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| | ==Crystal structure of Escherichia coli GenX in complex with elongation factor P== | | ==Crystal structure of Escherichia coli GenX in complex with elongation factor P== |
| - | <StructureSection load='3a5z' size='340' side='right' caption='[[3a5z]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='3a5z' size='340' side='right'caption='[[3a5z]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3a5z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A5Z FirstGlance]. <br> | + | <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> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a5y|3a5y]]</td></tr>
| + | <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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">genX, ECs5136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), efp, ECs5128 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=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> |
| - | <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>
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| - | <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=3a5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a5z OCA], [http://pdbe.org/3a5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a5z RCSB], [http://www.ebi.ac.uk/pdbsum/3a5z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3a5z ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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] | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a5/3a5z_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a5/3a5z_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | ==See Also== | | ==See Also== |
| - | *[[Elongation factor|Elongation factor]] | + | *[[Elongation factor 3D structures|Elongation factor 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[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: Elongation factor]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Lysyl-trna synthetase]]
| + | |
| - | [[Category: National project on protein structural and functional analyse]]
| + | |
| - | [[Category: Nppsfa]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Translation]]
| + | |
| - | [[Category: Trna]]
| + | |
| Structural highlights
Function
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][1] [2] [3]
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
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.
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[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yanagisawa T, Sumida T, Ishii R, Takemoto C, Yokoyama S. A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P. Nat Struct Mol Biol. 2010 Sep;17(9):1136-43. Epub 2010 Aug 22. PMID:20729861 doi:10.1038/nsmb.1889
- ↑ Roy H, Zou SB, Bullwinkle TJ, Wolfe BS, Gilreath MS, Forsyth CJ, Navarre WW, Ibba M. The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-β-lysine. Nat Chem Biol. 2011 Aug 14;7(10):667-9. PMID:21841797 doi:10.1038/nchembio.632
- ↑ Park JH, Johansson HE, Aoki H, Huang BX, Kim HY, Ganoza MC, Park MH. Post-translational modification by β-lysylation is required for activity of Escherichia coli elongation factor P (EF-P). J Biol Chem. 2012 Jan 20;287(4):2579-90. PMID:22128152 doi:10.1074/jbc.M111.309633
- ↑ Yanagisawa T, Sumida T, Ishii R, Takemoto C, Yokoyama S. A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P. Nat Struct Mol Biol. 2010 Sep;17(9):1136-43. Epub 2010 Aug 22. PMID:20729861 doi:10.1038/nsmb.1889
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