6u3j - Revision history

OCA at 07:43, 11 October 2023

OCA — Wed, 11 Oct 2023 07:43:35 GMT

←Older revision		Revision as of 07:43, 11 October 2023
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	<StructureSection load='6u3j' size='340' side='right'caption='[[6u3j]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6u3j' size='340' side='right'caption='[[6u3j]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u3j]] 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=6U3J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6U3J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u3j]] 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=6U3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U3J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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]] 2.25Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MLZ~~:~~N-METHYL-LYSINE~~'>~~MLZ~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">DHTKD1~~, ~~KIAA1630 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~<~~/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=6u3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3j OCA], [https://pdbe.org/6u3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u3j RCSB], [https://www.ebi.ac.uk/pdbsum/6u3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3j 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/Oxoglutarate_dehydrogenase_(succinyl-transferring) Oxoglutarate dehydrogenase (succinyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.2 1.2.4.2] </~~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=6u3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3j OCA], [~~http~~://pdbe.org/6u3j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6u3j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6u3j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3j ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/DHTK1_HUMAN DHTK1_HUMAN]] 2-aminoadipic 2-oxoadipic aciduria;Autosomal dominant Charcot-Marie-Tooth disease type 2Q. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/DHTK1_HUMAN DHTK1_HUMAN] 2-aminoadipic 2-oxoadipic aciduria;Autosomal dominant Charcot-Marie-Tooth disease type 2Q. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DHTK1_HUMAN DHTK1_HUMAN]] The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).	+	[https://www.uniprot.org/uniprot/DHTK1_HUMAN DHTK1_HUMAN] The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).
	<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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Khamrui, S]]	+	[[Category: Khamrui S]]
-	[[Category: Lazarus~~, M B]]~~	+	[[Category: Lazarus MB]]
-	~~[[Category: Lysine metabolism mitochondrial dehydrogenase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:35, 29 July 2020

OCA — Wed, 29 Jul 2020 11:35:42 GMT

←Older revision		Revision as of 11:35, 29 July 2020
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	==Structure of the 2-oxoadipate dehydrogenase DHTKD1==		==Structure of the 2-oxoadipate dehydrogenase DHTKD1==
-	<StructureSection load='6u3j' size='340' side='right'caption='[[6u3j]]' scene=''>	+	<StructureSection load='6u3j' size='340' side='right'caption='[[6u3j]], [[Resolution\|resolution]] 2.25Å' 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=6U3J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6U3J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u3j]] 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=6U3J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6U3J 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=6u3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3j OCA], [http://pdbe.org/6u3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u3j RCSB], [http://www.ebi.ac.uk/pdbsum/6u3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3j 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DHTKD1, KIAA1630 ([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/Oxoglutarate_dehydrogenase_(succinyl-transferring) Oxoglutarate dehydrogenase (succinyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.2 1.2.4.2] </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=6u3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3j OCA], [http://pdbe.org/6u3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u3j RCSB], [http://www.ebi.ac.uk/pdbsum/6u3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/DHTK1_HUMAN DHTK1_HUMAN]] 2-aminoadipic 2-oxoadipic aciduria;Autosomal dominant Charcot-Marie-Tooth disease type 2Q. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DHTK1_HUMAN DHTK1_HUMAN]] The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DHTKD1 is the E1 component of the 2-oxoadipate dehydrogenase complex, which is an enzyme involved in the catabolism of (hydroxy-)lysine and tryptophan. Mutations in DHTKD1 have been associated with 2-aminoadipic and 2-oxoadipic aciduria, Charcot-Marie-Tooth disease type 2Q and eosinophilic esophagitis, but the pathophysiology of these clinically distinct disorders remains elusive. Here, we report the identification of adipoylphosphonic acid and tenatoprazole as DHTKD1 inhibitors using targeted and high throughput screening, respectively. We furthermore elucidate the DHTKD1 crystal structure with thiamin diphosphate bound at 2.25 A. We also report the impact of 10 disease-associated missense mutations on DHTKD1. Whereas the majority of the DHTKD1 variants displayed impaired folding or reduced thermal stability in combination with absent or reduced enzyme activity, three variants showed no abnormalities. Our work provides chemical and structural tools for further understanding of the function of DHTKD1 and its role in several human pathologies.
		+
		+	Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex.,Leandro J, Khamrui S, Wang H, Suebsuwong C, Nemeria NS, Huynh K, Moustakim M, Secor C, Wang M, Dodatko T, Stauffer B, Wilson CG, Yu C, Arkin MR, Jordan F, Sanchez R, DeVita RJ, Lazarus MB, Houten SM ACS Chem Biol. 2020 Jul 9. doi: 10.1021/acschembio.0c00114. PMID:32633484<ref>PMID:32633484</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6u3j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Khamrui S]]	+	[[Category: Khamrui, S]]
-	[[Category: Lazarus MB]]	+	[[Category: Lazarus, M B]]
		+	[[Category: Lysine metabolism mitochondrial dehydrogenase]]
		+	[[Category: Oxidoreductase]]

OCA at 10:51, 22 July 2020

OCA — Wed, 22 Jul 2020 10:51:24 GMT

←Older revision		Revision as of 10:51, 22 July 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6u3j ~~is ON HOLD until Paper Publication~~	+	==Structure of the 2-oxoadipate dehydrogenase DHTKD1==
-		+	<StructureSection load='6u3j' size='340' side='right'caption='[[6u3j]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U3J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6U3J 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=6u3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3j OCA], [http://pdbe.org/6u3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u3j RCSB], [http://www.ebi.ac.uk/pdbsum/6u3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3j ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Khamrui S]]
		+	[[Category: Lazarus MB]]

OCA at 05:07, 29 April 2020

OCA — Wed, 29 Apr 2020 05:07:06 GMT

←Older revision		Revision as of 05:07, 29 April 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u3j is ON HOLD	+	The entry 6u3j is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 04:10, 22 April 2020

OCA — Wed, 22 Apr 2020 04:10:18 GMT

←Older revision		Revision as of 04:10, 22 April 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u3j is ON HOLD ~~until Paper Publication~~	+	The entry 6u3j is ON HOLD

	Authors:		Authors:

OCA at 08:09, 2 October 2019

OCA — Wed, 02 Oct 2019 08:09:06 GMT

←Older revision		Revision as of 08:09, 2 October 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u3j is ON HOLD	+	The entry 6u3j is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6u3j" [edit=sysop:move=sysop]

OCA — Wed, 28 Aug 2019 14:06:40 GMT

Protected "6u3j" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:06, 28 August 2019

OCA: New page: '''Unreleased structure''' The entry 6u3j is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 28 Aug 2019 14:06:38 GMT

New page: '''Unreleased structure''' The entry 6u3j is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6u3j is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]