5vn5 - Revision history

OCA at 14:11, 13 March 2024

OCA — Wed, 13 Mar 2024 14:11:28 GMT

←Older revision		Revision as of 14:11, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='5vn5' size='340' side='right'caption='[[5vn5]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5vn5' size='340' side='right'caption='[[5vn5]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vn5]] is a 3 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=5VN5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VN5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vn5]] is a 3 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=5VN5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VN5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.9Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ligY, SLG_07750 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=627192 SPHSK])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5vn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn5 OCA], [~~http~~://pdbe.org/5vn5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vn5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vn5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn5 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=5vn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn5 OCA], [https://pdbe.org/5vn5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vn5 RCSB], [https://www.ebi.ac.uk/pdbsum/5vn5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn5 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/G2IN02_SPHSK G2IN02_SPHSK]
-	Strain SYK-6 of the bacterium Sphingobium sp. catabolizes lignin-derived biphenyl via a meta-cleavage pathway. In this pathway, LigY is proposed to catalyze the hydrolysis of the meta-cleavage product (MCP) 4,11-dicarboxy-8-hydroxy-9-methoxy-2-hydroxy-6-oxo-6-phenyl-hexa-2,4-dienoate. Here, we validated this reaction by identifying 5-carboxyvanillate and 4-carboxy-2-hydroxypenta-2,4-dienoate as the products and determined the kcat and kcat/Km values as 9.3 +/- 0.6 s(-1) and 2.5 +/- 0.2 x 10(7) m(-1) s(-1), respectively. Sequence analyses and a 1.9 A resolution crystal structure established that LigY belongs to the amidohydrolase superfamily, unlike previously characterized MCP hydrolases, which are serine-dependent enzymes of the alpha/beta-hydrolase superfamily. The active-site architecture of LigY resembled that of alpha-amino-beta-carboxymuconic--semialdehyde decarboxylase, a class III amidohydrolase, with a single zinc ion coordinated by His-6, His-8, His-179, and Glu-282. Interestingly, we found that LigY lacks the acidic residue proposed to activate water for hydrolysis in other class III amidohydrolases. Moreover, substitution of His-223, a conserved residue proposed to activate water in other amidohydrolases, reduced the kcat to a much lesser extent than what has been reported for other amidohydrolases, suggesting that His-223 has a different role in LigY. Substitution of Arg-72, Tyr-190, Arg-234, or Glu-282 reduced LigY activity over 100-fold. On the basis of these results, we propose a catalytic mechanism involving substrate tautomerization, substrate-assisted activation of water for hydrolysis, and formation of a gem-diol intermediate. This last step diverges from what occurs in serine-dependent MCP hydrolases. This study provides insight into C-C-hydrolyzing enzymes and expands the known range of reactions catalyzed by the amidohydrolase superfamily.	+
-		+
-	The bacterial meta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the alpha/beta-hydrolase superfamily.,Kuatsjah E, Chan ACK, Kobylarz MJ, Murphy MEP, Eltis LD J Biol Chem. 2017 Nov 3;292(44):~~18290-18302. doi: 10.1074~~/~~jbc.M117.797696. Epub, 2017 Sep 20. PMID:28935670<ref>PMID:28935670<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5vn5" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sphsk~~]]	+	[[Category: Sphingobium sp. SYK-6]]
-	[[Category: Chan~~, A C.K~~]]	+	[[Category: Chan ACK]]
-	[[Category: Eltis~~, L D~~]]	+	[[Category: Eltis LD]]
-	[[Category: Kobylarz~~, M J~~]]	+	[[Category: Kobylarz MJ]]
-	[[Category: Kuatsjah, E]]	+	[[Category: Kuatsjah E]]
-	[[Category: Murphy~~, M E.P]]~~	+	[[Category: Murphy MEP]]
-	~~[[Category: Amidohydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lignin degradation]]~~	+
-	~~[[Category: Meta-cleavage product hydrolase~~]]	+

OCA at 08:27, 8 January 2020

OCA — Wed, 08 Jan 2020 08:27:17 GMT

←Older revision		Revision as of 08:27, 8 January 2020
Line 1:		Line 1:

	==Crystal structure of LigY from Sphingobium sp. strain SYK-6==		==Crystal structure of LigY from Sphingobium sp. strain SYK-6==
-	<StructureSection load='5vn5' size='340' side='right' caption='[[5vn5]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5vn5' size='340' side='right'caption='[[5vn5]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vn5]] is a 3 chain structure with sequence from [http://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=5VN5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VN5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vn5]] is a 3 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=5VN5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VN5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=CL:CHLORIDE+ION'>CL</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">ligY, SLG_07750 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=627192 ~~Sphingobium sp. SYK-6~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ligY, SLG_07750 ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5vn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn5 OCA], [http://pdbe.org/5vn5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vn5 RCSB], [http://www.ebi.ac.uk/pdbsum/5vn5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn5 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=5vn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn5 OCA], [http://pdbe.org/5vn5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vn5 RCSB], [http://www.ebi.ac.uk/pdbsum/5vn5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn5 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sphingobium sp. syk-6~~]]	+	[[Category: Large Structures]]
		+	[[Category: Sphsk]]
	[[Category: Chan, A C.K]]		[[Category: Chan, A C.K]]
	[[Category: Eltis, L D]]		[[Category: Eltis, L D]]

OCA at 19:02, 1 August 2018

OCA — Wed, 01 Aug 2018 19:02:12 GMT

←Older revision		Revision as of 19:02, 1 August 2018
Line 8:		Line 8:
	<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=5vn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn5 OCA], [http://pdbe.org/5vn5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vn5 RCSB], [http://www.ebi.ac.uk/pdbsum/5vn5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn5 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=5vn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn5 OCA], [http://pdbe.org/5vn5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vn5 RCSB], [http://www.ebi.ac.uk/pdbsum/5vn5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn5 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Strain SYK-6 of the bacterium Sphingobium sp. catabolizes lignin-derived biphenyl via a meta-cleavage pathway. In this pathway, LigY is proposed to catalyze the hydrolysis of the meta-cleavage product (MCP) 4,11-dicarboxy-8-hydroxy-9-methoxy-2-hydroxy-6-oxo-6-phenyl-hexa-2,4-dienoate. Here, we validated this reaction by identifying 5-carboxyvanillate and 4-carboxy-2-hydroxypenta-2,4-dienoate as the products and determined the kcat and kcat/Km values as 9.3 +/- 0.6 s(-1) and 2.5 +/- 0.2 x 10(7) m(-1) s(-1), respectively. Sequence analyses and a 1.9 A resolution crystal structure established that LigY belongs to the amidohydrolase superfamily, unlike previously characterized MCP hydrolases, which are serine-dependent enzymes of the alpha/beta-hydrolase superfamily. The active-site architecture of LigY resembled that of alpha-amino-beta-carboxymuconic--semialdehyde decarboxylase, a class III amidohydrolase, with a single zinc ion coordinated by His-6, His-8, His-179, and Glu-282. Interestingly, we found that LigY lacks the acidic residue proposed to activate water for hydrolysis in other class III amidohydrolases. Moreover, substitution of His-223, a conserved residue proposed to activate water in other amidohydrolases, reduced the kcat to a much lesser extent than what has been reported for other amidohydrolases, suggesting that His-223 has a different role in LigY. Substitution of Arg-72, Tyr-190, Arg-234, or Glu-282 reduced LigY activity over 100-fold. On the basis of these results, we propose a catalytic mechanism involving substrate tautomerization, substrate-assisted activation of water for hydrolysis, and formation of a gem-diol intermediate. This last step diverges from what occurs in serine-dependent MCP hydrolases. This study provides insight into C-C-hydrolyzing enzymes and expands the known range of reactions catalyzed by the amidohydrolase superfamily.
		+
		+	The bacterial meta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the alpha/beta-hydrolase superfamily.,Kuatsjah E, Chan ACK, Kobylarz MJ, Murphy MEP, Eltis LD J Biol Chem. 2017 Nov 3;292(44):18290-18302. doi: 10.1074/jbc.M117.797696. Epub, 2017 Sep 20. PMID:28935670<ref>PMID:28935670</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vn5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:48, 6 November 2017

OCA — Mon, 06 Nov 2017 11:48:32 GMT

←Older revision		Revision as of 11:48, 6 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vn5 is ~~ON HOLD~~	+	==Crystal structure of LigY from Sphingobium sp. strain SYK-6==
-		+	<StructureSection load='5vn5' size='340' side='right' caption='[[5vn5]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5vn5]] is a 3 chain structure with sequence from [http://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=5VN5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VN5 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ligY, SLG_07750 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=627192 Sphingobium sp. SYK-6])</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=5vn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn5 OCA], [http://pdbe.org/5vn5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vn5 RCSB], [http://www.ebi.ac.uk/pdbsum/5vn5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn5 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Sphingobium sp. syk-6]]
		+	[[Category: Chan, A C.K]]
		+	[[Category: Eltis, L D]]
		+	[[Category: Kobylarz, M J]]
		+	[[Category: Kuatsjah, E]]
		+	[[Category: Murphy, M E.P]]
		+	[[Category: Amidohydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Lignin degradation]]
		+	[[Category: Meta-cleavage product hydrolase]]

OCA: Protected "5vn5" [edit=sysop:move=sysop]

OCA — Wed, 10 May 2017 11:12:24 GMT

Protected "5vn5" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:12, 10 May 2017

OCA: New page: '''Unreleased structure''' The entry 5vn5 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 May 2017 11:12:23 GMT

New page: '''Unreleased structure''' The entry 5vn5 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5vn5 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]