4obw - Revision history

OCA at 12:38, 1 March 2024

2024-03-01T12:38:59Z

←Older revision		Revision as of 12:38, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<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>		<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>
-	</td></tr><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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.4Å</td></tr>
		+	<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>
	<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>		<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>
	</table>		</table>
	== Function ==		== 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).		[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.
-
-	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>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4obw" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:16, 25 January 2023

2023-01-25T07:16:02Z

←Older revision		Revision as of 07:16, 25 January 2023
Line 3:		Line 3:
	<StructureSection load='4obw' size='340' side='right'caption='[[4obw]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4obw' size='340' side='right'caption='[[4obw]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4obw]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. 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>	+	<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>
-	</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>~~	+	</td></tr><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>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4obx\|4obx]]</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=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>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">COQ5, DBI56, YML110C, YM8339.09C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>	+
-	<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>	+
-	<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~~://pdbe.org/4obw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4obw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4obw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4obw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[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).	+	[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase]]
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cao~~, D D~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Chen~~, Y X~~]]	+	[[Category: Cao DD]]
-	[[Category: Chi~~, C B~~]]	+	[[Category: Chen YX]]
-	[[Category: Dai~~, Y N~~]]	+	[[Category: Chi CB]]
-	[[Category: Jiang~~, Y L~~]]	+	[[Category: Dai YN]]
-	[[Category: Meng, F]]	+	[[Category: Jiang YL]]
-	[[Category: Ren~~, Y M~~]]	+	[[Category: Meng F]]
-	[[Category: Zhou~~, C Z~~]]	+	[[Category: Ren YM]]
-	[[Category: Zhou, K]]	+	[[Category: Zhou CZ]]
-	~~[[Category: Methyltransferase]]~~	+	[[Category: Zhou K]]
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:42, 10 April 2019

2019-04-10T08:42:33Z

←Older revision		Revision as of 08:42, 10 April 2019
Line 1:		Line 1:

	==crystal structure of yeast Coq5 in the SAM bound form==		==crystal structure of yeast Coq5 in the SAM bound form==
-	<StructureSection load='4obw' size='340' side='right' caption='[[4obw]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4obw' size='340' side='right'caption='[[4obw]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<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>	+	<table><tr><td colspan='2'>[[4obw]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. 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>
	</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>		</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>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4obx\|4obx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4obx\|4obx]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">COQ5, DBI56, YML110C, YM8339.09C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<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>		<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>
	<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://pdbe.org/4obw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4obw RCSB], [http://www.ebi.ac.uk/pdbsum/4obw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4obw ProSAT]</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=4obw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4obw OCA], [http://pdbe.org/4obw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4obw RCSB], [http://www.ebi.ac.uk/pdbsum/4obw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4obw ProSAT]</span></td></tr>
Line 25:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase]]		[[Category: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase]]
		+	[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Cao, D D]]		[[Category: Cao, D D]]
	[[Category: Chen, Y X]]		[[Category: Chen, Y X]]

OCA at 04:39, 5 August 2016

2016-08-05T04:39:25Z

←Older revision		Revision as of 04:39, 5 August 2016
Line 1:		Line 1:
		+
	==crystal structure of yeast Coq5 in the SAM bound form==		==crystal structure of yeast Coq5 in the SAM bound form==
	<StructureSection load='4obw' size='340' side='right' caption='[[4obw]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4obw' size='340' side='right' caption='[[4obw]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4obx\|4obx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4obx\|4obx]]</td></tr>
	<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>		<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>
-	<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>	+	<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://pdbe.org/4obw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4obw RCSB], [http://www.ebi.ac.uk/pdbsum/4obw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4obw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4obw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:51, 25 December 2014

2014-12-25T15:51:52Z

←Older revision		Revision as of 15:51, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<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>		<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>
-	</td></tr><tr><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><br>	+	</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>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4obx\|4obx]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4obx\|4obx]]</td></tr>
-	<tr><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>	+	<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>
-	<tr><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>	+	<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>
-	<table>	+	</table>
		+	== Function ==
		+	[[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).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase]]		[[Category: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase]]
-	[[Category: Cao, D D.]]	+	[[Category: Cao, D D]]
-	[[Category: Chen, Y X.]]	+	[[Category: Chen, Y X]]
-	[[Category: Chi, C B.]]	+	[[Category: Chi, C B]]
-	[[Category: Dai, Y N.]]	+	[[Category: Dai, Y N]]
-	[[Category: Jiang, Y L.]]	+	[[Category: Jiang, Y L]]
-	[[Category: Meng, F.]]	+	[[Category: Meng, F]]
-	[[Category: Ren, Y M.]]	+	[[Category: Ren, Y M]]
-	[[Category: Zhou, C Z.]]	+	[[Category: Zhou, C Z]]
-	[[Category: Zhou, K.]]	+	[[Category: Zhou, K]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 07:21, 10 September 2014

2014-09-10T07:21:04Z

←Older revision		Revision as of 07:21, 10 September 2014
Line 8:		Line 8:
	<tr><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>		<tr><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>
	<table>		<table>
		+	<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.
		+
		+	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>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 02:43, 7 August 2014

2014-08-07T02:43:07Z

←Older revision		Revision as of 02:43, 7 August 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==crystal structure of yeast Coq5 in the SAM bound form==
-		+	<StructureSection load='4obw' size='340' side='right' caption='[[4obw]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~The entry~~ 4obw is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<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>
-	~~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.	+	</td></tr><tr><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><br>
-		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4obx\|4obx]]</td></tr>
-	~~Description~~: ~~crystal structure of yeast Coq5 in the SAM bound form~~	+	<tr><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>
		+	<tr><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>
		+	<table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase]]
		+	[[Category: Cao, D D.]]
		+	[[Category: Chen, Y X.]]
		+	[[Category: Chi, C B.]]
		+	[[Category: Dai, Y N.]]
		+	[[Category: Jiang, Y L.]]
		+	[[Category: Meng, F.]]
		+	[[Category: Ren, Y M.]]
		+	[[Category: Zhou, C Z.]]
		+	[[Category: Zhou, K.]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Rossmann fold]]
		+	[[Category: Transferase]]

OCA at 07:06, 29 January 2014

2014-01-29T07:06:16Z

←Older revision		Revision as of 07:06, 29 January 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4obw is ON HOLD	+	The entry 4obw is ON HOLD until Paper Publication

	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.		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.

	Description: crystal structure of yeast Coq5 in the SAM bound form		Description: crystal structure of yeast Coq5 in the SAM bound form

OCA: Protected "4obw" [edit=sysop:move=sysop]

2014-01-15T07:45:43Z

Protected "4obw" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:45, 15 January 2014

OCA: New page: '''Unreleased structure''' The entry 4obw is ON HOLD 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. Description: crystal s...

2014-01-15T07:45:42Z

New page: '''Unreleased structure''' The entry 4obw is ON HOLD 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. Description: crystal s...

New page

'''Unreleased structure'''

The entry 4obw is ON HOLD

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.

Description: crystal structure of yeast Coq5 in the SAM bound form