6xm9 | pdb_00006xm9

Crystal structure of vanillin bound to Co-LSD4 from Sphingobium sp. strain SYK-6

spinqualitylabelsall models 6xm9, resolution 1.65Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6xm9 is a 1 chain structure with sequence from Sphsk. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ACT, CO, DMS, MG, V55 Gene: SLG_12860 (SPHSK) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Lignostilbene-alpha,beta-dioxygenases (LSDs) are iron-dependent oxygenases involved in the catabolism of lignin-derived stilbenes. Sphingobium sp. SYK-6 contains eight LSD homologs with undetermined physiological roles. To investigate which homologs are involved in the catabolism of dehydrodiconiferyl alcohol (DCA), derived from beta-5 linked lignin subunits, we heterologously produced the enzymes and screened their activities in lysates. The seven soluble enzymes all cleaved lignostilbene, but only LSD2, LSD3, and LSD4 exhibited high specific activity for 3-(4-hydroxy-3-(4-hydroxy-3-methoxystyryl)-5-methoxyphenyl) acrylate (DCA-S) relative to lignostilbene. LSD4 catalyzed the cleavage of DCA-S to 5-formylferulate and vanillin, and cleaved lignostilbene and DCA-S ( approximately 10(6) M(-1)s(-1)) with 10-fold greater specificity than pterostilbene and resveratrol. X-ray crystal structures of native LSD4 and the catalytically inactive cobalt-substituted Co-LSD4 at 1.45 A resolution revealed the same fold, metal ion coordination, and edge-to-edge dimeric structure as observed in related enzymes. Key catalytic residues, Phe-59, Tyr-101, and Lys-134, were also conserved. Structures of Co-LSD4.vanillin, Co-LSD4.lignostilbene, and Co-LSD4.DCA-S complexes revealed that Ser-283 forms a hydrogen bond with the hydroxyl group of the ferulyl portion of DCA-S. This residue is conserved in LSD2 and LSD4 but is alanine in LSD3. Substitution of Ser-283 with Ala minimally affected the specificity of LSD4 for either lignostilbene or DCA-S. By contrast, substitution with phenylalanine, as occurs in LSD5 and LSD6, reduced the specificity of the enzyme for both substrates by an order of magnitude. This study expands our understanding of an LSD critical to DCA catabolism as well as the physiological roles of other LSDs and their determinants of substrate specificity. Structural and functional analysis of lignostilbene dioxygenases from Sphingobium sp. SYK-6.,Kuatsjah E, Chan ACK, Katahira R, Haugen SJ, Beckham GT, Murphy MEP, Eltis LD J Biol Chem. 2021 May 6:100758. doi: 10.1016/j.jbc.2021.100758. PMID:33965373 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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