4bc2 - Revision history

OCA at 08:20, 23 October 2024

2024-10-23T08:20:07Z

← Older revision		Revision as of 08:20, 23 October 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/XYLB_HUMAN XYLB_HUMAN] Phosphorylates D-xylulose to produce D-xylulose 5-phosphate, a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis.<ref>PMID:23179721</ref>		[https://www.uniprot.org/uniprot/XYLB_HUMAN XYLB_HUMAN] Phosphorylates D-xylulose to produce D-xylulose 5-phosphate, a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis.<ref>PMID:23179721</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			D-Xylulokinase (XK; EC 2.7.1.17) catalyzes the ATP-dependent phosphorylation of D-xylulose (Xu) to produce xylulose-5-phosphate (Xu5P). In mammals, XK is the last enzyme in the glucuronate-xylulose pathway, active in the liver and kidneys, and is linked through its product Xu5P to the pentose phosphate pathway. XK may play an important role in metabolic disease, given that Xu5P is a key regulator of glucose metabolism and lipogenesis. We have expressed the product of a putative human XK gene, and identified it as the authentic human D-xylulokinase (hXK). NMR studies with a variety of sugars showed that hXK acts only on D-xylulose, and a coupled photometric assay established its key kinetic parameters as KM(Xu) = 24 +/- 3 muM and kcat = 35 +/- 5 s-1. Crystal structures were determined for hXK, on its own and in complexes with Xu, ADP and a fluorinated inhibitor. These reveal that hXK has two-domain fold characteristic of the sugar kinase/hsp70/actin superfamily, with glycerol kinase as its closest relative. Xu binds to domain-I and ADP to domain-II, but in this open form of hXK they are 10 A apart, implying that a large-scale conformational change is required for catalysis. Xu binds in its linear keto form, sandwiched between a Trp side chain and polar side chains that provide exquisite hydrogen bonding recognition. The hXK structure provides a basis for the design of specific inhibitors with which to probe its roles in sugar metabolism and metabolic disease.

			Structure and function of human xylulokinase, an enzyme with important roles in carbohydrate metabolism.,Bunker RD, Bulloch EM, Dickson JM, Loomes KM, Baker EN J Biol Chem. 2012 Nov 23. PMID:23179721<ref>PMID:23179721</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 4bc2" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:17, 1 May 2024

2024-05-01T07:17:35Z

← Older revision		Revision as of 07:17, 1 May 2024
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	<StructureSection load='4bc2' size='340' side='right'caption='[[4bc2]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='4bc2' size='340' side='right'caption='[[4bc2]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4bc2]] is a 3 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=4BC2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BC2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4bc2]] is a 3 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=4BC2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BC2 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</scene>~~, ~~<scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=XUL:D-XYLULOSE'>XUL</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]] 1.97Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=XUL:D-XYLULOSE'>XUL</scene></td></tr>
	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"><div style~~=~~'overflow~~: ~~auto; max-height: 3em;~~'>~~[[4b6t\|4b6t]], [[4b6y\|4b6y]], [[4bc3\|4bc3]], [[4bc4\|4bc4]], [[4bc5\|4bc5]]~~</~~div~~><~~/td></tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Xylulokinase Xylulokinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.17 2.7.1.17]~~ </~~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=4bc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bc2 OCA], [https://pdbe.org/4bc2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bc2 RCSB], [https://www.ebi.ac.uk/pdbsum/4bc2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bc2 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=4bc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bc2 OCA], [https://pdbe.org/4bc2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bc2 RCSB], [https://www.ebi.ac.uk/pdbsum/4bc2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bc2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/XYLB_HUMAN XYLB_HUMAN]] Phosphorylates D-xylulose to produce D-xylulose 5-phosphate, a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis.<ref>PMID:23179721</ref>		[https://www.uniprot.org/uniprot/XYLB_HUMAN XYLB_HUMAN] Phosphorylates D-xylulose to produce D-xylulose 5-phosphate, a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis.<ref>PMID:23179721</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	D-Xylulokinase (XK; EC 2.7.1.17) catalyzes the ATP-dependent phosphorylation of D-xylulose (Xu) to produce xylulose-5-phosphate (Xu5P). In mammals, XK is the last enzyme in the glucuronate-xylulose pathway, active in the liver and kidneys, and is linked through its product Xu5P to the pentose phosphate pathway. XK may play an important role in metabolic disease, given that Xu5P is a key regulator of glucose metabolism and lipogenesis. We have expressed the product of a putative human XK gene, and identified it as the authentic human D-xylulokinase (hXK). NMR studies with a variety of sugars showed that hXK acts only on D-xylulose, and a coupled photometric assay established its key kinetic parameters as KM(Xu) = 24 +/- 3 muM and kcat = 35 +/- 5 s-1. Crystal structures were determined for hXK, on its own and in complexes with Xu, ADP and a fluorinated inhibitor. These reveal that hXK has two-domain fold characteristic of the sugar kinase/hsp70/actin superfamily, with glycerol kinase as its closest relative. Xu binds to domain-I and ADP to domain-II, but in this open form of hXK they are 10 A apart, implying that a large-scale conformational change is required for catalysis. Xu binds in its linear keto form, sandwiched between a Trp side chain and polar side chains that provide exquisite hydrogen bonding recognition. The hXK structure provides a basis for the design of specific inhibitors with which to probe its roles in sugar metabolism and metabolic disease.

	Structure and function of human xylulokinase, an enzyme with important roles in carbohydrate metabolism.,Bunker RD, Bulloch EM, Dickson JM, Loomes KM, Baker EN J Biol Chem. 2012 Nov 23. PMID:23179721<ref>PMID:23179721</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4bc2" style="background-color:#fffaf0;"></div~~>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Xylulokinase]]~~		[[Category: Baker EN]]
	[[Category: Baker~~, E N~~]]		[[Category: Bunker RD]]
	[[Category: Bunker~~, R D~~]]		[[Category: Loomes KM]]
	[[Category: Loomes~~, K M]]~~
	~~[[Category: Fggy carbohydrate kinase]]~~
	~~[[Category: Glucuronate xylulokinase pathway]]~~
	~~[[Category: Transferase~~]]

OCA at 07:07, 31 August 2022

2022-08-31T07:07:36Z

OCA at 14:14, 8 July 2020

2020-07-08T14:14:16Z

← Older revision		Revision as of 14:14, 8 July 2020
Line 3:		Line 3:
	<StructureSection load='4bc2' size='340' side='right'caption='[[4bc2]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='4bc2' size='340' side='right'caption='[[4bc2]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4bc2]] is a 3 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=4BC2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4BC2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4bc2]] is a 3 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=4BC2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4BC2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=XUL:D-XYLULOSE'>XUL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=XUL:D-XYLULOSE'>XUL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4b6t\|4b6t]], [[4b6y\|4b6y]], [[4bc3\|4bc3]], [[4bc4\|4bc4]], [[4bc5\|4bc5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4b6t\|4b6t]], [[4b6y\|4b6y]], [[4bc3\|4bc3]], [[4bc4\|4bc4]], [[4bc5\|4bc5]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylulokinase Xylulokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.17 2.7.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylulokinase Xylulokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.17 2.7.1.17] </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=4bc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bc2 OCA], [http://pdbe.org/4bc2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4bc2 RCSB], [http://www.ebi.ac.uk/pdbsum/4bc2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4bc2 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=4bc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bc2 OCA], [http://pdbe.org/4bc2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4bc2 RCSB], [http://www.ebi.ac.uk/pdbsum/4bc2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4bc2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 14:00, 13 March 2019

2019-03-13T14:00:09Z

← Older revision		Revision as of 14:00, 13 March 2019
Line 1:		Line 1:

	==Crystal structure of human D-xylulokinase in complex with D-xylulose and adenosine diphosphate==		==Crystal structure of human D-xylulokinase in complex with D-xylulose and adenosine diphosphate==
	<StructureSection load='4bc2' size='340' side='right' caption='[[4bc2]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='4bc2' size='340' side='right'caption='[[4bc2]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4bc2]] is a 3 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=4BC2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BC2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4bc2]] is a 3 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=4BC2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BC2 FirstGlance]. <br>
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Xylulokinase]]		[[Category: Xylulokinase]]
	[[Category: Baker, E N]]		[[Category: Baker, E N]]

OCA at 20:00, 4 August 2016

2016-08-04T20:00:15Z

← Older revision		Revision as of 20:00, 4 August 2016
Line 1:		Line 1:

	==Crystal structure of human D-xylulokinase in complex with D-xylulose and adenosine diphosphate==		==Crystal structure of human D-xylulokinase in complex with D-xylulose and adenosine diphosphate==
	<StructureSection load='4bc2' size='340' side='right' caption='[[4bc2]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='4bc2' size='340' side='right' caption='[[4bc2]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4bc2]] is a 3 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=4BC2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BC2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4bc2]] is a 3 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=4BC2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BC2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=XUL:D-XYLULOSE'>XUL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=XUL:D-XYLULOSE'>XUL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4b6t\|4b6t]], [[4b6y\|4b6y]], [[4bc3\|4bc3]], [[4bc4\|4bc4]], [[4bc5\|4bc5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4b6t\|4b6t]], [[4b6y\|4b6y]], [[4bc3\|4bc3]], [[4bc4\|4bc4]], [[4bc5\|4bc5]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylulokinase Xylulokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.17 2.7.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylulokinase Xylulokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.17 2.7.1.17] </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=4bc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bc2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bc2 RCSB], [http://www.ebi.ac.uk/pdbsum/4bc2 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=4bc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bc2 OCA], [http://pdbe.org/4bc2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4bc2 RCSB], [http://www.ebi.ac.uk/pdbsum/4bc2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4bc2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4bc2" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Xylulokinase]]		[[Category: Xylulokinase]]
	[[Category: Baker, E N]]		[[Category: Baker, E N]]

OCA at 19:05, 24 December 2014

2014-12-24T19:05:02Z

← Older revision		Revision as of 19:05, 24 December 2014
Line 9:		Line 9:
	<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=4bc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bc2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bc2 RCSB], [http://www.ebi.ac.uk/pdbsum/4bc2 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=4bc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bc2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bc2 RCSB], [http://www.ebi.ac.uk/pdbsum/4bc2 PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/XYLB_HUMAN XYLB_HUMAN]] Phosphorylates D-xylulose to produce D-xylulose 5-phosphate, a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis.<ref>PMID:23179721</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 16:15, 9 December 2014

2014-12-09T16:15:55Z

← Older revision		Revision as of 16:15, 9 December 2014
Line 1:		Line 1:
	[[~~Image~~:~~4bc2~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of human D-xylulokinase in complex with D-xylulose and adenosine diphosphate==
			<StructureSection load='4bc2' size='340' side='right' caption='[[4bc2]], [[Resolution\|resolution]] 1.97Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4bc2]] is a 3 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=4BC2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BC2 FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=XUL:D-XYLULOSE'>XUL</scene></td></tr>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4b6t\|4b6t]], [[4b6y\|4b6y]], [[4bc3\|4bc3]], [[4bc4\|4bc4]], [[4bc5\|4bc5]]</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylulokinase Xylulokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.17 2.7.1.17] </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=4bc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bc2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bc2 RCSB], [http://www.ebi.ac.uk/pdbsum/4bc2 PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			D-Xylulokinase (XK; EC 2.7.1.17) catalyzes the ATP-dependent phosphorylation of D-xylulose (Xu) to produce xylulose-5-phosphate (Xu5P). In mammals, XK is the last enzyme in the glucuronate-xylulose pathway, active in the liver and kidneys, and is linked through its product Xu5P to the pentose phosphate pathway. XK may play an important role in metabolic disease, given that Xu5P is a key regulator of glucose metabolism and lipogenesis. We have expressed the product of a putative human XK gene, and identified it as the authentic human D-xylulokinase (hXK). NMR studies with a variety of sugars showed that hXK acts only on D-xylulose, and a coupled photometric assay established its key kinetic parameters as KM(Xu) = 24 +/- 3 muM and kcat = 35 +/- 5 s-1. Crystal structures were determined for hXK, on its own and in complexes with Xu, ADP and a fluorinated inhibitor. These reveal that hXK has two-domain fold characteristic of the sugar kinase/hsp70/actin superfamily, with glycerol kinase as its closest relative. Xu binds to domain-I and ADP to domain-II, but in this open form of hXK they are 10 A apart, implying that a large-scale conformational change is required for catalysis. Xu binds in its linear keto form, sandwiched between a Trp side chain and polar side chains that provide exquisite hydrogen bonding recognition. The hXK structure provides a basis for the design of specific inhibitors with which to probe its roles in sugar metabolism and metabolic disease.

	~~{{STRUCTURE_4bc2\| PDB=4bc2 \| SCENE= }}~~		Structure and function of human xylulokinase, an enzyme with important roles in carbohydrate metabolism.,Bunker RD, Bulloch EM, Dickson JM, Loomes KM, Baker EN J Biol Chem. 2012 Nov 23. PMID:23179721<ref>PMID:23179721</ref>

	~~===Crystal structure~~ of ~~human D-xylulokinase in complex with D-xylulose and adenosine diphosphate===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_23179721}}~~		== References ==
			<references/>
	==~~About this Structure~~==		__TOC__
	~~[[4bc2]] is a 3 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=4BC2 OCA].~~		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Xylulokinase]]		[[Category: Xylulokinase]]
	[[Category: Baker, E N.]]		[[Category: Baker, E N]]
	[[Category: Bunker, R D.]]		[[Category: Bunker, R D]]
	[[Category: Loomes, K M.]]		[[Category: Loomes, K M]]
	[[Category: Fggy carbohydrate kinase]]		[[Category: Fggy carbohydrate kinase]]
	[[Category: Glucuronate xylulokinase pathway]]		[[Category: Glucuronate xylulokinase pathway]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 10:40, 19 December 2012

2012-12-19T10:40:01Z

← Older revision		Revision as of 10:40, 19 December 2012
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	===Crystal structure of human D-xylulokinase in complex with D-xylulose and adenosine diphosphate===		===Crystal structure of human D-xylulokinase in complex with D-xylulose and adenosine diphosphate===

			{{ABSTRACT_PUBMED_23179721}}

	==About this Structure==		==About this Structure==

OCA at 10:06, 5 December 2012

2012-12-05T10:06:51Z

← Older revision		Revision as of 10:06, 5 December 2012
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	[[Image:4bc2.~~jpg~~\|left\|200px]]		[[Image:4bc2.png\|left\|200px]]

	{{STRUCTURE_4bc2\| PDB=4bc2 \| SCENE= }}		{{STRUCTURE_4bc2\| PDB=4bc2 \| SCENE= }}

← Older revision		Revision as of 07:07, 31 August 2022
Line 3:		Line 3:
	<StructureSection load='4bc2' size='340' side='right'caption='[[4bc2]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='4bc2' size='340' side='right'caption='[[4bc2]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4bc2]] is a 3 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=4BC2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=4BC2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4bc2]] is a 3 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=4BC2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BC2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=XUL:D-XYLULOSE'>XUL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=XUL:D-XYLULOSE'>XUL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4b6t\|4b6t]], [[4b6y\|4b6y]], [[4bc3\|4bc3]], [[4bc4\|4bc4]], [[4bc5\|4bc5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4b6t\|4b6t]], [[4b6y\|4b6y]], [[4bc3\|4bc3]], [[4bc4\|4bc4]], [[4bc5\|4bc5]]</div></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Xylulokinase Xylulokinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.17 2.7.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xylulokinase Xylulokinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.17 2.7.1.17] </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=4bc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bc2 OCA], [~~http~~://pdbe.org/4bc2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4bc2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4bc2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4bc2 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=4bc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bc2 OCA], [https://pdbe.org/4bc2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bc2 RCSB], [https://www.ebi.ac.uk/pdbsum/4bc2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bc2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/XYLB_HUMAN XYLB_HUMAN]] Phosphorylates D-xylulose to produce D-xylulose 5-phosphate, a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis.<ref>PMID:23179721</ref>		[[https://www.uniprot.org/uniprot/XYLB_HUMAN XYLB_HUMAN]] Phosphorylates D-xylulose to produce D-xylulose 5-phosphate, a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis.<ref>PMID:23179721</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==