4ur8 - Revision history

OCA at 10:33, 10 January 2024

OCA — Wed, 10 Jan 2024 10:33:44 GMT

←Older revision		Revision as of 10:33, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ur8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UR8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ur8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UR8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=OOG:2-OXOADIPIC+ACID'>OOG</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]] 2.097Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=OOG:2-OXOADIPIC+ACID'>OOG</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur8 OCA], [https://pdbe.org/4ur8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ur8 RCSB], [https://www.ebi.ac.uk/pdbsum/4ur8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ur8 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=4ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur8 OCA], [https://pdbe.org/4ur8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ur8 RCSB], [https://www.ebi.ac.uk/pdbsum/4ur8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ur8 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:33, 29 March 2023

OCA — Wed, 29 Mar 2023 07:33:40 GMT

←Older revision		Revision as of 07:33, 29 March 2023
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	<StructureSection load='4ur8' size='340' side='right'caption='[[4ur8]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4ur8' size='340' side='right'caption='[[4ur8]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ur8]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UR8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4UR8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ur8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UR8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=OOG:2-OXOADIPIC+ACID'>OOG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=OOG:2-OXOADIPIC+ACID'>OOG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ur5\|4ur5]], [[4ur7\|4ur7]]~~</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=4ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur8 OCA], [https://pdbe.org/4ur8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ur8 RCSB], [https://www.ebi.ac.uk/pdbsum/4ur8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ur8 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=4ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur8 OCA], [~~http~~://pdbe.org/4ur8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ur8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ur8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ur8 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KDGD_AGRFC KDGD_AGRFC]
	<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: Agrobacterium tumefaciens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hakulinen, N]]	+	[[Category: Hakulinen N]]
-	[[Category: Parkkinen, T]]	+	[[Category: Parkkinen T]]
-	[[Category: Rouvinen, J]]	+	[[Category: Rouvinen J]]
-	[[Category: Taberman, H]]	+	[[Category: Taberman H]]
-	~~[[Category: Biocatalysis]]~~	+
-	~~[[Category: D-galacturonic acid]]~~	+
-	~~[[Category: Decarboxylate]]~~	+
-	~~[[Category: Dehydratase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Oxidative pathway~~]]	+

OCA at 09:10, 21 May 2019

OCA — Tue, 21 May 2019 09:10:35 GMT

←Older revision		Revision as of 09:10, 21 May 2019
Line 1:		Line 1:

	==Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid==		==Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid==
-	<StructureSection load='4ur8' size='340' side='right' caption='[[4ur8]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='4ur8' size='340' side='right'caption='[[4ur8]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ur8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UR8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ur8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UR8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=OOG:2-OXOADIPIC+ACID'>OOG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=OOG:2-OXOADIPIC+ACID'>OOG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ur5\|4ur5]], [[4ur7\|4ur7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ur5\|4ur5]], [[4ur7\|4ur7]]</td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Hakulinen, N]]		[[Category: Hakulinen, N]]
	[[Category: Parkkinen, T]]		[[Category: Parkkinen, T]]

OCA at 10:23, 11 August 2016

OCA — Thu, 11 Aug 2016 10:23:58 GMT

←Older revision		Revision as of 10:23, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid==		==Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid==
	<StructureSection load='4ur8' size='340' side='right' caption='[[4ur8]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4ur8' size='340' side='right' caption='[[4ur8]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=OOG:2-OXOADIPIC+ACID'>OOG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=OOG:2-OXOADIPIC+ACID'>OOG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ur5\|4ur5]], [[4ur7\|4ur7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ur5\|4ur5]], [[4ur7\|4ur7]]</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=4ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ur8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ur8 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=4ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur8 OCA], [http://pdbe.org/4ur8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ur8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ur8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ur8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4ur8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:00, 28 January 2015

OCA — Wed, 28 Jan 2015 11:00:32 GMT

←Older revision		Revision as of 11:00, 28 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ur8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UR8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ur8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UR8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~CCU~~:~~(2Z,4Z)-HEXA-2,4-DIENEDIOIC~~+ACID'>~~CCU~~</scene>, <scene name='pdbligand=~~FMT~~:~~FORMIC~~+ACID'>~~FMT~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=OOG:2-OXOADIPIC+ACID'>OOG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ur5\|4ur5]], [[4ur7\|4ur7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ur5\|4ur5]], [[4ur7\|4ur7]]</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=4ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ur8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ur8 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=4ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ur8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ur8 PDBsum]</span></td></tr>

OCA at 12:44, 17 December 2014

OCA — Wed, 17 Dec 2014 12:44:47 GMT

←Older revision		Revision as of 12:44, 17 December 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid==
		+	<StructureSection load='4ur8' size='340' side='right' caption='[[4ur8]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ur8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UR8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCU:(2Z,4Z)-HEXA-2,4-DIENEDIOIC+ACID'>CCU</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ur5\|4ur5]], [[4ur7\|4ur7]]</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=4ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ur8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ur8 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Agrobacterium tumefaciens (At) strain C58 contains an oxidative enzyme pathway that can function on both D-glucuronic and D-galacturonic acid. The corresponding gene coding for At KDG dehydratase is located in the same gene cluster as those coding for uronate dehydrogenase (At Udh) and galactarolactone cycloisomerase (At Gci) which we have previously characterised. Here, we present the kinetic characterisation and crystal structure of At keto-deoxy-D-galactarate (KDG, 3-deoxy-2-keto-L-threo-hexulosarate) dehydratase, which catalyses the next step, the decarboxylating hydrolyase reaction of KDG to produce alpha-ketoglutaric semialdehyde (alpha-KGSA) and carbon dioxide. The crystal structures of At KDG dehydratase and its complexes with pyruvate and 2-oxoadipic acid, two substrate analogues, were determined to 1.7 A, 1.5 A, and 2.1 A resolutions, respectively. Furthermore, mass spectrometry was used to confirm reaction end-products. The results lead us to propose a structure-based mechanism for At KDG dehydratase, suggesting that while the enzyme belongs to the Class I aldolase protein family, it does not follow a typical retro-aldol condensation mechanism.

-	The ~~entry 4ur8 is ON HOLD until Paper Publication~~	+	The Structure and Function of a Decarboxylating Agrobacterium tumefaciens Keto-deoxy-D-galactarate Dehydratase.,Taberman H, Andberg MB, Parkkinen T, Janis J, Penttila M, Hakulinen N, Koivula A, Rouvinen J Biochemistry. 2014 Dec 2. PMID:25454257<ref>PMID:25454257</ref>

-	~~Authors: Taberman~~, H.~~, Parkkinen, T~~., Hakulinen, N., Rouvinen, J.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of keto-deoxy-~~D-~~galactarate dehydratase complexed with 2-oxoadipic~~ acid	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hakulinen, N]]
		+	[[Category: Parkkinen, T]]
		+	[[Category: Rouvinen, J]]
		+	[[Category: Taberman, H]]
		+	[[Category: Biocatalysis]]
		+	[[Category: D-galacturonic acid]]
		+	[[Category: Decarboxylate]]
		+	[[Category: Dehydratase]]
		+	[[Category: Lyase]]
		+	[[Category: Oxidative pathway]]

OCA at 07:02, 9 July 2014

OCA — Wed, 09 Jul 2014 07:02:44 GMT

←Older revision		Revision as of 07:02, 9 July 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ur8 is ON HOLD until ~~sometime in the future~~	+	The entry 4ur8 is ON HOLD until Paper Publication

	Authors: Taberman, H., Parkkinen, T., Hakulinen, N., Rouvinen, J.		Authors: Taberman, H., Parkkinen, T., Hakulinen, N., Rouvinen, J.

	Description: Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid		Description: Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid

OCA: Protected "4ur8" [edit=sysop:move=sysop]

OCA — Wed, 02 Jul 2014 07:38:38 GMT

Protected "4ur8" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:38, 2 July 2014

OCA: New page: '''Unreleased structure''' The entry 4ur8 is ON HOLD until sometime in the future Authors: Taberman, H., Parkkinen, T., Hakulinen, N., Rouvinen, J. Description: Crystal structure of ke...

OCA — Wed, 02 Jul 2014 07:38:37 GMT

New page: '''Unreleased structure''' The entry 4ur8 is ON HOLD until sometime in the future Authors: Taberman, H., Parkkinen, T., Hakulinen, N., Rouvinen, J. Description: Crystal structure of ke...

New page

'''Unreleased structure'''

The entry 4ur8 is ON HOLD until sometime in the future

Authors: Taberman, H., Parkkinen, T., Hakulinen, N., Rouvinen, J.

Description: Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid