5j84 - Revision history

OCA at 10:53, 6 September 2023

OCA — Wed, 06 Sep 2023 10:53:13 GMT

←Older revision		Revision as of 10:53, 6 September 2023
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	==Crystal structure of L-arabinonate dehydratase in holo-form==		==Crystal structure of L-arabinonate dehydratase in holo-form==
-	<StructureSection load='5j84' size='340' side='right' caption='[[5j84]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5j84' size='340' side='right'caption='[[5j84]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j84]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhilw Rhilw~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J84 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J84 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j84]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhizobium_leguminosarum_bv._trifolii_WSM2304 Rhizobium leguminosarum bv. trifolii WSM2304]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J84 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene~~>, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.4Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~KCX~~:~~LYSINE~~+~~NZ-CARBOXYLIC~~+~~ACID~~'>~~KCX~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Rleg2_2909 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=395492 RHILW])~~, ~~6981653 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=395492 RHILW])~~<~~/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=5j84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j84 OCA], [https://pdbe.org/5j84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j84 RCSB], [https://www.ebi.ac.uk/pdbsum/5j84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j84 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/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.9 4.2.1.9]~~ </~~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=5j84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j84 OCA], [~~http~~://pdbe.org/5j84 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j84 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j84 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j84 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ARAD_RHILW ARAD_RHILW] Catalyzes the dehydration of L-arabinonate to 2-dehydro-3-deoxy-L-arabinonate during L-arabinose degradation. Can also dehydrate D-galactonate and D-fuconate with good catalytic efficiency. Has weak activity with D-xylonate and D-gluconate.<ref>PMID:27102126</ref>
	<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: ~~Lyase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Rhilw~~]]	+	[[Category: Rhizobium leguminosarum bv. trifolii WSM2304]]
-	[[Category: Hakulinen, N]]	+	[[Category: Hakulinen N]]
-	[[Category: Rahman~~, M M~~]]	+	[[Category: Rahman MM]]
-	[[Category: Rouvinen, J]]	+	[[Category: Rouvinen J]]
-	~~[[Category: 2fe2s cluster]]~~	+
-	~~[[Category: L-arabinonate dehydratase]]~~	+
-	~~[[Category: L-arabonate dehydratase]]~~	+
-	~~[[Category: Pentonate dehydratase~~]]	+

OCA at 08:37, 10 January 2018

OCA — Wed, 10 Jan 2018 08:37:01 GMT

←Older revision		Revision as of 08:37, 10 January 2018
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	<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=5j84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j84 OCA], [http://pdbe.org/5j84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j84 RCSB], [http://www.ebi.ac.uk/pdbsum/5j84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j84 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=5j84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j84 OCA], [http://pdbe.org/5j84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j84 RCSB], [http://www.ebi.ac.uk/pdbsum/5j84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j84 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-l-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg(2+) ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of l-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.
		+
		+	The Crystal Structure of a Bacterial l-Arabinonate Dehydratase Contains a [2Fe-2S] Cluster.,Rahman MM, Andberg M, Thangaraj SK, Parkkinen T, Penttila M, Janis J, Koivula A, Rouvinen J, Hakulinen N ACS Chem Biol. 2017 Jul 21;12(7):1919-1927. doi: 10.1021/acschembio.7b00304. Epub, 2017 Jun 13. PMID:28574691<ref>PMID:28574691</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5j84" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:34, 16 November 2017

OCA — Thu, 16 Nov 2017 08:34:22 GMT

←Older revision		Revision as of 08:34, 16 November 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5j84 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of L-arabinonate dehydratase in holo-form==
-		+	<StructureSection load='5j84' size='340' side='right' caption='[[5j84]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~: ~~Rahman~~, M.M., ~~Rouvinen~~, J., ~~Hakulinen~~, N.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5j84]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhilw Rhilw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J84 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of L-arabinonate dehydratase in holo-form~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rleg2_2909 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=395492 RHILW]), 6981653 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=395492 RHILW])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.9 4.2.1.9] </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=5j84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j84 OCA], [http://pdbe.org/5j84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j84 RCSB], [http://www.ebi.ac.uk/pdbsum/5j84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j84 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lyase]]
		+	[[Category: Rhilw]]
	[[Category: Hakulinen, N]]		[[Category: Hakulinen, N]]
		+	[[Category: Rahman, M M]]
	[[Category: Rouvinen, J]]		[[Category: Rouvinen, J]]
-	[[Category: ~~Rahman, M.M~~]]	+	[[Category: 2fe2s cluster]]
		+	[[Category: L-arabinonate dehydratase]]
		+	[[Category: L-arabonate dehydratase]]
		+	[[Category: Pentonate dehydratase]]

OCA at 07:24, 19 April 2017

OCA — Wed, 19 Apr 2017 07:24:25 GMT

←Older revision		Revision as of 07:24, 19 April 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5j84 is ON HOLD	+	The entry 5j84 is ON HOLD until Paper Publication

	Authors: Rahman, M.M., Rouvinen, J., Hakulinen, N.		Authors: Rahman, M.M., Rouvinen, J., Hakulinen, N.

OCA at 09:48, 9 March 2017

OCA — Thu, 09 Mar 2017 09:48:44 GMT

←Older revision		Revision as of 09:48, 9 March 2017
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	Description: Crystal structure of L-arabinonate dehydratase in holo-form		Description: Crystal structure of L-arabinonate dehydratase in holo-form
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Rahman, M.M]]
	[[Category: Hakulinen, N]]		[[Category: Hakulinen, N]]
	[[Category: Rouvinen, J]]		[[Category: Rouvinen, J]]
		+	[[Category: Rahman, M.M]]

OCA: Protected "5j84" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:39:37 GMT

Protected "5j84" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:39, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j84 is ON HOLD Authors: Rahman, M.M., Rouvinen, J., Hakulinen, N. Description: Crystal structure of L-arabinonate dehydratase in holo-form [[Categ...

OCA — Wed, 11 May 2016 01:39:36 GMT

New page: '''Unreleased structure''' The entry 5j84 is ON HOLD Authors: Rahman, M.M., Rouvinen, J., Hakulinen, N. Description: Crystal structure of L-arabinonate dehydratase in holo-form [[Categ...

New page

'''Unreleased structure'''

The entry 5j84 is ON HOLD

Authors: Rahman, M.M., Rouvinen, J., Hakulinen, N.

Description: Crystal structure of L-arabinonate dehydratase in holo-form
[[Category: Unreleased Structures]]
[[Category: Rahman, M.M]]
[[Category: Hakulinen, N]]
[[Category: Rouvinen, J]]