5j5z - Revision history

OCA at 10:50, 6 September 2023

OCA — Wed, 06 Sep 2023 10:50:19 GMT

←Older revision		Revision as of 10:50, 6 September 2023
Line 1:		Line 1:

	==Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide dehydrogenase==		==Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide dehydrogenase==
-	<StructureSection load='5j5z' size='340' side='right' caption='[[5j5z]], [[Resolution\|resolution]] 1.84Å' scene=''>	+	<StructureSection load='5j5z' size='340' side='right'caption='[[5j5z]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j5z]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J5Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J5Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j5z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J5Z FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.84Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~DLD, GCSL, LAD, PHE3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Dihydrolipoyl_dehydrogenase Dihydrolipoyl dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.4 1.8.1.4]~~ </~~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=5j5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j5z OCA], [https://pdbe.org/5j5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j5z RCSB], [https://www.ebi.ac.uk/pdbsum/5j5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j5z 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=5j5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j5z OCA], [~~http~~://pdbe.org/5j5z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j5z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j5z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j5z ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN]] Note=Defects in DLD are involved in the development of congenital infantile lactic acidosis. Defects in DLD are a cause of maple syrup urine disease (MSUD) [MIM:[~~http~~://omim.org/entry/248600 248600]]. MSUD is characterized by mental and physical retardation, feeding problems and a maple syrup odor to the urine. The keto acids of the branched-chain amino acids are present in the urine, resulting from a block in oxidative decarboxylation.	+	[https://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN] Note=Defects in DLD are involved in the development of congenital infantile lactic acidosis. Defects in DLD are a cause of maple syrup urine disease (MSUD) [MIM:[https://omim.org/entry/248600 248600]. MSUD is characterized by mental and physical retardation, feeding problems and a maple syrup odor to the urine. The keto acids of the branched-chain amino acids are present in the urine, resulting from a block in oxidative decarboxylation.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN]] Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. Involved in the hyperactivation of spermatazoa during capacitation and in the spermatazoal acrosome reaction.	+	[https://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN] Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. Involved in the hyperactivation of spermatazoa during capacitation and in the spermatazoal acrosome reaction.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dihydrolipoyl dehydrogenase~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Adam-Vizi, V]]	+	[[Category: Adam-Vizi V]]
-	[[Category: Ambrus, A]]	+	[[Category: Ambrus A]]
-	[[Category: Mizsei, R]]	+	[[Category: Mizsei R]]
-	[[Category: Szabo, E]]	+	[[Category: Szabo E]]
-	[[Category: Torocsik, B]]	+	[[Category: Torocsik B]]
-	[[Category: Weiss~~, M S~~]]	+	[[Category: Weiss MS]]
-	[[Category: Zambo, Z]]	+	[[Category: Zambo Z]]
-	~~[[Category: Dihydrolipoamide dehydrogenase]]~~	+
-	~~[[Category: Disease-causing mutant]]~~	+
-	~~[[Category: E3 deficiency]]~~	+
-	~~[[Category: E3 subunit]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:30, 4 July 2018

OCA — Wed, 04 Jul 2018 07:30:29 GMT

←Older revision		Revision as of 07:30, 4 July 2018
Line 13:		Line 13:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN]] Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. Involved in the hyperactivation of spermatazoa during capacitation and in the spermatazoal acrosome reaction.		[[http://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN]] Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. Involved in the hyperactivation of spermatazoa during capacitation and in the spermatazoal acrosome reaction.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report the crystal structures of the human (dihydro)lipoamide dehydrogenase (hLADH, hE3) and its disease-causing homodimer interface mutant D444V-hE3 at 2.27 and 1.84A resolution, respectively. The wild type structure is a unique uncomplexed, unliganded hE3 structure with the true canonical sequence. Based on the structural information a novel molecular pathomechanism is proposed for the impaired catalytic activity and enhanced capacity for reactive oxygen species generation of the pathogenic mutant. The mechanistic model involves a previously much ignored solvent accessible channel leading to the active site that might be perturbed also by other disease-causing homodimer interface substitutions of this enzyme.
		+
		+	Crystal structures of the disease-causing D444V mutant and the relevant wild type human dihydrolipoamide dehydrogenase.,Szabo E, Mizsei R, Wilk P, Zambo Z, Torocsik B, Weiss MS, Adam-Vizi V, Ambrus A Free Radic Biol Med. 2018 Jun 20;124:214-220. doi:, 10.1016/j.freeradbiomed.2018.06.008. PMID:29908278<ref>PMID:29908278</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5j5z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dihydrolipoamide dehydrogenase\|Dihydrolipoamide dehydrogenase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:56, 28 March 2018

OCA — Wed, 28 Mar 2018 06:56:31 GMT

←Older revision		Revision as of 06:56, 28 March 2018
Line 3:		Line 3:
	<StructureSection load='5j5z' size='340' side='right' caption='[[5j5z]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='5j5z' size='340' side='right' caption='[[5j5z]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J5Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j5z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J5Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DLD, GCSL, LAD, PHE3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrolipoyl_dehydrogenase Dihydrolipoyl dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.4 1.8.1.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrolipoyl_dehydrogenase Dihydrolipoyl dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.4 1.8.1.4] </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=5j5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j5z OCA], [http://pdbe.org/5j5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j5z RCSB], [http://www.ebi.ac.uk/pdbsum/5j5z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j5z 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=5j5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j5z OCA], [http://pdbe.org/5j5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j5z RCSB], [http://www.ebi.ac.uk/pdbsum/5j5z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j5z ProSAT]</span></td></tr>
Line 15:		Line 16:
	</StructureSection>		</StructureSection>
	[[Category: Dihydrolipoyl dehydrogenase]]		[[Category: Dihydrolipoyl dehydrogenase]]
		+	[[Category: Human]]
	[[Category: Adam-Vizi, V]]		[[Category: Adam-Vizi, V]]
	[[Category: Ambrus, A]]		[[Category: Ambrus, A]]

OCA at 07:23, 15 November 2017

OCA — Wed, 15 Nov 2017 07:23:29 GMT

←Older revision		Revision as of 07:23, 15 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5j5z is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide dehydrogenase==
-		+	<StructureSection load='5j5z' size='340' side='right' caption='[[5j5z]], [[Resolution\|resolution]] 1.84Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5j5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J5Z FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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/Dihydrolipoyl_dehydrogenase Dihydrolipoyl dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.4 1.8.1.4] </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=5j5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j5z OCA], [http://pdbe.org/5j5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j5z RCSB], [http://www.ebi.ac.uk/pdbsum/5j5z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j5z ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN]] Note=Defects in DLD are involved in the development of congenital infantile lactic acidosis. Defects in DLD are a cause of maple syrup urine disease (MSUD) [MIM:[http://omim.org/entry/248600 248600]]. MSUD is characterized by mental and physical retardation, feeding problems and a maple syrup odor to the urine. The keto acids of the branched-chain amino acids are present in the urine, resulting from a block in oxidative decarboxylation.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN]] Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. Involved in the hyperactivation of spermatazoa during capacitation and in the spermatazoal acrosome reaction.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dihydrolipoyl dehydrogenase]]
		+	[[Category: Adam-Vizi, V]]
		+	[[Category: Ambrus, A]]
		+	[[Category: Mizsei, R]]
		+	[[Category: Szabo, E]]
		+	[[Category: Torocsik, B]]
		+	[[Category: Weiss, M S]]
		+	[[Category: Zambo, Z]]
		+	[[Category: Dihydrolipoamide dehydrogenase]]
		+	[[Category: Disease-causing mutant]]
		+	[[Category: E3 deficiency]]
		+	[[Category: E3 subunit]]
		+	[[Category: Oxidoreductase]]

OCA at 15:05, 15 May 2016

OCA — Sun, 15 May 2016 15:05:31 GMT

←Older revision		Revision as of 15:05, 15 May 2016
Line 3:		Line 3:
	The entry 5j5z is ON HOLD until Paper Publication		The entry 5j5z is ON HOLD until Paper Publication

-	Authors: ~~Szabo, E., Mizsei, R., Zambo, Z., Torocsik, B., Weiss, M.S., Adam-Vizi, V., Ambrus, A.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Ambrus, A]]
-	[[Category: Szabo, E]]
-	[[Category: Mizsei, R]]
-	[[Category: Torocsik, B]]
-	[[Category: Zambo, Z]]
-	[[Category: Adam-Vizi, V]]
-	[[Category: Weiss, M.S]]

OCA: Protected "5j5z" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:31:29 GMT

Protected "5j5z" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:31, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j5z is ON HOLD until Paper Publication Authors: Szabo, E., Mizsei, R., Zambo, Z., Torocsik, B., Weiss, M.S., Adam-Vizi, V., Ambrus, A. Description...

OCA — Wed, 11 May 2016 01:31:28 GMT

New page: '''Unreleased structure''' The entry 5j5z is ON HOLD until Paper Publication Authors: Szabo, E., Mizsei, R., Zambo, Z., Torocsik, B., Weiss, M.S., Adam-Vizi, V., Ambrus, A. Description...

New page

'''Unreleased structure'''

The entry 5j5z is ON HOLD until Paper Publication

Authors: Szabo, E., Mizsei, R., Zambo, Z., Torocsik, B., Weiss, M.S., Adam-Vizi, V., Ambrus, A.

Description:
[[Category: Unreleased Structures]]
[[Category: Ambrus, A]]
[[Category: Szabo, E]]
[[Category: Mizsei, R]]
[[Category: Torocsik, B]]
[[Category: Zambo, Z]]
[[Category: Adam-Vizi, V]]
[[Category: Weiss, M.S]]