4pdn
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4pdn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_KTE5 Escherichia coli KTE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PDN FirstGlance]. <br> | <table><tr><td colspan='2'>[[4pdn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_KTE5 Escherichia coli KTE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PDN FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.448Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=4pdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pdn OCA], [https://pdbe.org/4pdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pdn RCSB], [https://www.ebi.ac.uk/pdbsum/4pdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pdn 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=4pdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pdn OCA], [https://pdbe.org/4pdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pdn RCSB], [https://www.ebi.ac.uk/pdbsum/4pdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pdn ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/A0A0J9X1Z5_ECOLX A0A0J9X1Z5_ECOLX] | [https://www.uniprot.org/uniprot/A0A0J9X1Z5_ECOLX A0A0J9X1Z5_ECOLX] | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | EF-P is a bacterial tRNA-mimic protein, which accelerates the ribosome-catalyzed polymerization of poly-prolines. In Escherichia coli, EF-P is post-translationally modified on a conserved lysine residue. The post-translational modification is performed in a two-step reaction involving the addition of a beta-lysine moiety and the subsequent hydroxylation, catalyzed by PoxA and YfcM, respectively. The beta-lysine moiety was previously shown to enhance the rate of poly-proline synthesis, but the role of the hydroxylation is poorly understood. We solved the crystal structure of YfcM and performed functional analyses to determine the hydroxylation mechanism. In addition, YfcM appears to be structurally distinct from any other hydroxylase structures reported so far. The structure of YfcM is similar to that of the ribonuclease YbeY, even though they do not share sequence homology. Furthermore, YfcM has a metal ion-coordinating motif, similar to YbeY. The metal ion-coordinating motif of YfcM resembles a 2-His-1-carboxylate motif, which coordinates an Fe(II) ion and forms the catalytic site of non-heme iron enzymes. Our findings showed that the metal ion-coordinating motif of YfcM plays an essential role in the hydroxylation of the beta-lysylated lysine residue of EF-P. Taken together, our results suggested the potential catalytic mechanism of hydroxylation by YfcM. | ||
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| - | The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation.,Kobayashi K, Katz A, Rajkovic A, Ishii R, Branson OE, Freitas MA, Ishitani R, Ibba M, Nureki O Nucleic Acids Res. 2014 Oct 29;42(19):12295-305. doi: 10.1093/nar/gku898. Epub, 2014 Oct 1. PMID:25274739<ref>PMID:25274739</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4pdn" style="background-color:#fffaf0;"></div> | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
Crystal structure of E. coli YfcM
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