4lyd | pdb_00004lyd

Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 from Sphingomonas wittichii RW1

spinqualitylabelsall models 4lyd, resolution 2.26Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4lyd is a 1 chain structure with sequence from Sphww. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Related: 4lxg, 4lxh, 4lxi Gene: dxnB2, Swit_3055 (SPHWW) Activity: 2,6-dioxo-6-phenylhexa-3-enoate hydrolase, with EC number 3.7.1.8 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed DxnB2 and BphD are meta-cleavage product (MCP) hydrolases that catalyze C-C bond hydrolysis of the biphenyl metabolite 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA). BphD is a bottleneck in the bacterial degradation of polychlorinated biphenyls (PCBs) by the Bph catabolic pathway due in part to inhibition by 3-Cl HOPDAs. By contrast, DxnB2 from Sphingomonas wittichii RW1 catalyzes the hydrolysis of 3-Cl HOPDAs more efficiently. X-ray crystallographic studies of the catalytically inactive S105A variant of DxnB2 complexed with 3-Cl HOPDA revealed a binding mode in which C1 through C6 of the dienoate are coplanar. The chlorine substituent is accommodated by a hydrophobic pocket that is larger than the homologous site in BphDLB400 from Burkholderia xenovorans LB400. The planar binding mode observed in the crystalline complex was consistent with the hyper- and hypsochromically shifted absorption spectra of 3-Cl and 3,9,11-triCl HOPDA, respectively, bound to S105A in solution. Moreover, ES(red), an intermediate possessing a bathochromically shifted spectrum observed in the turnover of HOPDA, was not detected, suggesting that substrate destabilization was rate-limiting in the turnover of these PCB metabolites. Interestingly, electron density for the first alpha-helix of the lid domain was poorly defined in the dimeric DxnB2 structures, unlike in the tetrameric BphDLB400. Structural comparison of MCP hydrolases identified the NC-loop, connecting the lid to the alpha/beta-hydrolase core domain, as a determinant in the oligomeric state and suggests its involvement in catalysis. Finally, an increased mobility of the DxnB2 lid may contribute to the enzyme's ability to hydrolyze PCB metabolites, highlighting how lid architecture contributes to substrate specificity in alpha/beta-hydrolases. The Lid Domain of the MCP Hydrolase DxnB2 Contributes to the Reactivity toward Recalcitrant PCB Metabolites.,Ruzzini AC, Bhowmik S, Yam KC, Ghosh S, Bolin JT, Eltis LD Biochemistry. 2013 Aug 20;52(33):5685-95. doi: 10.1021/bi400774m. Epub 2013 Aug, 9. PMID:23879719 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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