4y9d - Revision history

OCA at 13:02, 1 March 2024

OCA — Fri, 01 Mar 2024 13:02:56 GMT

←Older revision		Revision as of 13:02, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4y9d]] 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=4Y9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y9D FirstGlance]. <br>		<table><tr><td colspan='2'>[[4y9d]] 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=4Y9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y9D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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]] 2.012Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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=4y9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y9d OCA], [https://pdbe.org/4y9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y9d RCSB], [https://www.ebi.ac.uk/pdbsum/4y9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y9d 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=4y9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y9d OCA], [https://pdbe.org/4y9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y9d RCSB], [https://www.ebi.ac.uk/pdbsum/4y9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y9d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/G2IN91_SPHSK G2IN91_SPHSK]		[https://www.uniprot.org/uniprot/G2IN91_SPHSK G2IN91_SPHSK]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars, and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high-value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of beta-Aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. beta-Aryl ether units are typically abundant in lignin, corresponding to 50-70% of all the inter-monomer linkages. Consequently, a comprehensive understanding of enzymatic beta-ether cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the beta-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites, and on the catalytic mechanisms of these enzymes, comparing them to other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.
-
-	Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin beta-aryl Ether Cleavage Pathway from Sphingobium sp SYK-6.,Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD J Biol Chem. 2016 Mar 3. pii: jbc.M115.700427. PMID:26940872<ref>PMID:26940872</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4y9d" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:04, 3 May 2023

OCA — Wed, 03 May 2023 08:04:09 GMT

←Older revision		Revision as of 08:04, 3 May 2023
Line 3:		Line 3:
	<StructureSection load='4y9d' size='340' side='right'caption='[[4y9d]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='4y9d' size='340' side='right'caption='[[4y9d]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y9d]] is a 1 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=4Y9D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Y9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y9d]] 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=4Y9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y9D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y98\|4y98]]</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=4y9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y9d OCA], [https://pdbe.org/4y9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y9d RCSB], [https://www.ebi.ac.uk/pdbsum/4y9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y9d ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ligD ([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=4y9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y9d OCA], [~~http~~://pdbe.org/4y9d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4y9d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4y9d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4y9d ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G2IN91_SPHSK G2IN91_SPHSK]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sphsk~~]]	+	[[Category: Sphingobium sp. SYK-6]]
-	[[Category: Adams~~, P D~~]]	+	[[Category: Adams PD]]
-	[[Category: Heins~~, R A~~]]	+	[[Category: Heins RA]]
-	[[Category: McAndrew~~, R P~~]]	+	[[Category: McAndrew RP]]
-	[[Category: Pereira~~, J H~~]]	+	[[Category: Pereira JH]]
-	[[Category: Sale~~, K L~~]]	+	[[Category: Sale KL]]
-	[[Category: Simmons~~, B A]]~~	+	[[Category: Simmons BA]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Short chain dehydrogenase/reductase sdr family~~]]	+

OCA at 06:58, 12 June 2019

OCA — Wed, 12 Jun 2019 06:58:33 GMT

←Older revision		Revision as of 06:58, 12 June 2019
Line 1:		Line 1:

	==Crystal structure of LigD in complex with NADH from Sphingobium sp. strain SYK-6==		==Crystal structure of LigD in complex with NADH from Sphingobium sp. strain SYK-6==
-	<StructureSection load='4y9d' size='340' side='right' caption='[[4y9d]], [[Resolution\|resolution]] 2.01Å' scene=''>	+	<StructureSection load='4y9d' size='340' side='right'caption='[[4y9d]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y9d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y9d]] is a 1 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=4Y9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y9D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y98\|4y98]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y98\|4y98]]</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=4y9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y9d OCA], [http://pdbe.org/4y9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y9d RCSB], [http://www.ebi.ac.uk/pdbsum/4y9d PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ligD ([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=4y9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y9d OCA], [http://pdbe.org/4y9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y9d RCSB], [http://www.ebi.ac.uk/pdbsum/4y9d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y9d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sphsk]]
	[[Category: Adams, P D]]		[[Category: Adams, P D]]
	[[Category: Heins, R A]]		[[Category: Heins, R A]]

OCA at 18:39, 10 May 2016

OCA — Tue, 10 May 2016 18:39:00 GMT

←Older revision		Revision as of 18:39, 10 May 2016
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=4y9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y9d OCA], [http://pdbe.org/4y9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y9d RCSB], [http://www.ebi.ac.uk/pdbsum/4y9d 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=4y9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y9d OCA], [http://pdbe.org/4y9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y9d RCSB], [http://www.ebi.ac.uk/pdbsum/4y9d PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars, and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high-value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of beta-Aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. beta-Aryl ether units are typically abundant in lignin, corresponding to 50-70% of all the inter-monomer linkages. Consequently, a comprehensive understanding of enzymatic beta-ether cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the beta-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites, and on the catalytic mechanisms of these enzymes, comparing them to other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.
		+
		+	Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin beta-aryl Ether Cleavage Pathway from Sphingobium sp SYK-6.,Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD J Biol Chem. 2016 Mar 3. pii: jbc.M115.700427. PMID:26940872<ref>PMID:26940872</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4y9d" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 03:46, 10 March 2016

OCA — Thu, 10 Mar 2016 03:46:53 GMT

←Older revision		Revision as of 03:46, 10 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4y9d ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of LigD in complex with NADH from Sphingobium sp. strain SYK-6==
-		+	<StructureSection load='4y9d' size='340' side='right' caption='[[4y9d]], [[Resolution\|resolution]] 2.01Å' scene=''>
-	~~Authors~~: ~~Pereira, J~~.H.~~, McAndrew, R~~.P.~~, Heins, R~~.A.~~, Sale, K~~.L.~~, Simmons, B.A., Adams, P.D~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4y9d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y9D FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y98\|4y98]]</td></tr>
-	[[~~Category~~: ~~Pereira~~, J.H]]	+	<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=4y9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y9d OCA], [http://pdbe.org/4y9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y9d RCSB], [http://www.ebi.ac.uk/pdbsum/4y9d PDBsum]</span></td></tr>
-	[[Category: ~~Mcandrew~~, R.P]]	+	</table>
-	[[Category: Heins, R.A]]	+	__TOC__
-	[[Category: ~~Adams~~, P.D]]	+	</StructureSection>
-	[[Category: Sale, K.L]]	+	[[Category: Adams, P D]]
-	[[Category: Simmons, B.A]]	+	[[Category: Heins, R A]]
		+	[[Category: McAndrew, R P]]
		+	[[Category: Pereira, J H]]
		+	[[Category: Sale, K L]]
		+	[[Category: Simmons, B A]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Short chain dehydrogenase/reductase sdr family]]

OCA at 23:29, 30 November 2015

OCA — Mon, 30 Nov 2015 23:29:22 GMT

←Older revision		Revision as of 23:29, 30 November 2015
Line 9:		Line 9:
	[[Category: Pereira, J.H]]		[[Category: Pereira, J.H]]
	[[Category: Mcandrew, R.P]]		[[Category: Mcandrew, R.P]]
-	[[Category: Adams, P.D]]
	[[Category: Heins, R.A]]		[[Category: Heins, R.A]]
		+	[[Category: Adams, P.D]]
	[[Category: Sale, K.L]]		[[Category: Sale, K.L]]
	[[Category: Simmons, B.A]]		[[Category: Simmons, B.A]]

OCA at 11:19, 1 April 2015

OCA — Wed, 01 Apr 2015 11:19:57 GMT

←Older revision		Revision as of 11:19, 1 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4y9d is ON HOLD	+	The entry 4y9d is ON HOLD until Paper Publication

	Authors: Pereira, J.H., McAndrew, R.P., Heins, R.A., Sale, K.L., Simmons, B.A., Adams, P.D.		Authors: Pereira, J.H., McAndrew, R.P., Heins, R.A., Sale, K.L., Simmons, B.A., Adams, P.D.

OCA: Protected "4y9d" [edit=sysop:move=sysop]

OCA — Wed, 25 Feb 2015 12:50:59 GMT

Protected "4y9d" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:50, 25 February 2015

OCA: New page: '''Unreleased structure''' The entry 4y9d is ON HOLD Authors: Pereira, J.H., McAndrew, R.P., Heins, R.A., Sale, K.L., Simmons, B.A., Adams, P.D. Description: [[Category: Unreleased St...

OCA — Wed, 25 Feb 2015 12:50:57 GMT

New page: '''Unreleased structure''' The entry 4y9d is ON HOLD Authors: Pereira, J.H., McAndrew, R.P., Heins, R.A., Sale, K.L., Simmons, B.A., Adams, P.D. Description: [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 4y9d is ON HOLD

Authors: Pereira, J.H., McAndrew, R.P., Heins, R.A., Sale, K.L., Simmons, B.A., Adams, P.D.

Description:
[[Category: Unreleased Structures]]
[[Category: Pereira, J.H]]
[[Category: Mcandrew, R.P]]
[[Category: Adams, P.D]]
[[Category: Heins, R.A]]
[[Category: Sale, K.L]]
[[Category: Simmons, B.A]]