6aa8 - Revision history

OCA at 09:22, 22 November 2023

2023-11-22T09:22:23Z

←Older revision		Revision as of 09:22, 22 November 2023
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	<StructureSection load='6aa8' size='340' side='right'caption='[[6aa8]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6aa8' size='340' side='right'caption='[[6aa8]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6aa8]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cloab Cloab~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AA8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6AA8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6aa8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_acetobutylicum_ATCC_824 Clostridium acetobutylicum ATCC 824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AA8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 2.1Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>hbd, CA_C2708 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=272562 CLOAB])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/3~~-~~hydroxybutyryl~~-~~CoA_dehydrogenase 3-hydroxybutyryl-CoA dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.157 1.1.1.157]~~ </~~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=6aa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aa8 OCA], [https://pdbe.org/6aa8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6aa8 RCSB], [https://www.ebi.ac.uk/pdbsum/6aa8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6aa8 ProSAT]</span></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=6aa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aa8 OCA], [~~http~~://pdbe.org/6aa8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6aa8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6aa8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6aa8 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/HBD_CLOAB HBD_CLOAB]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6aa8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6aa8" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Journal:Acta Cryst F:S2053230X18014814\|Journal:Acta Cryst F:S2053230X18014814]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~3-hydroxybutyryl-CoA dehydrogenase]]~~	+	[[Category: Clostridium acetobutylicum ATCC 824]]
-	~~[[Category: Cloab~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Taguchi, S]]	+	[[Category: Taguchi S]]
-	[[Category: Takenoya, M]]	+	[[Category: Takenoya M]]
-	[[Category: Yajima, S]]	+	[[Category: Yajima S]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 21:27, 28 October 2020

2020-10-28T21:27:23Z

←Older revision		Revision as of 21:27, 28 October 2020
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	==Crystal structure of (S)-3-hydroxybutyryl-coenzymeA dehydrogenase from Clostridium acetobutylicum complexed with NAD+==		==Crystal structure of (S)-3-hydroxybutyryl-coenzymeA dehydrogenase from Clostridium acetobutylicum complexed with NAD+==
-	<StructureSection load='6aa8' size='340' side='right' caption='[[6aa8]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='6aa8' size='340' side='right'caption='[[6aa8]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6aa8]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AA8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca.weizmann~~.~~ac.il/oca-docs~~/fgij/fg.htm?mol=6AA8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6aa8]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Cloab Cloab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AA8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6AA8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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">hbd, CA_C2708 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272562 CLOAB])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyryl-CoA_dehydrogenase 3-hydroxybutyryl-CoA dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.157 1.1.1.157] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyryl-CoA_dehydrogenase 3-hydroxybutyryl-CoA dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.157 1.1.1.157] </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=6aa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aa8 OCA], [http://pdbe.org/6aa8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aa8 RCSB], [http://www.ebi.ac.uk/pdbsum/6aa8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aa8 ProSAT]</span></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=6aa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aa8 OCA], [http://pdbe.org/6aa8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aa8 RCSB], [http://www.ebi.ac.uk/pdbsum/6aa8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aa8 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	(S)-3-Hydroxybutyryl-CoA dehydrogenase (HBD) has been gaining increased attention recently as it is a key enzyme in the enantiomeric formation of (S)-3-hydroxybutyryl-CoA [(S)-3HB-CoA]. It converts acetoacetyl-CoA to (S)-3HB-CoA in the synthetic metabolic pathway. (S)-3HB-CoA is further modified to form (S)-3-hydroxybutyrate, which is a source of biodegradable polymers. During the course of a study to develop biodegradable polymers, attempts were made to determine the crystal structure of HBD from Clostridium acetobutylicum (CacHBD), and the crystal structures of both apo and NAD(+)-bound forms of CacHBD were determined. The crystals belonged to different space groups: P212121 and P21. However, both structures adopted a hexamer composed of three dimers in the asymmetric unit, and this oligomerization was additionally confirmed by gel-filtration column chromatography. Furthermore, to investigate the catalytic residues of CacHBD, the enzymatic activities of the wild type and of three single-amino-acid mutants were analyzed, in which the Ser, His and Asn residues that are conserved in the HBDs from C. acetobutylicum, C. butyricum and Ralstonia eutropha, as well as in the L-3-hydroxyacyl-CoA dehydrogenases from Homo sapiens and Escherichia coli, were substituted by alanines. The S117A and N188A mutants abolished the activity, while the H138A mutant showed a slightly lower Km value and a significantly lower kcat value than the wild type. Therefore, in combination with the crystal structures, it was shown that His138 is involved in catalysis and that Ser117 and Asn188 may be important for substrate recognition to place the keto group of the substrate in the correct position for reaction.
		+
		+	Crystal structure and kinetic analyses of a hexameric form of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum.,Takenoya M, Taguchi S, Yajima S Acta Crystallogr F Struct Biol Commun. 2018 Nov 1;74(Pt 11):733-740. doi:, 10.1107/S2053230X18014814. Epub 2018 Oct 31. PMID:30387779<ref>PMID:30387779</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6aa8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Journal:Acta Cryst F:S2053230X18014814\|Journal:Acta Cryst F:S2053230X18014814]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: 3-hydroxybutyryl-CoA dehydrogenase]]		[[Category: 3-hydroxybutyryl-CoA dehydrogenase]]
		+	[[Category: Cloab]]
		+	[[Category: Large Structures]]
	[[Category: Taguchi, S]]		[[Category: Taguchi, S]]
	[[Category: Takenoya, M]]		[[Category: Takenoya, M]]

OCA at 12:10, 7 November 2018

2018-11-07T12:10:47Z

←Older revision		Revision as of 12:10, 7 November 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6aa8 is ON HOLD until Paper Publication~~	+	==Crystal structure of (S)-3-hydroxybutyryl-coenzymeA dehydrogenase from Clostridium acetobutylicum complexed with NAD+==
-		+	<StructureSection load='6aa8' size='340' side='right' caption='[[6aa8]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors: Takenoya, M., Taguchi, S., Yajima, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6aa8]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AA8 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of (S)-3-hydroxybutyryl-coenzymeA dehydrogenase from Clostridium acetobutylicum complexed with NAD+	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyryl-CoA_dehydrogenase 3-hydroxybutyryl-CoA dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.157 1.1.1.157] </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=6aa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aa8 OCA], [http://pdbe.org/6aa8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aa8 RCSB], [http://www.ebi.ac.uk/pdbsum/6aa8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aa8 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 3-hydroxybutyryl-CoA dehydrogenase]]
	[[Category: Taguchi, S]]		[[Category: Taguchi, S]]
	[[Category: Takenoya, M]]		[[Category: Takenoya, M]]
	[[Category: Yajima, S]]		[[Category: Yajima, S]]
		+	[[Category: Complex]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]

OCA at 16:52, 1 August 2018

2018-08-01T16:52:56Z

←Older revision		Revision as of 16:52, 1 August 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6aa8 is ON HOLD	+	The entry 6aa8 is ON HOLD until Paper Publication

-	Authors: Takenoya, M~~., Ito, S., Sasaki, S~~., Taguchi, S., Yajima, S.	+	Authors: Takenoya, M., Taguchi, S., Yajima, S.

	Description: Crystal structure of (S)-3-hydroxybutyryl-coenzymeA dehydrogenase from Clostridium acetobutylicum complexed with NAD+		Description: Crystal structure of (S)-3-hydroxybutyryl-coenzymeA dehydrogenase from Clostridium acetobutylicum complexed with NAD+
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Taguchi, S]]		[[Category: Taguchi, S]]
-	[[Category: Ito, S]]
	[[Category: Takenoya, M]]		[[Category: Takenoya, M]]
-	[[Category: Sasaki, S]]
	[[Category: Yajima, S]]		[[Category: Yajima, S]]

OCA: Protected "6aa8" [edit=sysop:move=sysop]

2018-07-25T05:43:30Z

Protected "6aa8" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:43, 25 July 2018

OCA: New page: '''Unreleased structure''' The entry 6aa8 is ON HOLD Authors: Takenoya, M., Ito, S., Sasaki, S., Taguchi, S., Yajima, S. Description: Crystal structure of (S)-3-hydroxybutyryl-coenzyme...

2018-07-25T05:43:29Z

New page: '''Unreleased structure''' The entry 6aa8 is ON HOLD Authors: Takenoya, M., Ito, S., Sasaki, S., Taguchi, S., Yajima, S. Description: Crystal structure of (S)-3-hydroxybutyryl-coenzyme...

New page

'''Unreleased structure'''

The entry 6aa8 is ON HOLD

Authors: Takenoya, M., Ito, S., Sasaki, S., Taguchi, S., Yajima, S.

Description: Crystal structure of (S)-3-hydroxybutyryl-coenzymeA dehydrogenase from Clostridium acetobutylicum complexed with NAD+
[[Category: Unreleased Structures]]
[[Category: Taguchi, S]]
[[Category: Ito, S]]
[[Category: Takenoya, M]]
[[Category: Sasaki, S]]
[[Category: Yajima, S]]