4obx: Difference between revisions

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'''Unreleased structure'''


The entry 4obx is ON HOLD  until Paper Publication
==Crystal structure of yeast Coq5 in the apo form==
<StructureSection load='4obx' size='340' side='right'caption='[[4obx]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4obx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OBX FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</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=4obx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4obx OCA], [https://pdbe.org/4obx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4obx RCSB], [https://www.ebi.ac.uk/pdbsum/4obx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4obx ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/COQ5_YEAST COQ5_YEAST] Methyltransferase required for the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Saccharomyces cerevisiae Coq5 is an S-adenosyl methionine (SAM)-dependent methyltransferase (SAM-MTase) that catalyzes the only C-methylation step in the coenzyme Q (CoQ) biosynthesis pathway, in which 2-methoxy-6-polyprenyl-1,4-benzoquinone (DDMQH2) is converted to 2-methoxy-5-methyl-6-polyprenyl-1,4-benzoquinone (DMQH2). Crystal structures of Coq5 were determined in the apo form (Coq5-apo) at 2.2 A resolution and in the SAM-bound form (Coq5-SAM) at 2.4 A resolution, representing the first pair of structures for the yeast CoQ biosynthetic enzymes. Coq5 displays a typical class I SAM-MTase structure with two minor variations beyond the core domain, both of which are considered to participate in dimerization and/or substrate recognition. Slight conformational changes at the active-site pocket were observed upon binding of SAM. Structure-based computational simulation using an analogue of DDMQH2 enabled us to identify the binding pocket and entrance tunnel of the substrate. Multiple-sequence alignment showed that the residues contributing to the dimeric interface and the SAM- and DDMQH2-binding sites are highly conserved in Coq5 and homologues from diverse species. A putative catalytic mechanism of Coq5 was proposed in which Arg201 acts as a general base to initiate catalysis with the help of a water molecule.


Authors: Dai, Y.N., Zhou, K., Cao, D.D., Jiang, Y.L., Meng, F., Chi, C.B., Ren, Y.M., Chen, Y.X., Zhou, C.Z.
Crystal structures and catalytic mechanism of the C-methyltransferase Coq5 provide insights into a key step of the yeast coenzyme Q synthesis pathway.,Dai YN, Zhou K, Cao DD, Jiang YL, Meng F, Chi CB, Ren YM, Chen Y, Zhou CZ Acta Crystallogr D Biol Crystallogr. 2014 Aug 1;70(Pt 8):2085-92. doi:, 10.1107/S1399004714011559. Epub 2014 Jul 25. PMID:25084328<ref>PMID:25084328</ref>


Description: Crystal structure of yeast Coq5 in the apo form
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4obx" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Cao DD]]
[[Category: Chen YX]]
[[Category: Chi CB]]
[[Category: Dai YN]]
[[Category: Jiang YL]]
[[Category: Meng F]]
[[Category: Ren YM]]
[[Category: Zhou CZ]]
[[Category: Zhou K]]
Retrieved from "https://proteopedia.org/4obx"