6zzq - Revision history

OCA at 12:00, 1 February 2024

2024-02-01T12:00:59Z

←Older revision		Revision as of 12:00, 1 February 2024
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	<StructureSection load='6zzq' size='340' side='right'caption='[[6zzq]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='6zzq' size='340' side='right'caption='[[6zzq]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6zzq]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aciba Aciba~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZZQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ZZQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zzq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZZQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZZQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AAE:ACETOACETIC+ACID'>AAE</scene>~~, ~~<scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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">~~A7M79_09600, BGC29_06470 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=470 ACIBA])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAE:ACETOACETIC+ACID'>AAE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6zzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zzq OCA], [~~http~~://pdbe.org/6zzq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6zzq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6zzq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6zzq 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=6zzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zzq OCA], [https://pdbe.org/6zzq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zzq RCSB], [https://www.ebi.ac.uk/pdbsum/6zzq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zzq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1E3M3N6_ACIBA A0A1E3M3N6_ACIBA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aciba~~]]	+	[[Category: Acinetobacter baumannii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gloster~~, T M~~]]	+	[[Category: Gloster TM]]
-	[[Category: Machado~~, T F.G~~]]	+	[[Category: Machado TFG]]
-	[[Category: McMahon~~, S A~~]]	+	[[Category: McMahon SA]]
-	[[Category: Oehler, V]]	+	[[Category: Oehler V]]
-	[[Category: Silva~~, R G.da]]~~	+	[[Category: Da Silva RG]]
-	~~[[Category: Mesophilic enzyme]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Short-chain dehydrogenase/reductase~~]]	+

OCA at 08:27, 20 January 2021

2021-01-20T08:27:37Z

←Older revision		Revision as of 08:27, 20 January 2021
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	==Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Acinetobacter baumannii complexed with NAD+ and acetoacetate==		==Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Acinetobacter baumannii complexed with NAD+ and acetoacetate==
-	<StructureSection load='6zzq' size='340' side='right'caption='[[6zzq]]' scene=''>	+	<StructureSection load='6zzq' size='340' side='right'caption='[[6zzq]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZZQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZZQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zzq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciba Aciba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZZQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZZQ FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zzq OCA], [http://pdbe.org/6zzq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zzq RCSB], [http://www.ebi.ac.uk/pdbsum/6zzq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zzq ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAE:ACETOACETIC+ACID'>AAE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">A7M79_09600, BGC29_06470 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zzq OCA], [http://pdbe.org/6zzq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zzq RCSB], [http://www.ebi.ac.uk/pdbsum/6zzq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zzq ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The enzyme (R)-3-hydroxybutyrate dehydrogenase (HBDH) catalyzes the enantioselective reduction of 3-oxocarboxylates to (R)-3-hydroxycarboxylates, the monomeric precursors of biodegradable polyesters. Despite its application in asymmetric reduction, which prompted several engineering attempts of this enzyme, the order of chemical events in the active site, their contributions to limit the reaction rate, and interactions between the enzyme and non-native 3-oxocarboxylates have not been explored. Here, a combination of kinetic isotope effects, protein crystallography, and quantum mechanics/molecular mechanics (QM/MM) calculations were employed to dissect the HBDH mechanism. Initial velocity patterns and primary deuterium kinetic isotope effects establish a steady-state ordered kinetic mechanism for acetoacetate reduction by a psychrophilic and a mesophilic HBDH, where hydride transfer is not rate limiting. Primary deuterium kinetic isotope effects on the reduction of 3-oxovalerate indicate that hydride transfer becomes more rate limiting with this non-native substrate. Solvent and multiple deuterium kinetic isotope effects suggest hydride and proton transfers occur in the same transition state. Crystal structures were solved for both enzymes complexed to NAD(+):acetoacetate and NAD(+):3-oxovalerate, illustrating the structural basis for the stereochemistry of the 3-hydroxycarboxylate products. QM/MM calculations using the crystal structures as a starting point predicted a higher activation energy for 3-oxovalerate reduction catalyzed by the mesophilic HBDH, in agreement with the higher reaction rate observed experimentally for the psychrophilic orthologue. Both transition states show concerted, albeit not synchronous, proton and hydride transfers to 3-oxovalerate. Setting the MM partial charges to zero results in identical reaction activation energies with both orthologues, suggesting the difference in activation energy between the reactions catalyzed by cold- and warm-adapted HBDHs arises from differential electrostatic stabilization of the transition state. Mutagenesis and phylogenetic analysis reveal the catalytic importance of His150 and Asn145 in the respective orthologues.
		+
		+	Dissecting the Mechanism of (R)-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry.,Machado TFG, Purg M, McMahon SA, Read BJ, Oehler V, Aqvist J, Gloster TM, da Silva RG ACS Catal. 2020 Dec 18;10(24):15019-15032. doi: 10.1021/acscatal.0c04736. Epub, 2020 Dec 7. PMID:33391858<ref>PMID:33391858</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zzq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aciba]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gloster TM]]	+	[[Category: Gloster, T M]]
-	[[Category: Machado ~~TFG~~]]	+	[[Category: Machado, T F.G]]
-	[[Category: McMahon SA]]	+	[[Category: McMahon, S A]]
-	[[Category: Oehler V]]	+	[[Category: Oehler, V]]
-	[[Category: Da Silva RG]]	+	[[Category: Silva, R G.da]]
		+	[[Category: Mesophilic enzyme]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Short-chain dehydrogenase/reductase]]

OCA at 06:22, 7 October 2020

2020-10-07T06:22:07Z

←Older revision		Revision as of 06:22, 7 October 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6zzq is ~~ON HOLD~~	+	==Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Acinetobacter baumannii complexed with NAD+ and acetoacetate==
-		+	<StructureSection load='6zzq' size='340' side='right'caption='[[6zzq]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZZQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZZQ FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zzq OCA], [http://pdbe.org/6zzq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zzq RCSB], [http://www.ebi.ac.uk/pdbsum/6zzq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zzq ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gloster TM]]
		+	[[Category: Machado TFG]]
		+	[[Category: McMahon SA]]
		+	[[Category: Oehler V]]
		+	[[Category: Da Silva RG]]

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

2020-08-12T08:17:40Z

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

←Older revision

Revision as of 08:17, 12 August 2020

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

2020-08-12T08:17:39Z

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

New page

'''Unreleased structure'''

The entry 6zzq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]