3a5y: Difference between revisions

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{{Seed}}
[[Image:3a5y.jpg|left|200px]]


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==Crystal structure of GenX from Escherichia coli in complex with lysyladenylate analog==
The line below this paragraph, containing "STRUCTURE_3a5y", creates the "Structure Box" on the page.
<StructureSection load='3a5y' size='340' side='right'caption='[[3a5y]], [[Resolution|resolution]] 1.90&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'>[[3a5y]] is a 4 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=3A5Y 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]] 1.9&#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=KAA:5-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE'>KAA</scene></td></tr>
{{STRUCTURE_3a5y|  PDB=3a5y  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3a5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a5y OCA], [https://pdbe.org/3a5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a5y RCSB], [https://www.ebi.ac.uk/pdbsum/3a5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a5y ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/EPMA_ECOLI EPMA_ECOLI] 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'. The substrate (R)-beta-lysine is 100-fold more efficient than either (S)-beta-lysine or L-alpha-lysine. Cannot ligate lysine to any tRNA.[HAMAP-Rule:MF_00174]<ref>PMID:20729861</ref> <ref>PMID:21841797</ref> <ref>PMID:22128152</ref>
== 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/main_output.php?pdb_ID=3a5y 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.


===Crystal structure of GenX from Escherichia coli in complex with lysyladenylate analog===
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>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
3A5Y is a 4 chains structure with sequences 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 class="pdbe-citations 3a5y" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Lysine--tRNA ligase]]
[[Category: Large Structures]]
[[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 paralog]]
[[Category: Ligase]]
[[Category: Lysyl-trna synthetase]]
[[Category: Lysyladenylate analog]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Translation]]
[[Category: Trna]]
 
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Retrieved from "https://proteopedia.org/3a5y"