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4y98

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Crystal structure of LigD-apo form from Sphingobium sp. strain SYK-6

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 <StructureSection load='4y98' size='340' side='right'caption='[[4y98]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4y98]] 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=4Y98 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y98 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4y98]] 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=4Y98 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y98 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4y9d|4y9d]]</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]] 2.648&#8491;</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'>[https://proteopedia.org/fgij/fg.htm?mol=4y98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y98 OCA], [https://pdbe.org/4y98 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y98 RCSB], [https://www.ebi.ac.uk/pdbsum/4y98 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y98 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=4y98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y98 OCA], [http://pdbe.org/4y98 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y98 RCSB], [http://www.ebi.ac.uk/pdbsum/4y98 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y98 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/G2IN91_SPHSK G2IN91_SPHSK]
-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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4y98" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[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]]

4y98

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Crystal structure of LigD-apo form from Sphingobium sp. strain SYK-6

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