6eeu - Revision history

OCA at 14:41, 13 March 2024

OCA — Wed, 13 Mar 2024 14:41:04 GMT

←Older revision		Revision as of 14:41, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6eeu' size='340' side='right'caption='[[6eeu]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='6eeu' size='340' side='right'caption='[[6eeu]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6eeu]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"pseudomonas_desmolytica"_gray_and_thornton_1928 "pseudomonas desmolytica" gray and thornton 1928~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EEU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6EEU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6eeu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Delftia_acidovorans Delftia acidovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EEU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EEU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.93Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>Daci_0287 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~80866~~ "~~Pseudomonas desmolytica~~" ~~Gray and Thornton 1928])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Hydroxymethylglutaryl-CoA_reductase Hydroxymethylglutaryl-CoA reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.88 1.1.1.88]~~ </~~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=6eeu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eeu OCA], [https://pdbe.org/6eeu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6eeu RCSB], [https://www.ebi.ac.uk/pdbsum/6eeu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6eeu 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=6eeu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eeu OCA], [~~http~~://pdbe.org/6eeu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6eeu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6eeu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6eeu ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A9BQX8_DELAS A9BQX8_DELAS]
-	The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR) catalyzes the first committed step of the mevalonate pathway, which is used across biology in the biosynthesis of countless metabolites. HMGR consumes 2 equiv of the cofactor NAD(P)H to perform the four-electron reduction of HMG-CoA to mevalonate toward the production of steroids and isoprenoids, the largest class of natural products. Recent structural data have shown that HMGR contains a highly mobile C-terminal domain (CTD) that is believed to adopt many different conformations to permit binding and dissociation of the substrate, cofactors, and products at specific points during the reaction cycle. Here, we have characterized the HMGR from Delftia acidovorans as an NADH-specific enzyme and determined crystal structures of the enzyme in unbound, mevalonate-bound, and NADH- and citrate-bound states. Together, these structures depict ligand binding in both the active site and the cofactor-binding site while illustrating how a conserved helical motif confers NAD(P)H cofactor specificity. Unexpectedly, the NADH-bound structure also reveals a new conformation of the CTD, in which the domain has "flipped" upside-down, while directly binding the cofactor. By capturing these structural snapshots, this work not only expands the known range of HMGR domain movement but also provides valuable insight into the catalytic mechanism of this biologically important enzyme.	+
-		+
-	~~New Crystallographic Snapshots of Large Domain Movements in Bacterial 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase.,Ragwan ER, Arai E, Kung Y Biochemistry. 2018 Sep 19. doi~~: ~~10.1021~~/~~acs.biochem.8b00869. PMID:30199631<ref>PMID:30199631<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6eeu" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[HMG-CoA Reductase 3D structures\|HMG-CoA Reductase 3D structures]]		*[[HMG-CoA Reductase 3D structures\|HMG-CoA Reductase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pseudomonas desmolytica gray and thornton 1928]]~~	+	[[Category: Delftia acidovorans]]
-	~~[[Category: Hydroxymethylglutaryl-CoA reductase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arai, E]]	+	[[Category: Arai E]]
-	[[Category: Kung, Y]]	+	[[Category: Kung Y]]
-	[[Category: Ragwan~~, E R]]~~	+	[[Category: Ragwan ER]]
-	~~[[Category: Mevalonate pathway]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:15, 1 January 2020

OCA — Wed, 01 Jan 2020 11:15:29 GMT

←Older revision		Revision as of 11:15, 1 January 2020
Line 1:		Line 1:

	==Structure of class II HMG-CoA reductase from Delftia acidovorans==		==Structure of class II HMG-CoA reductase from Delftia acidovorans==
-	<StructureSection load='6eeu' size='340' side='right' caption='[[6eeu]], [[Resolution\|resolution]] 1.93Å' scene=''>	+	<StructureSection load='6eeu' size='340' side='right'caption='[[6eeu]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6eeu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_desmolytica"_gray_and_thornton_1928 "pseudomonas desmolytica" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EEU FirstGlance]. <br>		<table><tr><td colspan='2'>[[6eeu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_desmolytica"_gray_and_thornton_1928 "pseudomonas desmolytica" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EEU FirstGlance]. <br>
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 6eeu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6eeu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[HMG-CoA Reductase 3D structures\|HMG-CoA Reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	[[Category: Pseudomonas desmolytica gray and thornton 1928]]		[[Category: Pseudomonas desmolytica gray and thornton 1928]]
	[[Category: Hydroxymethylglutaryl-CoA reductase]]		[[Category: Hydroxymethylglutaryl-CoA reductase]]
		+	[[Category: Large Structures]]
	[[Category: Arai, E]]		[[Category: Arai, E]]
	[[Category: Kung, Y]]		[[Category: Kung, Y]]

OCA at 08:49, 3 October 2018

OCA — Wed, 03 Oct 2018 08:49:15 GMT

←Older revision		Revision as of 08:49, 3 October 2018
Line 3:		Line 3:
	<StructureSection load='6eeu' size='340' side='right' caption='[[6eeu]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='6eeu' size='340' side='right' caption='[[6eeu]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6eeu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EEU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6eeu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_desmolytica"_gray_and_thornton_1928 "pseudomonas desmolytica" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EEU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Daci_0287 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=80866 "Pseudomonas desmolytica" Gray and Thornton 1928])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxymethylglutaryl-CoA_reductase Hydroxymethylglutaryl-CoA reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.88 1.1.1.88] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxymethylglutaryl-CoA_reductase Hydroxymethylglutaryl-CoA reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.88 1.1.1.88] </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=6eeu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eeu OCA], [http://pdbe.org/6eeu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eeu RCSB], [http://www.ebi.ac.uk/pdbsum/6eeu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eeu 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=6eeu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eeu OCA], [http://pdbe.org/6eeu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eeu RCSB], [http://www.ebi.ac.uk/pdbsum/6eeu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eeu ProSAT]</span></td></tr>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pseudomonas desmolytica gray and thornton 1928]]
	[[Category: Hydroxymethylglutaryl-CoA reductase]]		[[Category: Hydroxymethylglutaryl-CoA reductase]]
	[[Category: Arai, E]]		[[Category: Arai, E]]

OCA at 08:09, 26 September 2018

OCA — Wed, 26 Sep 2018 08:09:03 GMT

←Older revision		Revision as of 08:09, 26 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6eeu is ~~ON HOLD until Paper~~ Publication	+	==Structure of class II HMG-CoA reductase from Delftia acidovorans==
		+	<StructureSection load='6eeu' size='340' side='right' caption='[[6eeu]], [[Resolution\|resolution]] 1.93Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6eeu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EEU FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxymethylglutaryl-CoA_reductase Hydroxymethylglutaryl-CoA reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.88 1.1.1.88] </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=6eeu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eeu OCA], [http://pdbe.org/6eeu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eeu RCSB], [http://www.ebi.ac.uk/pdbsum/6eeu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eeu ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR) catalyzes the first committed step of the mevalonate pathway, which is used across biology in the biosynthesis of countless metabolites. HMGR consumes 2 equiv of the cofactor NAD(P)H to perform the four-electron reduction of HMG-CoA to mevalonate toward the production of steroids and isoprenoids, the largest class of natural products. Recent structural data have shown that HMGR contains a highly mobile C-terminal domain (CTD) that is believed to adopt many different conformations to permit binding and dissociation of the substrate, cofactors, and products at specific points during the reaction cycle. Here, we have characterized the HMGR from Delftia acidovorans as an NADH-specific enzyme and determined crystal structures of the enzyme in unbound, mevalonate-bound, and NADH- and citrate-bound states. Together, these structures depict ligand binding in both the active site and the cofactor-binding site while illustrating how a conserved helical motif confers NAD(P)H cofactor specificity. Unexpectedly, the NADH-bound structure also reveals a new conformation of the CTD, in which the domain has "flipped" upside-down, while directly binding the cofactor. By capturing these structural snapshots, this work not only expands the known range of HMGR domain movement but also provides valuable insight into the catalytic mechanism of this biologically important enzyme.

-	~~Authors~~:	+	New Crystallographic Snapshots of Large Domain Movements in Bacterial 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase.,Ragwan ER, Arai E, Kung Y Biochemistry. 2018 Sep 19. doi: 10.1021/acs.biochem.8b00869. PMID:30199631<ref>PMID:30199631</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6eeu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hydroxymethylglutaryl-CoA reductase]]
		+	[[Category: Arai, E]]
		+	[[Category: Kung, Y]]
		+	[[Category: Ragwan, E R]]
		+	[[Category: Mevalonate pathway]]
		+	[[Category: Oxidoreductase]]

OCA at 08:41, 5 September 2018

OCA — Wed, 05 Sep 2018 08:41:43 GMT

←Older revision		Revision as of 08:41, 5 September 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6eeu is ON HOLD	+	The entry 6eeu is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6eeu" [edit=sysop:move=sysop]

OCA — Wed, 22 Aug 2018 04:46:35 GMT

Protected "6eeu" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:46, 22 August 2018

OCA: New page: '''Unreleased structure''' The entry 6eeu is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 Aug 2018 04:46:34 GMT

New page: '''Unreleased structure''' The entry 6eeu is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6eeu is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]