4xt0: Difference between revisions

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<StructureSection load='4xt0' size='340' side='right'caption='[[4xt0]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
<StructureSection load='4xt0' size='340' side='right'caption='[[4xt0]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4xt0]] 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=4XT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XT0 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4xt0]] 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=4XT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XT0 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.07&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ligF ([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=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=4xt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xt0 OCA], [http://pdbe.org/4xt0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xt0 RCSB], [http://www.ebi.ac.uk/pdbsum/4xt0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xt0 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=4xt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xt0 OCA], [https://pdbe.org/4xt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xt0 RCSB], [https://www.ebi.ac.uk/pdbsum/4xt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xt0 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/LIGF_SPHPI LIGF_SPHPI]] Lignin degradation enzyme.
[https://www.uniprot.org/uniprot/G2IN92_SPHSK G2IN92_SPHSK]  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via beta-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent beta-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because beta-aryl ether bonds account for 50-70% of all interunit linkages in lignin, understanding the mechanism of enzymatic beta-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.
 
Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of beta-Aryl Ether Bonds in Lignin.,Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN Jr J Biol Chem. 2016 Mar 4;291(10):5234-46. doi: 10.1074/jbc.M115.694307. Epub 2015 , Dec 4. PMID:26637355<ref>PMID:26637355</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4xt0" 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: Bingman, C A]]
[[Category: Bingman CA]]
[[Category: Donohue, T J]]
[[Category: Donohue TJ]]
[[Category: Helmich, K E]]
[[Category: Helmich KE]]
[[Category: Phillips, G N]]
[[Category: Phillips Jr GN]]
[[Category: Beta-etherase]]
[[Category: Glutathione]]
[[Category: Gst]]
[[Category: Ligf]]
[[Category: Lignase]]
[[Category: Thioredoxin]]
[[Category: Transferase]]

Latest revision as of 16:01, 1 March 2024

Crystal Structure of Beta-etherase LigF from Sphingobium sp. strain SYK-6Crystal Structure of Beta-etherase LigF from Sphingobium sp. strain SYK-6

Structural highlights

4xt0 is a 1 chain structure with sequence from Sphingobium sp. SYK-6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.07Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

G2IN92_SPHSK

4xt0, resolution 2.07Å

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