7cta
From Proteopedia
(Difference between revisions)
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==Crystal structure of Cx-SAM bound CmoB from Vibrio vulnificus== | ==Crystal structure of Cx-SAM bound CmoB from Vibrio vulnificus== | ||
| - | <StructureSection load='7cta' size='340' side='right'caption='[[7cta]]' scene=''> | + | <StructureSection load='7cta' size='340' side='right'caption='[[7cta]], [[Resolution|resolution]] 2.90Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CTA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CTA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7cta]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus_MO6-24/O Vibrio vulnificus MO6-24/O]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CTA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CTA FirstGlance]. <br> |
| - | </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=7cta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cta OCA], [https://pdbe.org/7cta PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cta RCSB], [https://www.ebi.ac.uk/pdbsum/7cta PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cta ProSAT]</span></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]] 2.9Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GEK:(2S)-4-[{[(2S,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL}(CARBOXYLATOMETHYL)SULFONIO]-2-AMMONIOBUTANOATE'>GEK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7cta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cta OCA], [https://pdbe.org/7cta PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cta RCSB], [https://www.ebi.ac.uk/pdbsum/7cta PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cta ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/CMOB_VIBVU CMOB_VIBVU] Catalyzes carboxymethyl transfer from carboxy-S-adenosyl-L-methionine (Cx-SAM) to 5-hydroxyuridine (ho5U) to form 5-carboxymethoxyuridine (cmo5U) at position 34 in tRNAs.[HAMAP-Rule:MF_01590] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | CmoB utilizes carboxy-S-adenosyl-l-methionine (CxSAM) to carry out unusual carboxymethyl transfer to form 5-carboxymethoxyuridine (cmo(5)U) of several tRNA species in Gram-negative bacteria. In this report, we present three X-ray crystal structures of CmoB from Vibrio vulnificus representing different states in the course of the reaction pathway; i.e., apo-, substrate-bound, and product-bound forms. Especially, the crystal structure of apo-CmoB unveils a novel open state of the enzyme, capturing unprecedented conformational dynamics around the substrate-binding site. The apo-structure demonstrates that the open conformation favors the release of CxSAM thus representing an inactive form. Our crystal structures of CmoB complexed with CxSAM and S-adenosyl-l-homocysteine (SAH) and combined binding assay results support the proposed mechanism underlying the cofactor selectivity, where CmoB preferentially senses negative charge around amino acid residues Lys-91, Tyr-200, and Arg-315. | ||
| + | |||
| + | Structural snapshots of CmoB in various states during wobble uridine modification of tRNA.,Jeong S, Kim J Biochem Biophys Res Commun. 2021 Jan 1;534:604-609. doi:, 10.1016/j.bbrc.2020.11.033. Epub 2020 Nov 17. PMID:33213836<ref>PMID:33213836</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7cta" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Vibrio vulnificus MO6-24/O]] | ||
[[Category: Jeong S]] | [[Category: Jeong S]] | ||
[[Category: Kim J]] | [[Category: Kim J]] | ||
Current revision
Crystal structure of Cx-SAM bound CmoB from Vibrio vulnificus
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