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| | ==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 [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 Sphingobium sp. SYK-6])</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.
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| - | 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>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 5vn5" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Sphingobium sp. syk-6]] | + | [[Category: Large Structures]] |
| - | [[Category: Chan, A C.K]] | + | [[Category: Sphingobium sp. SYK-6]] |
| - | [[Category: Eltis, L D]] | + | [[Category: Chan ACK]] |
| - | [[Category: Kobylarz, M J]] | + | [[Category: Eltis LD]] |
| - | [[Category: Kuatsjah, E]] | + | [[Category: Kobylarz MJ]] |
| - | [[Category: Murphy, M E.P]] | + | [[Category: Kuatsjah E]] |
| - | [[Category: Amidohydrolase]]
| + | [[Category: Murphy MEP]] |
| - | [[Category: Hydrolase]]
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| - | [[Category: Lignin degradation]]
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| - | [[Category: Meta-cleavage product hydrolase]]
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