protein lysylation' by an Escherichia coli lysyl-tRNA synthetase paralog, GenX/PoxA/YjeA. X-ray crystallographic analysis shows that the structure of the GenX protein resembles that of a class II aaRS. Further in vitro studies reveal that it specifically aminoacylates EF-P with lysine. The shape of the protein substrate mimics that of the L-shaped tRNA, and its lysylation site corresponds to the tRNA 3' end. Thus, we show how the aaRS architecture can be adapted to achieve aminoacylation of a specific protein. Moreover, in vivo analyses reveal that the translation elongation factor P (EF-P) lysylation by GenX is enhanced by YjeK (lysine 2,3-aminomutase paralog), which is encoded next to the EF-P gene, and might convert alpha-lysyl-EF-P to beta-lysyl-EF-P. In vivo analyses indicate that the EF-P modification by GenX and YjeK is essential for cell survival.


==Function==
A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.,Yanagisawa T, Sumida T, Ishii R, Takemoto C, Yokoyama S Nat Struct Mol Biol. 2010 Sep;17(9):1136-43. Epub 2010 Aug 22. PMID:20729861<ref>PMID:20729861</ref>
[[http://www.uniprot.org/uniprot/C3SGA2_ECOLX C3SGA2_ECOLX]] With EpmB is involved in the beta-lysylation step of the post-translational modification of translation elongation factor P (EF-P) on 'Lys-34'. Catalyzes the ATP-dependent activation of (R)-beta-lysine produced by EpmB, forming a lysyl-adenylate, from which the beta-lysyl moiety is then transferred to the epsilon-amino group of EF-P 'Lys-34' (By similarity).[HAMAP-Rule:MF_00174]


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[3a5y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A5Y OCA].
</div>
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:020729861</ref><references group="xtra"/><references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Lysine--tRNA ligase]]
[[Category: Lysine--tRNA ligase]]
[[Category: Ishii, R.]]
[[Category: Ishii, R]]
[[Category: Sumida, T.]]
[[Category: Sumida, T]]
[[Category: Yanagisawa, T.]]
[[Category: Yanagisawa, T]]
[[Category: Yokoyama, S.]]
[[Category: Yokoyama, S]]
[[Category: Aminoacyl-trna synthetase]]
[[Category: Aminoacyl-trna synthetase]]
[[Category: Aminoacyl-trna synthetase paralog]]
[[Category: Aminoacyl-trna synthetase paralog]]
Line 24: Line 43:
[[Category: National project on protein structural and functional analyse]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Nppsfa]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Structural genomic]]
[[Category: Rsgi]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Translation]]
[[Category: Translation]]
[[Category: Trna]]
[[Category: Trna]]
Retrieved from "https://proteopedia.org/3a5y"