3a5z

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{{STRUCTURE_3a5z| PDB=3a5z | SCENE= }}
 
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===Crystal structure of Escherichia coli GenX in complex with elongation factor P===
 
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{{ABSTRACT_PUBMED_20729861}}
 
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==Function==
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==Crystal structure of Escherichia coli GenX in complex with elongation factor P==
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[[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] [[http://www.uniprot.org/uniprot/C3SGD7_ECOLX C3SGD7_ECOLX]] Involved in peptide bond synthesis. Alleviates ribosome stalling that occurs when 3 or more consecutive Pro residues or the sequence PPG is present in a protein, possibly by augmenting the peptidyl transferase activity of the ribosome. Modification of Lys-34 is required for alleviation (By similarity).[HAMAP-Rule:MF_00141]
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<StructureSection load='3a5z' size='340' side='right'caption='[[3a5z]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3a5z]] is a 8 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=3A5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A5Z FirstGlance]. <br>
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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]] 2.5&#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>
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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=3a5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a5z OCA], [https://pdbe.org/3a5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a5z RCSB], [https://www.ebi.ac.uk/pdbsum/3a5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a5z ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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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/a5/3a5z_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=3a5z 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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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.
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==About this Structure==
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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>
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[[3a5z]] is a 8 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=3A5Z OCA].
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==See Also==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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*[[Elongation factor|Elongation factor]]
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</div>
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<div class="pdbe-citations 3a5z" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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<ref group="xtra">PMID:020729861</ref><references group="xtra"/><references/>
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*[[Elongation factor 3D structures|Elongation factor 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Lysine--tRNA ligase]]
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[[Category: Large Structures]]
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[[Category: Ishii, R.]]
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[[Category: Ishii R]]
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[[Category: Sumida, T.]]
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[[Category: Sumida T]]
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[[Category: Yanagisawa, T.]]
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[[Category: Yanagisawa T]]
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[[Category: Yokoyama, S.]]
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[[Category: Yokoyama S]]
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[[Category: Aminoacyl-trna synthetase]]
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[[Category: Aminoacyl-trna synthetase paralog]]
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[[Category: Elongation factor]]
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[[Category: Ligase]]
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[[Category: Lysyl-trna synthetase]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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[[Category: Translation]]
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[[Category: Trna]]
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Current revision

Crystal structure of Escherichia coli GenX in complex with elongation factor P

PDB ID 3a5z

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