6dxs - Revision history

OCA at 06:15, 11 October 2023

OCA — Wed, 11 Oct 2023 06:15:28 GMT

←Older revision		Revision as of 06:15, 11 October 2023
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	==Crystal structure of the LigJ hydratase E284Q mutant substrate complex with (3Z)-2-keto-4-carboxy-3-hexenedioate==		==Crystal structure of the LigJ hydratase E284Q mutant substrate complex with (3Z)-2-keto-4-carboxy-3-hexenedioate==
-	<StructureSection load='6dxs' size='340' side='right' caption='[[6dxs]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='6dxs' size='340' side='right'caption='[[6dxs]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dxs]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sphsk Sphsk~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dxs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingobium_sp._SYK-6 Sphingobium sp. SYK-6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DXS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=HJ7:(2Z)-4-oxobut-2-ene-1,2,4-tricarboxylic+acid'>HJ7</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.65Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[6dxq\|6dxq~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HJ7:(2Z)-4-oxobut-2-ene-1,2,4-tricarboxylic+acid'>HJ7</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ligJ, SLG_12520 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~627192 SPHSK])</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=6dxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxs OCA], [https://pdbe.org/6dxs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dxs RCSB], [https://www.ebi.ac.uk/pdbsum/6dxs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxs 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/4-oxalmesaconate_hydratase 4-oxalmesaconate hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.83 4.2.1.83]~~ </~~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=6dxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxs OCA], [~~http~~://pdbe.org/6dxs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dxs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dxs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxs ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/LIGJ_SPHSK LIGJ_SPHSK] Contributes to the degradation of lignin at the level of the protocatechuate 4,5-cleavage pathway. Catalyzes the hydration of the double bond of (3Z)-2-keto-4-carboxy-3-hexenedioate (KCH) to (4S)-4-carboxy-4-hydroxy-2-oxoadipate (CHA, also named (2S)-2-hydroxy-4-oxobutane-1,2,4-tricarboxylate) (PubMed:29658701, PubMed:30207699). Is involved in the catabolism of both vanillate and syringate (PubMed:11092855).<ref>PMID:11092855</ref> <ref>PMID:29658701</ref> <ref>PMID:30207699</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: ~~4-oxalmesaconate hydratase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Sphsk~~]]	+	[[Category: Sphingobium sp. SYK-6]]
-	[[Category: Hogancamp~~, T N~~]]	+	[[Category: Hogancamp TN]]
-	[[Category: Mabanglo~~, M F~~]]	+	[[Category: Mabanglo MF]]
-	[[Category: Raushel~~, F M]]~~	+	[[Category: Raushel FM]]
-	~~[[Category: Amidohydrolase]]~~	+
-	~~[[Category: Hydratase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Lyase-lyase inhibitor complex~~]]	+

OCA at 08:37, 17 October 2018

OCA — Wed, 17 Oct 2018 08:37:23 GMT

←Older revision		Revision as of 08:37, 17 October 2018
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	<StructureSection load='6dxs' size='340' side='right' caption='[[6dxs]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='6dxs' size='340' side='right' caption='[[6dxs]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dxs]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dxs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphsk Sphsk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DXS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HJ7:(2Z)-4-oxobut-2-ene-1,2,4-tricarboxylic+acid'>HJ7</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HJ7:(2Z)-4-oxobut-2-ene-1,2,4-tricarboxylic+acid'>HJ7</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dxq\|6dxq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dxq\|6dxq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ligJ, SLG_12520 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=627192 SPHSK])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-oxalmesaconate_hydratase 4-oxalmesaconate hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.83 4.2.1.83] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-oxalmesaconate_hydratase 4-oxalmesaconate hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.83 4.2.1.83] </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=6dxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxs OCA], [http://pdbe.org/6dxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dxs RCSB], [http://www.ebi.ac.uk/pdbsum/6dxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxs 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=6dxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxs OCA], [http://pdbe.org/6dxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dxs RCSB], [http://www.ebi.ac.uk/pdbsum/6dxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxs ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: 4-oxalmesaconate hydratase]]		[[Category: 4-oxalmesaconate hydratase]]
		+	[[Category: Sphsk]]
	[[Category: Hogancamp, T N]]		[[Category: Hogancamp, T N]]
	[[Category: Mabanglo, M F]]		[[Category: Mabanglo, M F]]

OCA at 08:06, 26 September 2018

OCA — Wed, 26 Sep 2018 08:06:01 GMT

←Older revision		Revision as of 08:06, 26 September 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6dxs is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the LigJ hydratase E284Q mutant substrate complex with (3Z)-2-keto-4-carboxy-3-hexenedioate==
		+	<StructureSection load='6dxs' size='340' side='right' caption='[[6dxs]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dxs]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DXS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HJ7:(2Z)-4-oxobut-2-ene-1,2,4-tricarboxylic+acid'>HJ7</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dxq\|6dxq]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-oxalmesaconate_hydratase 4-oxalmesaconate hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.83 4.2.1.83] </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=6dxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxs OCA], [http://pdbe.org/6dxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dxs RCSB], [http://www.ebi.ac.uk/pdbsum/6dxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxs ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	LigJ from the soil bacterium Sphingobium sp. SYK-6 catalyzes the reversible hydration of (3Z)-2-keto-4-carboxy-3-hexenedioate (KCH) to 4-carboxy-4-hydroxy-2-oxoadipate (CHA) in the degradation of lignin in the protocatechuate (PCA) 4,5-cleavage pathway. LigJ is a member of the amidohydrolase superfamily and an enzyme in cog2159. The three-dimensional crystal structure of wild-type LigJ was solved in the presence (PDB id: 6DXQ) and absence of the product CHA (PDB id: 6DWV). The protein folds as a distorted (beta/alpha)8-barrel and a single zinc ion is bound in the active site at the C-terminal end of the central beta-barrel. The product CHA is ligated to the zinc ion in the active site via the displacement of the side-chain carboxylate of Glu-284 and a single water molecule from the coordination shell of the metal center in LigJ. The product-bound structure reveals that the enzyme catalyzes the hydration of KCH with the formation of a chiral center at C4 with S-stereochemistry. The mutant E284Q was unable to catalyze the hydration of KCH to CHA and the structure of this mutant was determined in the presence of the substrate KCH (PDB id: 6DXS). Based on the structure of LigJ in the presence of KCH and CHA it is proposed that the side chain carboxylate of Glu-284 functions as a general base in the abstraction of a water molecule for nucleophilic attack at C4 of the substrate. The reaction is facilitated by the delocalization of the negative charge to the metal center via the carbonyl group at C2 of the substrate. C3 of the substrate is subsequently protonated by Glu-284 functioning as a general acid. The overall reaction occurs by the syn-addition of water to the double bond between C4 and C3 of the substrate KCH. The kinetic constants for the hydration of KCH to CHA by LigJ at pH 8.0 are 25 s-1 and 2.6 x 106 M-1 s-1 for kcat and kcat/Km, respectively.

-	~~Authors~~: ~~Mabanglo~~, ~~M.F~~., ~~Raushel~~, F.M.~~, Hogancamp, T~~.N.	+	Structure and Reaction Mechanism of the LigJ Hydratase: An Enzyme Critical for the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway.,Hogancamp TN, Mabanglo MF, Raushel FM Biochemistry. 2018 Sep 12. doi: 10.1021/acs.biochem.8b00713. PMID:30207699<ref>PMID:30207699</ref>

-	~~Description: Crystal structure~~ of the ~~LigJ hydratase E284Q mutant substrate complex with (3Z)~~-2-~~keto-4-carboxy-3-hexenedioate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Hogancamp, T.N]]	+	<div class="pdbe-citations 6dxs" style="background-color:#fffaf0;"></div>
-	[[Category: Mabanglo, M.F]]	+	== References ==
-	[[Category: Raushel, F.M]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 4-oxalmesaconate hydratase]]
		+	[[Category: Hogancamp, T N]]
		+	[[Category: Mabanglo, M F]]
		+	[[Category: Raushel, F M]]
		+	[[Category: Amidohydrolase]]
		+	[[Category: Hydratase]]
		+	[[Category: Lyase]]
		+	[[Category: Lyase-lyase inhibitor complex]]

OCA at 18:04, 19 September 2018

OCA — Wed, 19 Sep 2018 18:04:14 GMT

←Older revision		Revision as of 18:04, 19 September 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Mabanglo, M.F., Raushel, F.M., Hogancamp, T.N.		Authors: Mabanglo, M.F., Raushel, F.M., Hogancamp, T.N.

OCA at 05:57, 12 September 2018

OCA — Wed, 12 Sep 2018 05:57:51 GMT

←Older revision		Revision as of 05:57, 12 September 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: Mabanglo, M.F., Raushel, F.M.	+	Authors: Mabanglo, M.F., Raushel, F.M., Hogancamp, T.N.

	Description: Crystal structure of the LigJ hydratase E284Q mutant substrate complex with (3Z)-2-keto-4-carboxy-3-hexenedioate		Description: Crystal structure of the LigJ hydratase E284Q mutant substrate complex with (3Z)-2-keto-4-carboxy-3-hexenedioate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Hogancamp, T.N]]
	[[Category: Mabanglo, M.F]]		[[Category: Mabanglo, M.F]]
	[[Category: Raushel, F.M]]		[[Category: Raushel, F.M]]

OCA at 05:50, 25 July 2018

OCA — Wed, 25 Jul 2018 05:50:51 GMT

←Older revision		Revision as of 05:50, 25 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Mabanglo, M.F., Raushel, F.M.		Authors: Mabanglo, M.F., Raushel, F.M.

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

OCA — Wed, 11 Jul 2018 04:06:07 GMT

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

←Older revision

Revision as of 04:06, 11 July 2018

OCA: New page: '''Unreleased structure''' The entry 6dxs is ON HOLD Authors: Mabanglo, M.F., Raushel, F.M. Description: Crystal structure of the LigJ hydratase E284Q mutant substrate complex with (3Z...

OCA — Wed, 11 Jul 2018 04:06:06 GMT

New page: '''Unreleased structure''' The entry 6dxs is ON HOLD Authors: Mabanglo, M.F., Raushel, F.M. Description: Crystal structure of the LigJ hydratase E284Q mutant substrate complex with (3Z...

New page

'''Unreleased structure'''

The entry 6dxs is ON HOLD

Authors: Mabanglo, M.F., Raushel, F.M.

Description: Crystal structure of the LigJ hydratase E284Q mutant substrate complex with (3Z)-2-keto-4-carboxy-3-hexenedioate
[[Category: Unreleased Structures]]
[[Category: Mabanglo, M.F]]
[[Category: Raushel, F.M]]