3a5z

From Proteopedia

(Difference between revisions)

Revision as of 16:18, 22 December 2021

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

Structural highlights

3a5z is a 8 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3a5y
Gene:	genX, ECs5136 ("Bacillus coli" Migula 1895), efp, ECs5128 ("Bacillus coli" Migula 1895)
Activity:	Lysine--tRNA ligase, with EC number 6.1.1.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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] [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]

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^[1]

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

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3a5z"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Escherichia coli GenX in complex with elongation factor P==
-<StructureSection load='3a5z' size='340' side='right' caption='[[3a5z]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='3a5z' size='340' side='right'caption='[[3a5z]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == 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/"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 [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='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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a5y|3a5y]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a5y|3a5y]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">genX, ECs5136 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), efp, ECs5128 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysine--tRNA_ligase Lysine--tRNA ligase], with EC number [https://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=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>
+<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>
 </table>
 == 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/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] [[https://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]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 ==See Also==
-*[[Elongation factor|Elongation factor]]
+*[[Elongation factor 3D structures|Elongation factor 3D structures]]
 == References ==
 <references/>
@@ Line 39: / Line 39: @@
 </StructureSection>
 [[Category: Bacillus coli migula 1895]]
+[[Category: Large Structures]]
 [[Category: Lysine--tRNA ligase]]
 [[Category: Ishii, R]]

3a5z

From Proteopedia

Revision as of 16:18, 22 December 2021

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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