6xm8 - Revision history

OCA at 14:55, 18 October 2023

2023-10-18T14:55:20Z

←Older revision		Revision as of 14:55, 18 October 2023
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	<StructureSection load='6xm8' size='340' side='right'caption='[[6xm8]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6xm8' size='340' side='right'caption='[[6xm8]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xm8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Sphsk Sphsk~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XM8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xm8]] is a 1 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=6XM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XM8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=V5P:lignostilbene'>V5P</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]] 1.85Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SLG_12860 ([https://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=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=V5P:lignostilbene'>V5P</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=6xm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xm8 OCA], [https://pdbe.org/6xm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xm8 RCSB], [https://www.ebi.ac.uk/pdbsum/6xm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xm8 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=6xm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xm8 OCA], [https://pdbe.org/6xm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xm8 RCSB], [https://www.ebi.ac.uk/pdbsum/6xm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xm8 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G2IQT9_SPHSK G2IQT9_SPHSK]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sphsk~~]]	+	[[Category: Sphingobium sp. SYK-6]]
-	[[Category: Beckham~~, G T~~]]	+	[[Category: Beckham GT]]
-	[[Category: Chan~~, A C~~]]	+	[[Category: Chan AC]]
-	[[Category: Eltis~~, L D~~]]	+	[[Category: Eltis LD]]
-	[[Category: Katahira, R]]	+	[[Category: Katahira R]]
-	[[Category: Kuatsjah, E]]	+	[[Category: Kuatsjah E]]
-	[[Category: Murphy~~, M E]]~~	+	[[Category: Murphy ME]]
-	~~[[Category: Bacterial aromatic catabolism]]~~	+
-	~~[[Category: Carotenoid cleavage dioxygenase]]~~	+
-	~~[[Category: Lignostilbene dioxygenase]]~~	+
-	~~[[Category: Non-heme iron oxygenase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:25, 26 May 2021

2021-05-26T09:25:09Z

←Older revision		Revision as of 09:25, 26 May 2021
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	==Crystal structure of lignostilbene bound to Co-LSD4 from Sphingobium sp. strain SYK-6==		==Crystal structure of lignostilbene bound to Co-LSD4 from Sphingobium sp. strain SYK-6==
-	<StructureSection load='6xm8' size='340' side='right'caption='[[6xm8]]' scene=''>	+	<StructureSection load='6xm8' size='340' side='right'caption='[[6xm8]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XM8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xm8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphsk Sphsk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XM8 FirstGlance]. <br>
-	</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=6xm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xm8 OCA], [https://pdbe.org/6xm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xm8 RCSB], [https://www.ebi.ac.uk/pdbsum/6xm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xm8 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=V5P:lignostilbene'>V5P</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SLG_12860 ([https://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=6xm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xm8 OCA], [https://pdbe.org/6xm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xm8 RCSB], [https://www.ebi.ac.uk/pdbsum/6xm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xm8 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lignostilbene-alpha,beta-dioxygenases (LSDs) are iron-dependent oxygenases involved in the catabolism of lignin-derived stilbenes. Sphingobium sp. SYK-6 contains eight LSD homologs with undetermined physiological roles. To investigate which homologs are involved in the catabolism of dehydrodiconiferyl alcohol (DCA), derived from beta-5 linked lignin subunits, we heterologously produced the enzymes and screened their activities in lysates. The seven soluble enzymes all cleaved lignostilbene, but only LSD2, LSD3, and LSD4 exhibited high specific activity for 3-(4-hydroxy-3-(4-hydroxy-3-methoxystyryl)-5-methoxyphenyl) acrylate (DCA-S) relative to lignostilbene. LSD4 catalyzed the cleavage of DCA-S to 5-formylferulate and vanillin, and cleaved lignostilbene and DCA-S ( approximately 10(6) M(-1)s(-1)) with 10-fold greater specificity than pterostilbene and resveratrol. X-ray crystal structures of native LSD4 and the catalytically inactive cobalt-substituted Co-LSD4 at 1.45 A resolution revealed the same fold, metal ion coordination, and edge-to-edge dimeric structure as observed in related enzymes. Key catalytic residues, Phe-59, Tyr-101, and Lys-134, were also conserved. Structures of Co-LSD4.vanillin, Co-LSD4.lignostilbene, and Co-LSD4.DCA-S complexes revealed that Ser-283 forms a hydrogen bond with the hydroxyl group of the ferulyl portion of DCA-S. This residue is conserved in LSD2 and LSD4 but is alanine in LSD3. Substitution of Ser-283 with Ala minimally affected the specificity of LSD4 for either lignostilbene or DCA-S. By contrast, substitution with phenylalanine, as occurs in LSD5 and LSD6, reduced the specificity of the enzyme for both substrates by an order of magnitude. This study expands our understanding of an LSD critical to DCA catabolism as well as the physiological roles of other LSDs and their determinants of substrate specificity.
		+
		+	Structural and functional analysis of lignostilbene dioxygenases from Sphingobium sp. SYK-6.,Kuatsjah E, Chan ACK, Katahira R, Haugen SJ, Beckham GT, Murphy MEP, Eltis LD J Biol Chem. 2021 May 6:100758. doi: 10.1016/j.jbc.2021.100758. PMID:33965373<ref>PMID:33965373</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6xm8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Beckham GT]]	+	[[Category: Sphsk]]
-	[[Category: Chan AC]]	+	[[Category: Beckham, G T]]
-	[[Category: Eltis LD]]	+	[[Category: Chan, A C]]
-	[[Category: Katahira R]]	+	[[Category: Eltis, L D]]
-	[[Category: Kuatsjah E]]	+	[[Category: Katahira, R]]
-	[[Category: Murphy ME]]	+	[[Category: Kuatsjah, E]]
		+	[[Category: Murphy, M E]]
		+	[[Category: Bacterial aromatic catabolism]]
		+	[[Category: Carotenoid cleavage dioxygenase]]
		+	[[Category: Lignostilbene dioxygenase]]
		+	[[Category: Non-heme iron oxygenase]]
		+	[[Category: Oxidoreductase]]

OCA at 09:17, 12 May 2021

2021-05-12T09:17:57Z

←Older revision		Revision as of 09:17, 12 May 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6xm8 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of lignostilbene bound to Co-LSD4 from Sphingobium sp. strain SYK-6==
-		+	<StructureSection load='6xm8' size='340' side='right'caption='[[6xm8]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XM8 FirstGlance]. <br>
-	~~Description~~:	+	</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=6xm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xm8 OCA], [https://pdbe.org/6xm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xm8 RCSB], [https://www.ebi.ac.uk/pdbsum/6xm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xm8 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Beckham GT]]
		+	[[Category: Chan AC]]
		+	[[Category: Eltis LD]]
		+	[[Category: Katahira R]]
		+	[[Category: Kuatsjah E]]
		+	[[Category: Murphy ME]]

OCA at 09:23, 29 July 2020

2020-07-29T09:23:57Z

←Older revision		Revision as of 09:23, 29 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6xm8 is ON HOLD	+	The entry 6xm8 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6xm8" [edit=sysop:move=sysop]

2020-07-08T10:58:33Z

Protected "6xm8" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:58, 8 July 2020

OCA: New page: '''Unreleased structure''' The entry 6xm8 is ON HOLD Authors: Description: Category: Unreleased Structures

2020-07-08T10:58:32Z

New page: '''Unreleased structure''' The entry 6xm8 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6xm8 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]