4qii - Revision history

OCA at 15:06, 8 November 2023

OCA — Wed, 08 Nov 2023 15:06:33 GMT

←Older revision		Revision as of 15:06, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qii]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QII FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qii]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QII FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2NE:SALICYLYL+COA'>2NE</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.64Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2NE:SALICYLYL+COA'>2NE</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=4qii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qii OCA], [https://pdbe.org/4qii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qii RCSB], [https://www.ebi.ac.uk/pdbsum/4qii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qii 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=4qii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qii OCA], [https://pdbe.org/4qii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qii RCSB], [https://www.ebi.ac.uk/pdbsum/4qii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qii ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:31, 15 February 2023

OCA — Wed, 15 Feb 2023 11:31:23 GMT

←Older revision		Revision as of 11:31, 15 February 2023
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	<StructureSection load='4qii' size='340' side='right'caption='[[4qii]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='4qii' size='340' side='right'caption='[[4qii]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qii]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QII OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QII FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qii]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QII FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2NE:SALICYLYL+COA'>2NE</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2NE:SALICYLYL+COA'>2NE</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qij\|4qij]]</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=4qii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qii OCA], [https://pdbe.org/4qii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qii RCSB], [https://www.ebi.ac.uk/pdbsum/4qii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qii ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,4-dihydroxy-2-naphthoyl-CoA_synthase 1,4-dihydroxy-2-naphthoyl-CoA synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </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=4qii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qii OCA], [~~http~~://pdbe.org/4qii PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qii RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qii PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qii ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MENB_MYCTU MENB_MYCTU]] Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).<ref>PMID:12909628</ref>	+	[https://www.uniprot.org/uniprot/MENB_MYCTU MENB_MYCTU] Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).<ref>PMID:12909628</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 1,4-dihydroxy-2-naphthoyl-CoA synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Guo~~, Z H~~]]	+	[[Category: Guo ZH]]
-	[[Category: Song~~, H G~~]]	+	[[Category: Song HG]]
-	[[Category: Sung~~, H P~~]]	+	[[Category: Sung HP]]
-	[[Category: Tse~~, Y S]]~~	+	[[Category: Tse YS]]
-	~~[[Category: 4-dihydroxy-2-naphthoyl-coenzyme some]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Synthase~~]]	+

OCA at 08:39, 24 April 2019

OCA — Wed, 24 Apr 2019 08:39:55 GMT

←Older revision		Revision as of 08:39, 24 April 2019
Line 1:		Line 1:

	==Crystal Structure of type II MenB from Mycobacteria tuberculosis==		==Crystal Structure of type II MenB from Mycobacteria tuberculosis==
-	<StructureSection load='4qii' size='340' side='right' caption='[[4qii]], [[Resolution\|resolution]] 1.64Å' scene=''>	+	<StructureSection load='4qii' size='340' side='right'caption='[[4qii]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qii]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QII OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QII FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qii]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QII OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QII FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2NE:SALICYLYL+COA'>2NE</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2NE:SALICYLYL+COA'>2NE</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qij\|4qij]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qij\|4qij]]</td></tr>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: 1,4-dihydroxy-2-naphthoyl-CoA synthase]]		[[Category: 1,4-dihydroxy-2-naphthoyl-CoA synthase]]
		+	[[Category: Large Structures]]
		+	[[Category: Myctu]]
	[[Category: Guo, Z H]]		[[Category: Guo, Z H]]
	[[Category: Song, H G]]		[[Category: Song, H G]]

OCA at 02:39, 5 August 2016

OCA — Fri, 05 Aug 2016 02:39:48 GMT

←Older revision		Revision as of 02:39, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of type II MenB from Mycobacteria tuberculosis==		==Crystal Structure of type II MenB from Mycobacteria tuberculosis==
	<StructureSection load='4qii' size='340' side='right' caption='[[4qii]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='4qii' size='340' side='right' caption='[[4qii]], [[Resolution\|resolution]] 1.64Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qij\|4qij]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qij\|4qij]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,4-dihydroxy-2-naphthoyl-CoA_synthase 1,4-dihydroxy-2-naphthoyl-CoA synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,4-dihydroxy-2-naphthoyl-CoA_synthase 1,4-dihydroxy-2-naphthoyl-CoA synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </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=4qii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qii OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qii RCSB], [http://www.ebi.ac.uk/pdbsum/4qii 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=4qii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qii OCA], [http://pdbe.org/4qii PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qii RCSB], [http://www.ebi.ac.uk/pdbsum/4qii PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qii 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 4qii" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:06, 24 December 2014

OCA — Wed, 24 Dec 2014 22:06:06 GMT

←Older revision		Revision as of 22:06, 24 December 2014
Line 8:		Line 8:
	<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=4qii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qii OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qii RCSB], [http://www.ebi.ac.uk/pdbsum/4qii 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=4qii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qii OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qii RCSB], [http://www.ebi.ac.uk/pdbsum/4qii PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MENB_MYCTU MENB_MYCTU]] Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).<ref>PMID:12909628</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 12:43, 19 November 2014

OCA — Wed, 19 Nov 2014 12:43:55 GMT

←Older revision		Revision as of 12:43, 19 November 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal Structure of type II MenB from Mycobacteria tuberculosis==
		+	<StructureSection load='4qii' size='340' side='right' caption='[[4qii]], [[Resolution\|resolution]] 1.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4qii]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QII OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QII FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2NE:SALICYLYL+COA'>2NE</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qij\|4qij]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,4-dihydroxy-2-naphthoyl-CoA_synthase 1,4-dihydroxy-2-naphthoyl-CoA synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </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=4qii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qii OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qii RCSB], [http://www.ebi.ac.uk/pdbsum/4qii PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	1,4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase catalyzes an essential intramolecular Claisen condensation in menaquinone biosynthesis and is an important target for the development of new antibiotics. This enzyme in Mycobacterium tuberculosis is cofactor-free and is classified as a type II DHNA-CoA synthase, differing from type I enzymes, which rely on exogenous bicarbonate for catalysis. Its crystal structures in complex with product analogues have been determined at high resolution to reveal ligand-dependent structural changes, which include the ordering of a 27-residue active-site loop (amino acids 107-133) and the reorientation of the carboxy-terminal helix (amino acids 289-301) that forms part of the active site from the opposing subunit across the trimer-trimer interface. These structural changes result in closure of the active site to the bulk solution, which is likely to take place through an induced-fit mechanism, similar to that observed for type I DHNA-CoA synthases. These findings demonstrate that the ligand-dependent conformational changes are a conserved feature of all DHNA-CoA synthases, providing new insights into the catalytic mechanism of this essential tubercular enzyme.

-	~~The entry 4qii is ON HOLD until Paper Publication~~	+	Ligand-dependent active-site closure revealed in the crystal structure of Mycobacterium tuberculosis MenB complexed with product analogues.,Song H, Sung HP, Tse YS, Jiang M, Guo Z Acta Crystallogr D Biol Crystallogr. 2014 Nov;70(Pt 11):2959-69. doi:, 10.1107/S1399004714019440. Epub 2014 Oct 23. PMID:25372686<ref>PMID:25372686</ref>

-	~~Authors: Song~~, H.G., ~~Tse~~, ~~Y.S.~~, Sung, H.P~~., Guo~~, ~~Z.H.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal Structure of type II MenB from Mycobacteria tuberculosis~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 1,4-dihydroxy-2-naphthoyl-CoA synthase]]
		+	[[Category: Guo, Z H]]
		+	[[Category: Song, H G]]
		+	[[Category: Sung, H P]]
		+	[[Category: Tse, Y S]]
		+	[[Category: 4-dihydroxy-2-naphthoyl-coenzyme some]]
		+	[[Category: Lyase]]
		+	[[Category: Synthase]]

OCA at 06:37, 18 June 2014

OCA — Wed, 18 Jun 2014 06:37:20 GMT

←Older revision		Revision as of 06:37, 18 June 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: ~~SONG~~ H.G., ~~TSE~~ Y.S., ~~SUNG~~ H.P., ~~GUO~~ Z.H.	+	Authors: Song, H.G., Tse, Y.S., Sung, H.P., Guo, Z.H.

	Description: Crystal Structure of type II MenB from Mycobacteria tuberculosis		Description: Crystal Structure of type II MenB from Mycobacteria tuberculosis

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

OCA — Wed, 11 Jun 2014 08:06:55 GMT

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

←Older revision

Revision as of 08:06, 11 June 2014

OCA: New page: '''Unreleased structure''' The entry 4qii is ON HOLD Authors: SONG H.G., TSE Y.S., SUNG H.P., GUO Z.H. Description: Crystal Structure of type II MenB from Mycobacteria tuberculosis

OCA — Wed, 11 Jun 2014 08:06:53 GMT

New page: '''Unreleased structure''' The entry 4qii is ON HOLD Authors: SONG H.G., TSE Y.S., SUNG H.P., GUO Z.H. Description: Crystal Structure of type II MenB from Mycobacteria tuberculosis

New page

'''Unreleased structure'''

The entry 4qii is ON HOLD

Authors: SONG H.G., TSE Y.S., SUNG H.P., GUO Z.H.

Description: Crystal Structure of type II MenB from Mycobacteria tuberculosis