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| | <StructureSection load='6ojr' size='340' side='right'caption='[[6ojr]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='6ojr' size='340' side='right'caption='[[6ojr]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6ojr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_devorans"_zimmermann_1890 "bacillus devorans" zimmermann 1890]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ojr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OJR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.3Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lignostilbene_alpha-beta-dioxygenase Lignostilbene alpha-beta-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.43 1.13.11.43] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6ojr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ojr OCA], [http://pdbe.org/6ojr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ojr RCSB], [http://www.ebi.ac.uk/pdbsum/6ojr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ojr 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=6ojr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ojr OCA], [https://pdbe.org/6ojr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ojr RCSB], [https://www.ebi.ac.uk/pdbsum/6ojr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ojr ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/LSDX1_SPHPI LSDX1_SPHPI]] Catalyzes the cleavage of the interphenyl double bond (C alpha-C beta) of lignin-derived polyphenolic diaryl-propane type compounds (Stilbene).<ref>PMID:1368688</ref> <ref>PMID:7763879</ref> <ref>PMID:7763880</ref> <ref>PMID:14506920</ref> | + | [https://www.uniprot.org/uniprot/LSDX1_SPHPI LSDX1_SPHPI] Catalyzes the cleavage of the interphenyl double bond (C alpha-C beta) of lignin-derived polyphenolic diaryl-propane type compounds (Stilbene).<ref>PMID:1368688</ref> <ref>PMID:7763879</ref> <ref>PMID:7763880</ref> <ref>PMID:14506920</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus devorans zimmermann 1890]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lignostilbene alpha-beta-dioxygenase]] | + | [[Category: Sphingomonas paucimobilis]] |
| - | [[Category: Eltis, L D]] | + | [[Category: Eltis LD]] |
| - | [[Category: Kobylarz, M J]] | + | [[Category: Kobylarz MJ]] |
| - | [[Category: Kuatsjah, E]] | + | [[Category: Kuatsjah E]] |
| - | [[Category: Liu, A K.N]] | + | [[Category: Liu AKN]] |
| - | [[Category: Murphy, M E.P]] | + | [[Category: Murphy MEP]] |
| - | [[Category: Verstraete, M M]] | + | [[Category: Verstraete MM]] |
| - | [[Category: Aromatic compound]]
| + | |
| - | [[Category: Bacterial catabolism]]
| + | |
| - | [[Category: Carotenoid cleavage oxygenase]]
| + | |
| - | [[Category: Lignin degradation]]
| + | |
| - | [[Category: Lignostilbene]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
LSDX1_SPHPI Catalyzes the cleavage of the interphenyl double bond (C alpha-C beta) of lignin-derived polyphenolic diaryl-propane type compounds (Stilbene).[1] [2] [3] [4]
Publication Abstract from PubMed
Lignostilbene-alpha,beta-dioxygenase A (LsdA) from the bacterium Sphingomonas paucimobilis TMY1009 is a non-heme iron oxygenase that catalyzes the cleavage of lignostilbene, a compound arising in lignin transformation, to two vanillin molecules. To examine LsdA's substrate specificity, we heterologously produced the dimeric enzyme with the help of chaperones. When tested on several substituted stilbenes, LsdA exhibited greatest specificity for lignostilbene (k cat (app)/K M (app)= 1.00 +/- 0.04 x 10(6) M(-1)s(-1)). These experiments further indicated that the substrate's 4-hydroxy moiety is required for catalysis, and that this moiety cannot be replaced with a methoxy group. Phenylazophenol inhibited the LsdA-catalyzed cleavage of lignostilbene in a reversible, mixed fashion (K ic = 6 +/- 1 microM, Kiu = 24 +/- 4 microM). An X-ray crystal structure of LsdA at 2.3 A resolution revealed a seven-bladed beta-propeller fold with an iron cofactor coordinated by four histidines, in agreement with previous observations on related carotenoid cleavage oxygenases. We noted that residues at the dimer interface are also present in LsdB, another lignostilbene dioxygenase in S. paucimobilis TMY1009, rationalizing LsdA and LsdB homo- and heterodimerization in vivo A structure of a LsdA.phenylazophenol complex identified Phe-59, Tyr-101, and Lys-134 as contacting the 4-hydroxyphenyl moiety of the inhibitor. Phe-59 and Tyr-101 substitutions with His and Phe, respectively, reduced LsdA activity (k cat (app)) ~15- and 10-fold. The K134M variant did not detectably cleave lignostilbene, indicating that Lys-134 plays a key catalytic role. This study expands our mechanistic understanding of LsdA and related stilbene-cleaving dioxygenases.
Identification of functionally important residues and structural features in a bacterial lignostilbene dioxygenase.,Kuatsjah E, Verstraete MM, Kobylarz MJ, Liu AKN, Murphy MEP, Eltis LD J Biol Chem. 2019 Jul 10. pii: RA119.009428. doi: 10.1074/jbc.RA119.009428. PMID:31292192[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kamoda S, Samejima M. Cloning of a lignostilbene-alpha,beta-dioxygenase gene from Pseudomonas paucimobilis TMY1009. Agric Biol Chem. 1991 May;55(5):1411-2. PMID:1368688
- ↑ Kamoda S, Saburi Y. Cloning, expression, and sequence analysis of a lignostilbene-alpha,beta-dioxygenase gene from Pseudomonas paucimobilis TMY1009. Biosci Biotechnol Biochem. 1993 Jun;57(6):926-30. PMID:7763879
- ↑ Kamoda S, Saburi Y. Structural and enzymatical comparison of lignostilbene-alpha,beta-dioxygenase isozymes, I, II, and III, from Pseudomonas paucimobilis TMY1009. Biosci Biotechnol Biochem. 1993 Jun;57(6):931-4. doi: 10.1271/bbb.57.931. PMID:7763880 doi:http://dx.doi.org/10.1271/bbb.57.931
- ↑ Han SY, Inoue H, Terada T, Kamoda S, Saburi Y, Sekimata K, Saito T, Kobayashi M, Shinozaki K, Yoshida S, Asami T. N-benzylideneaniline and N-benzylaniline are potent inhibitors of lignostilbene-alpha,beta-dioxygenase, a key enzyme in oxidative cleavage of the central double bond of lignostilbene. J Enzyme Inhib Med Chem. 2003 Jun;18(3):279-83. doi: 10.1080/1475636031000080207. PMID:14506920 doi:http://dx.doi.org/10.1080/1475636031000080207
- ↑ Kuatsjah E, Verstraete MM, Kobylarz MJ, Liu AKN, Murphy MEP, Eltis LD. Identification of functionally important residues and structural features in a bacterial lignostilbene dioxygenase. J Biol Chem. 2019 Jul 10. pii: RA119.009428. doi: 10.1074/jbc.RA119.009428. PMID:31292192 doi:http://dx.doi.org/10.1074/jbc.RA119.009428
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