3khu - Revision history

OCA at 08:16, 6 September 2023

OCA — Wed, 06 Sep 2023 08:16:00 GMT

←Older revision		Revision as of 08:16, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3khu' size='340' side='right'caption='[[3khu]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3khu' size='340' side='right'caption='[[3khu]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3khu]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KHU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3khu]] is a 6 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=3KHU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KHU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=EPE:4-(~~2~~-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</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"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3itk\|3itk]], [[2q3e\|2q3e]], [[2qg4\|2qg4]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">UGDH~~ (~~[https://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'>[https://en.wikipedia.org/wiki/UDP~~-~~glucose_6~~-~~dehydrogenase UDP~~-~~glucose 6-dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22]~~ </~~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=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [https://pdbe.org/3khu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [https://www.ebi.ac.uk/pdbsum/3khu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3khu 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=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [https://pdbe.org/3khu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [https://www.ebi.ac.uk/pdbsum/3khu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3khu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/UGDH_HUMAN UGDH_HUMAN]] Involved in the biosynthesis of glycosaminoglycans; hyaluronan, chondroitin sulfate, and heparan sulfate.	+	[https://www.uniprot.org/uniprot/UGDH_HUMAN UGDH_HUMAN] Involved in the biosynthesis of glycosaminoglycans; hyaluronan, chondroitin sulfate, and heparan sulfate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: UDP-glucose 6-dehydrogenase]]~~	+	[[Category: Arrowsmith CH]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Bountra C]]
-	[[Category: Bountra, C]]	+	[[Category: Chaikuad A]]
-	[[Category: Chaikuad, A]]	+	[[Category: Edwards AM]]
-	~~[[Category: Delft, F von~~]]	+	[[Category: Egger S]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Filippakopoulos P]]
-	[[Category: Egger, S]]	+	[[Category: Guo K]]
-	[[Category: Filippakopoulos, P]]	+	[[Category: Kavanagh KL]]
-	[[Category: Guo, K]]	+	[[Category: Muniz JRC]]
-	[[Category: Kavanagh~~, K L~~]]	+	[[Category: Nidetzky B]]
-	[[Category: Muniz~~, J R.C~~]]	+	[[Category: Oppermann U]]
-	[[Category: Nidetzky, B]]	+	[[Category: Sethi R]]
-	[[Category: Oppermann, U]]	+	[[Category: Weigelt J]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Yue WW]]
-	[[Category: Sethi, R]]	+	[[Category: Von Delft F]]
-	[[Category: Weigelt, J]]	+
-	[[Category: Yue~~, W W~~]]	+
-	[[Category: ~~Oxidoreductase]]~~	+
-	~~[[Category: Sgc]]~~	+
-	~~[[Category: Thiohemiacetal intermediate~~]]	+

OCA at 12:25, 13 October 2021

OCA — Wed, 13 Oct 2021 12:25:33 GMT

←Older revision		Revision as of 12:25, 13 October 2021
Line 1:		Line 1:

	==Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate==		==Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate==
-	<StructureSection load='3khu' size='340' side='right' caption='[[3khu]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3khu' size='340' side='right'caption='[[3khu]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3khu]] is a 6 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=3KHU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3KHU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3khu]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KHU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3itk\|3itk]], [[2q3e\|2q3e]], [[2qg4\|2qg4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3itk\|3itk]], [[2q3e\|2q3e]], [[2qg4\|2qg4]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UGDH ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UGDH ([https://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/UDP-glucose_6-dehydrogenase UDP-glucose 6-dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/UDP-glucose_6-dehydrogenase UDP-glucose 6-dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22] </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=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [~~http~~://pdbe.org/3khu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3khu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3khu 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=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [https://pdbe.org/3khu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [https://www.ebi.ac.uk/pdbsum/3khu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3khu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/UGDH_HUMAN UGDH_HUMAN]] Involved in the biosynthesis of glycosaminoglycans; hyaluronan, chondroitin sulfate, and heparan sulfate.	+	[[https://www.uniprot.org/uniprot/UGDH_HUMAN UGDH_HUMAN]] Involved in the biosynthesis of glycosaminoglycans; hyaluronan, chondroitin sulfate, and heparan sulfate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: UDP-glucose 6-dehydrogenase]]		[[Category: UDP-glucose 6-dehydrogenase]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]

OCA at 09:42, 26 December 2018

OCA — Wed, 26 Dec 2018 09:42:37 GMT

←Older revision		Revision as of 09:42, 26 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate==		==Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate==
	<StructureSection load='3khu' size='340' side='right' caption='[[3khu]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3khu' size='340' side='right' caption='[[3khu]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UGDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UGDH ([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/UDP-glucose_6-dehydrogenase UDP-glucose 6-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_6-dehydrogenase UDP-glucose 6-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22] </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=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [http://pdbe.org/3khu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [http://www.ebi.ac.uk/pdbsum/3khu 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=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [http://pdbe.org/3khu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [http://www.ebi.ac.uk/pdbsum/3khu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3khu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/3khu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/3khu_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 03:22, 8 February 2016

OCA — Mon, 08 Feb 2016 03:22:53 GMT

←Older revision		Revision as of 03:22, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3khu' size='340' side='right' caption='[[3khu]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3khu' size='340' side='right' caption='[[3khu]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3khu]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KHU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3khu]] is a 6 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=3KHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KHU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3itk\|3itk]], [[2q3e\|2q3e]], [[2qg4\|2qg4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3itk\|3itk]], [[2q3e\|2q3e]], [[2qg4\|2qg4]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UGDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UGDH ([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/UDP-glucose_6-dehydrogenase UDP-glucose 6-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_6-dehydrogenase UDP-glucose 6-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22] </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=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [http://www.ebi.ac.uk/pdbsum/3khu 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=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [http://pdbe.org/3khu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [http://www.ebi.ac.uk/pdbsum/3khu PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3khu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3khu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: UDP-glucose 6-dehydrogenase]]		[[Category: UDP-glucose 6-dehydrogenase]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]

OCA at 20:13, 24 December 2014

OCA — Wed, 24 Dec 2014 20:13:18 GMT

←Older revision		Revision as of 20:13, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3khu]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KHU FirstGlance]. <br>		<table><tr><td colspan='2'>[[3khu]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KHU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3itk\|3itk]], [[2q3e\|2q3e]], [[2qg4\|2qg4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3itk\|3itk]], [[2q3e\|2q3e]], [[2qg4\|2qg4]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UGDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UGDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_6-dehydrogenase UDP-glucose 6-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_6-dehydrogenase UDP-glucose 6-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [http://www.ebi.ac.uk/pdbsum/3khu 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=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [http://www.ebi.ac.uk/pdbsum/3khu PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UGDH_HUMAN UGDH_HUMAN]] Involved in the biosynthesis of glycosaminoglycans; hyaluronan, chondroitin sulfate, and heparan sulfate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 25:		Line 27:
	Structural and kinetic evidence that the catalytic reaction of human UDP-glucose 6-dehydrogenase involves covalent thiohemiacetal and thioester enzyme intermediates.,Egger S, Chaikuad A, Klimacek M, Kavanagh KL, Oppermann U, Nidetzky B J Biol Chem. 2011 Nov 28. PMID:22123821<ref>PMID:22123821</ref>		Structural and kinetic evidence that the catalytic reaction of human UDP-glucose 6-dehydrogenase involves covalent thiohemiacetal and thioester enzyme intermediates.,Egger S, Chaikuad A, Klimacek M, Kavanagh KL, Oppermann U, Nidetzky B J Biol Chem. 2011 Nov 28. PMID:22123821<ref>PMID:22123821</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 33:		Line 35:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: UDP-glucose 6-dehydrogenase]]		[[Category: UDP-glucose 6-dehydrogenase]]
-	[[Category: Arrowsmith, C H.]]	+	[[Category: Arrowsmith, C H]]
-	[[Category: Bountra, C.]]	+	[[Category: Bountra, C]]
-	[[Category: Chaikuad, A.]]	+	[[Category: Chaikuad, A]]
-	[[Category: Delft, F von.]]	+	[[Category: Delft, F von]]
-	[[Category: Edwards, A M.]]	+	[[Category: Edwards, A M]]
-	[[Category: Egger, S.]]	+	[[Category: Egger, S]]
-	[[Category: Filippakopoulos, P.]]	+	[[Category: Filippakopoulos, P]]
-	[[Category: Guo, K.]]	+	[[Category: Guo, K]]
-	[[Category: Kavanagh, K L.]]	+	[[Category: Kavanagh, K L]]
-	[[Category: Muniz, J R.C.]]	+	[[Category: Muniz, J R.C]]
-	[[Category: Nidetzky, B.]]	+	[[Category: Nidetzky, B]]
-	[[Category: Oppermann, U.]]	+	[[Category: Oppermann, U]]
-	[[Category: ~~SGC,~~ Structural ~~Genomics Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sethi, R.]]	+	[[Category: Sethi, R]]
-	[[Category: Weigelt, J.]]	+	[[Category: Weigelt, J]]
-	[[Category: Yue, W W.]]	+	[[Category: Yue, W W]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Sgc]]		[[Category: Sgc]]
-	[[Category: Structural genomic]]
-	[[Category: Structural genomics consortium]]
	[[Category: Thiohemiacetal intermediate]]		[[Category: Thiohemiacetal intermediate]]

OCA at 09:50, 21 May 2014

OCA — Wed, 21 May 2014 09:50:23 GMT

←Older revision		Revision as of 09:50, 21 May 2014
Line 1:		Line 1:
-	[[~~Image:~~3khu.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate==
		+	<StructureSection load='3khu' size='340' side='right' caption='[[3khu]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3khu]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KHU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3itk\|3itk]], [[2q3e\|2q3e]], [[2qg4\|2qg4]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UGDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_6-dehydrogenase UDP-glucose 6-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3khu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3khu RCSB], [http://www.ebi.ac.uk/pdbsum/3khu PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/3khu_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Biosynthesis of UDP-glucuronic acid by UDP-glucose 6-dehydrogenase (UGDH)5 occurs through four-electron oxidation of the C6 primary alcohol of UDP-glucose in two NAD+-dependent steps. The catalytic reaction of UGDH is thought to involve a Cys nucleophile that promotes formation of a thiohemiacetal enzyme intermediate in the course of the first oxidation step. The thiohemiacetal undergoes further oxidation into a thioester, and hydrolysis of the thioester completes the catalytic cycle. Herein we present crystallographic and kinetic evidence for the human form of UGDH that clarifies participation of covalent catalysis in the enzymatic mechanism. Substitution of the putative catalytic base for water attack on thioester (Glu161) by an incompetent analog (Gln161) gave a UGDH variant (E161Q) in which the hydrolysis step had become completely rate limiting so that a thioester enzyme intermediate accumulated at steady state. Using crystallization of E161Q in the presence of 5 mM UDP-glucose and 2 mM NAD+, we succeeded in intercepting a thiohemiacetal enzyme intermediate and determined its structure at 2.3 Angstrom resolution. Cys276 was covalently modified in the structure, establishing a role for it as catalytic nucelophile of the reaction. The reactive C6 of thiohemiacetal was in a position suitable to become further oxidized by hydride transfer to NAD+. The proposed catalytic mechanism of human UGDH involves Lys220 as general base for alcohol oxidation on UDP-glucose and as oxyanion stabilizer during formation and breakdown of the thiohemiacetal and thioester enzyme intermediates. Water bonded to Asp280 deprotonates Cys276 for function as aldehyde trap and also provides oxyanion stabilization. Glu161 is the Bronsted base catalytically promoting the thioester hydrolysis.

-	<!--	+	Structural and kinetic evidence that the catalytic reaction of human UDP-glucose 6-dehydrogenase involves covalent thiohemiacetal and thioester enzyme intermediates.,Egger S, Chaikuad A, Klimacek M, Kavanagh KL, Oppermann U, Nidetzky B J Biol Chem. 2011 Nov 28. PMID:22123821<ref>PMID:22123821</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3khu"~~, ~~creates the "Structure Box" on the page.~~	+
-	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded)~~,	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3khu\| PDB=3khu \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22123821}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22123821 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22123821}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3khu]] is a 6 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022123821<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: UDP-glucose 6-dehydrogenase]]		[[Category: UDP-glucose 6-dehydrogenase]]

OCA at 05:39, 11 January 2012

OCA — Wed, 11 Jan 2012 05:39:54 GMT

←Older revision		Revision as of 05:39, 11 January 2012
Line 11:		Line 11:
	===Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate===		===Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22123821}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22123821 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22123821}}

	==About this Structure==		==About this Structure==
	[[3khu]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA].		[[3khu]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022123821</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: UDP-glucose 6-dehydrogenase]]		[[Category: UDP-glucose 6-dehydrogenase]]

OCA: Protected "3khu" [edit=sysop:move=sysop]

OCA — Wed, 07 Dec 2011 07:15:09 GMT

Protected "3khu" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:15, 7 December 2011

OCA at 07:15, 7 December 2011

OCA — Wed, 07 Dec 2011 07:15:06 GMT

←Older revision		Revision as of 07:15, 7 December 2011
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3khu.png\|left\|200px]]
-	[[Image:3khu.~~jpg~~\|left\|200px]]	+

	<!--		<!--
Line 14:		Line 13:

	==About this Structure==		==About this Structure==
-	~~3KHU~~ is a 6 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA].	+	[[3khu]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHU OCA].
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: UDP-glucose 6-dehydrogenase]]		[[Category: UDP-glucose 6-dehydrogenase]]
Line 38:		Line 37:
	[[Category: Structural genomics consortium]]		[[Category: Structural genomics consortium]]
	[[Category: Thiohemiacetal intermediate]]		[[Category: Thiohemiacetal intermediate]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 18 20:23:48 2009''

OCA: New page: {{Seed}} 200px