4obw

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==crystal structure of yeast Coq5 in the SAM bound form==
==crystal structure of yeast Coq5 in the SAM bound form==
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<StructureSection load='4obw' size='340' side='right' caption='[[4obw]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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<StructureSection load='4obw' size='340' side='right'caption='[[4obw]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4obw]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OBW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OBW FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4obw]] 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=4OBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OBW FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4obx|4obx]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-methoxy-6-polyprenyl-1,4-benzoquinol_methylase 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.201 2.1.1.201] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4obw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4obw OCA], [https://pdbe.org/4obw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4obw RCSB], [https://www.ebi.ac.uk/pdbsum/4obw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4obw ProSAT]</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=4obw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4obw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4obw RCSB], [http://www.ebi.ac.uk/pdbsum/4obw PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://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).
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[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).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase]]
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[[Category: Large Structures]]
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[[Category: Cao, D D]]
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[[Category: Saccharomyces cerevisiae S288C]]
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[[Category: Chen, Y X]]
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[[Category: Cao DD]]
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[[Category: Chi, C B]]
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[[Category: Chen YX]]
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[[Category: Dai, Y N]]
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[[Category: Chi CB]]
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[[Category: Jiang, Y L]]
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[[Category: Dai YN]]
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[[Category: Meng, F]]
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[[Category: Jiang YL]]
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[[Category: Ren, Y M]]
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[[Category: Meng F]]
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[[Category: Zhou, C Z]]
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[[Category: Ren YM]]
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[[Category: Zhou, K]]
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[[Category: Zhou CZ]]
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[[Category: Methyltransferase]]
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[[Category: Zhou K]]
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[[Category: Rossmann fold]]
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[[Category: Transferase]]
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Current revision

crystal structure of yeast Coq5 in the SAM bound form

PDB ID 4obw

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