4h8a - Revision history

OCA at 15:01, 20 September 2023

OCA — Wed, 20 Sep 2023 15:01:30 GMT

←Older revision		Revision as of 15:01, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4h8a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[4h8a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H8A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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=4h8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h8a OCA], [https://pdbe.org/4h8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h8a RCSB], [https://www.ebi.ac.uk/pdbsum/4h8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h8a 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=4h8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h8a OCA], [https://pdbe.org/4h8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h8a RCSB], [https://www.ebi.ac.uk/pdbsum/4h8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h8a ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:04, 3 November 2022

OCA — Thu, 03 Nov 2022 08:04:46 GMT

←Older revision		Revision as of 08:04, 3 November 2022
Line 1:		Line 1:

	==Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH==		==Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH==
-	<StructureSection load='4h8a' size='340' side='right' caption='[[4h8a]], [[Resolution\|resolution]] 1.64Å' scene=''>	+	<StructureSection load='4h8a' size='340' side='right'caption='[[4h8a]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h8a]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H8A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4H8A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h8a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H8A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allD, glxB8, ylbC, b0517, JW0505 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4h8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h8a OCA], [https://pdbe.org/4h8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h8a RCSB], [https://www.ebi.ac.uk/pdbsum/4h8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h8a 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/Ureidoglycolate_dehydrogenase Ureidoglycolate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.154 1.1.1.154] </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=4h8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h8a OCA], [~~http~~://pdbe.org/4h8a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4h8a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4h8a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4h8a ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ALLD_ECOLI ALLD_ECOLI]] Involved in the anaerobic utilization of allantoin.	+	[https://www.uniprot.org/uniprot/ALLD_ECOLI ALLD_ECOLI] Involved in the anaerobic utilization of allantoin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
-	[[Category: ~~Ureidoglycolate dehydrogenase~~]]	+	[[Category: Large Structures]]
-	[[Category: Kim, M]]	+	[[Category: Kim M]]
-	[[Category: Rhee, S]]	+	[[Category: Rhee S]]
-	[[Category: Shin, I]]	+	[[Category: Shin I]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 22:23, 5 August 2016

OCA — Fri, 05 Aug 2016 22:23:25 GMT

←Older revision		Revision as of 22:23, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH==		==Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH==
	<StructureSection load='4h8a' size='340' side='right' caption='[[4h8a]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='4h8a' size='340' side='right' caption='[[4h8a]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h8a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H8A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h8a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H8A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allD, glxB8, ylbC, b0517, JW0505 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allD, glxB8, ylbC, b0517, JW0505 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ureidoglycolate_dehydrogenase Ureidoglycolate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.154 1.1.1.154] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ureidoglycolate_dehydrogenase Ureidoglycolate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.154 1.1.1.154] </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=4h8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h8a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h8a RCSB], [http://www.ebi.ac.uk/pdbsum/4h8a 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=4h8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h8a OCA], [http://pdbe.org/4h8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h8a RCSB], [http://www.ebi.ac.uk/pdbsum/4h8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h8a 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 4h8a" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Ureidoglycolate dehydrogenase]]		[[Category: Ureidoglycolate dehydrogenase]]
	[[Category: Kim, M]]		[[Category: Kim, M]]

OCA at 22:26, 25 December 2014

OCA — Thu, 25 Dec 2014 22:26:02 GMT

←Older revision		Revision as of 22:26, 25 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4h8a.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH==
		+	<StructureSection load='4h8a' size='340' side='right' caption='[[4h8a]], [[Resolution\|resolution]] 1.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4h8a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H8A FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allD, glxB8, ylbC, b0517, JW0505 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ureidoglycolate_dehydrogenase Ureidoglycolate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.154 1.1.1.154] </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=4h8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h8a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h8a RCSB], [http://www.ebi.ac.uk/pdbsum/4h8a PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ALLD_ECOLI ALLD_ECOLI]] Involved in the anaerobic utilization of allantoin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nitrogen metabolism is one of essential processes in living organisms. The catabolic pathways of nitrogenous compounds play a pivotal role in the storage and recovery of nitrogen. In Escherichia coli, two different, interconnecting metabolic routes drive nitrogen utilization through purine degradation metabolites. The enzyme (S)-ureidoglycolate dehydrogenase (AllD), which is a member of l-sulfolactate dehydrogenase-like family, converts (S)-ureidoglycolate, a key intermediate in the purine degradation pathway, to oxalurate in an NAD(P)-dependent manner. Therefore, AllD is a metabolic branch-point enzyme for nitrogen metabolism in E. coli. Here, we report crystal structures of AllD in its apo form, in a binary complex with NADH cofactor, and in a ternary complex with NADH and glyoxylate, a possible spontaneous degradation product of oxalurate. Structural analyses revealed that NADH in an extended conformation is bound to an NADH-binding fold with three distinct domains that differ from those of the canonical NADH-binding fold. We also characterized ligand-induced structural changes, as well as the binding mode of glyoxylate, in the active site near the NADH nicotinamide ring. Based on structural and kinetic analyses, we concluded that AllD selectively utilizes NAD(+) as a cofactor, and further propose that His116 acts as a general catalytic base and that a hydride transfer is possible on the B-face of the nicotinamide ring of the cofactor. Other residues conserved in the active sites of this novel l-sulfolactate dehydrogenase-like family also play essential roles in catalysis.

-	~~{{STRUCTURE_4h8a\| PDB=4h8a \| SCENE= }}~~	+	Structural and functional insights into (s)-ureidoglycolate dehydrogenase, a metabolic branch point enzyme in nitrogen utilization.,Kim MI, Shin I, Cho S, Lee J, Rhee S PLoS One. 2012;7(12):e52066. doi: 10.1371/journal.pone.0052066. Epub 2012 Dec 20. PMID:23284870<ref>PMID:23284870</ref>

-	~~===Crystal structure~~ of ~~ureidoglycolate dehydrogenase in binary complex with NADH===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_23284870}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[4h8a]] is a 2 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H8A OCA].~~	+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ureidoglycolate dehydrogenase]]		[[Category: Ureidoglycolate dehydrogenase]]
-	[[Category: Kim, M.]]	+	[[Category: Kim, M]]
-	[[Category: Rhee, S.]]	+	[[Category: Rhee, S]]
-	[[Category: Shin, I.]]	+	[[Category: Shin, I]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]

OCA at 08:48, 16 January 2013

OCA — Wed, 16 Jan 2013 08:48:50 GMT

←Older revision		Revision as of 08:48, 16 January 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4h8a.jpg\|left\|200px]]

-	~~The entry~~ 4h8a ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4h8a\| PDB=4h8a \| SCENE= }}

-	~~Authors: Rhee, S., Shin, I., Kim, M.~~	+	===Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH===

-	~~Description: Crystal~~ structure ~~of ureidoglycolate dehydrogenase in binary complex~~ with ~~NADH~~	+	{{ABSTRACT_PUBMED_23284870}}
		+
		+	==About this Structure==
		+	[[4h8a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H8A OCA].
		+	[[Category: Escherichia coli]]
		+	[[Category: Ureidoglycolate dehydrogenase]]
		+	[[Category: Kim, M.]]
		+	[[Category: Rhee, S.]]
		+	[[Category: Shin, I.]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]

OCA at 06:57, 10 October 2012

OCA — Wed, 10 Oct 2012 06:57:08 GMT

←Older revision		Revision as of 06:57, 10 October 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4h8a is ON HOLD	+	The entry 4h8a is ON HOLD until Paper Publication

-	Authors: Rhee, S, Shin, I, Kim, M	+	Authors: Rhee, S., Shin, I., Kim, M.

	Description: Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH		Description: Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH

OCA: Protected "4h8a" [edit=sysop:move=sysop]

OCA — Wed, 03 Oct 2012 05:49:18 GMT

Protected "4h8a" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:49, 3 October 2012

OCA: New page: '''Unreleased structure''' The entry 4h8a is ON HOLD Authors: Rhee, S, Shin, I, Kim, M Description: Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH

OCA — Wed, 03 Oct 2012 05:49:17 GMT

New page: '''Unreleased structure''' The entry 4h8a is ON HOLD Authors: Rhee, S, Shin, I, Kim, M Description: Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH

New page

'''Unreleased structure'''

The entry 4h8a is ON HOLD

Authors: Rhee, S, Shin, I, Kim, M

Description: Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH