5x5u - Revision history

OCA at 07:54, 22 November 2023

OCA — Wed, 22 Nov 2023 07:54:19 GMT

←Older revision		Revision as of 07:54, 22 November 2023
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	<StructureSection load='5x5u' size='340' side='right'caption='[[5x5u]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5x5u' size='340' side='right'caption='[[5x5u]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5u]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_29145 Atcc 29145~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X5U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Azospirillum_brasilense Azospirillum brasilense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X5U FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.3Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5x5t\|5x5t]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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">araE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192 ATCC 29145])~~</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=5x5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5u OCA], [https://pdbe.org/5x5u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x5u RCSB], [https://www.ebi.ac.uk/pdbsum/5x5u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5u 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=5x5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5u OCA], [~~http~~://pdbe.org/5x5u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x5u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x5u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5u ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~KGSDH_AZOBR KGSDH_AZOBR]~~] Catalyzes the NAD(P)(+)-dependent oxidation of alpha-ketoglutaric semialdehyde (alphaKGSA) to alpha-ketoglutarate. Is involved in a degradation pathway of L-arabinose that allows A.brasilense to grow on L-arabinose as a sole carbon source. Prefers NAD(+) to NADP(+) as a cosubstrate. Displays broad substrate specificity: exhibits the highest activity with alphaKGSA and succinic semialdehyde as substrates, but to a lesser extent, is also active with glutaraldehyde, benzaldehyde, and a number of aldehydes from C3 to C8.<ref>PMID:16835232</ref>	+	[https://www.uniprot.org/uniprot/KGSD1_AZOBR KGSD1_AZOBR] Catalyzes the NAD(P)(+)-dependent oxidation of alpha-ketoglutaric semialdehyde (alphaKGSA) to alpha-ketoglutarate. Is involved in a degradation pathway of L-arabinose that allows A.brasilense to grow on L-arabinose as a sole carbon source. Prefers NAD(+) to NADP(+) as a cosubstrate. Displays broad substrate specificity: exhibits the highest activity with alphaKGSA and succinic semialdehyde as substrates, but to a lesser extent, is also active with glutaraldehyde, benzaldehyde, and a number of aldehydes from C3 to C8.<ref>PMID:16835232</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: ~~Atcc 29145~~]]	+	[[Category: Azospirillum brasilense]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim, K J]]	+	[[Category: Kim K-J]]
-	[[Category: Son, H F]]	+	[[Category: Son H-F]]
-	~~[[Category: Alpha-ketoglutarate semialdehyde dehydrogenase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 05:41, 13 May 2020

OCA — Wed, 13 May 2020 05:41:46 GMT

←Older revision		Revision as of 05:41, 13 May 2020
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-	==Crystal ~~strcuture~~ of alpha-ketoglutarate-semialdehyde dehydrogenase (KGSADH) complexed with NAD==	+	==Crystal structure of alpha-ketoglutarate-semialdehyde dehydrogenase (KGSADH) complexed with NAD==
-	<StructureSection load='5x5u' size='340' side='right' caption='[[5x5u]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5x5u' size='340' side='right'caption='[[5x5u]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5U OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X5U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29145 Atcc 29145]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X5U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5t\|5x5t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5t\|5x5t]]</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=5x5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5u OCA], [http://pdbe.org/5x5u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5u RCSB], [http://www.ebi.ac.uk/pdbsum/5x5u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5u ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">araE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192 ATCC 29145])</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=5x5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5u OCA], [http://pdbe.org/5x5u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5u RCSB], [http://www.ebi.ac.uk/pdbsum/5x5u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5x5u" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x5u" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Succinate-semialdehyde dehydrogenase\|Succinate-semialdehyde dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 29145]]
		+	[[Category: Large Structures]]
	[[Category: Kim, K J]]		[[Category: Kim, K J]]
	[[Category: Son, H F]]		[[Category: Son, H F]]
	[[Category: Alpha-ketoglutarate semialdehyde dehydrogenase]]		[[Category: Alpha-ketoglutarate semialdehyde dehydrogenase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 12:48, 10 May 2017

OCA — Wed, 10 May 2017 12:48:04 GMT

←Older revision		Revision as of 12:48, 10 May 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5x5u is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal strcuture of alpha-ketoglutarate-semialdehyde dehydrogenase (KGSADH) complexed with NAD==
		+	<StructureSection load='5x5u' size='340' side='right' caption='[[5x5u]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x5u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X5U FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5t\|5x5t]]</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=5x5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5u OCA], [http://pdbe.org/5x5u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5u RCSB], [http://www.ebi.ac.uk/pdbsum/5x5u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5u ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KGSDH_AZOBR KGSDH_AZOBR]] Catalyzes the NAD(P)(+)-dependent oxidation of alpha-ketoglutaric semialdehyde (alphaKGSA) to alpha-ketoglutarate. Is involved in a degradation pathway of L-arabinose that allows A.brasilense to grow on L-arabinose as a sole carbon source. Prefers NAD(+) to NADP(+) as a cosubstrate. Displays broad substrate specificity: exhibits the highest activity with alphaKGSA and succinic semialdehyde as substrates, but to a lesser extent, is also active with glutaraldehyde, benzaldehyde, and a number of aldehydes from C3 to C8.<ref>PMID:16835232</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	3-Hydroxypropionic acid (3-HP) is an important platform chemical to be converted to acrylic acid and acrylamide. Aldehyde dehydrogenase (ALDH), an enzyme that catalyzes the reaction of 3-hydroxypropionaldehyde (3-HPA) to 3-HP, determines 3-HP production rate during the conversion of glycerol to 3-HP. To elucidate molecular mechanism of 3-HP production, we determined the first crystal structure of a 3-HP producing ALDH, alpha-ketoglutarate-semialdehyde dehydrogenase from Azospirillum basilensis (AbKGSADH), in its apo-form and in complex with NAD+. Although showing an overall structure similar to other ALDHs, the AbKGSADH enzyme had an optimal substrate binding site for accepting 3-HPA as a substrate. Molecular docking simulation of 3-HPA into the AbKGSADH structure revealed that the residues Asn159, Gln160 and Arg163 stabilize the aldehyde- and the hydroxyl-groups of 3-HPA through hydrogen bonds, and several hydrophobic residues, such as Phe156, Val286, Ile288, and Phe450, provide the optimal size and shape for 3-HPA binding. We also compared AbKGSADH with other reported 3-HP producing ALDHs for the crucial amino acid residues for enzyme catalysis and substrate binding, which provides structural implications on how these enzymes utilize 3-HPA as a substrate.

-	~~Authors: Son, H.~~-F., ~~Kim~~, K.-J.	+	Structural insights into the production of 3-hydroxypropionic acid by aldehyde dehydrogenase from Azospirillum brasilense.,Son HF, Park S, Yoo TH, Jung GY, Kim KJ Sci Rep. 2017 Apr 10;7:46005. doi: 10.1038/srep46005. PMID:28393833<ref>PMID:28393833</ref>

-	~~Description: Crystal strcuture~~ of ~~alpha~~-~~ketoglutarate~~-~~semialdehyde dehydrogenase (KGSADH) complexed with NAD~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Kim, K.-J]]	+	<div class="pdbe-citations 5x5u" style="background-color:#fffaf0;"></div>
-	[[Category: Son, H.-F]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kim, K J]]
		+	[[Category: Son, H F]]
		+	[[Category: Alpha-ketoglutarate semialdehyde dehydrogenase]]
		+	[[Category: Oxidoreductase]]

OCA at 12:17, 5 April 2017

OCA — Wed, 05 Apr 2017 12:17:21 GMT

←Older revision		Revision as of 12:17, 5 April 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x5u is ON HOLD	+	The entry 5x5u is ON HOLD until Paper Publication

	Authors: Son, H.-F., Kim, K.-J.		Authors: Son, H.-F., Kim, K.-J.

OCA: Protected "5x5u" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:47:29 GMT

Protected "5x5u" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:47, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x5u is ON HOLD Authors: Son, H.-F., Kim, K.-J. Description: Crystal strcuture of alpha-ketoglutarate-semialdehyde dehydrogenase (KGSADH) complexed...

OCA — Thu, 09 Mar 2017 15:47:28 GMT

New page: '''Unreleased structure''' The entry 5x5u is ON HOLD Authors: Son, H.-F., Kim, K.-J. Description: Crystal strcuture of alpha-ketoglutarate-semialdehyde dehydrogenase (KGSADH) complexed...

New page

'''Unreleased structure'''

The entry 5x5u is ON HOLD

Authors: Son, H.-F., Kim, K.-J.

Description: Crystal strcuture of alpha-ketoglutarate-semialdehyde dehydrogenase (KGSADH) complexed with NAD
[[Category: Unreleased Structures]]
[[Category: Kim, K.-J]]
[[Category: Son, H.-F]]