3w08 | pdb_00003w08

Crystal structure of aldoxime dehydratase

spinqualitylabelsall models 3w08, resolution 1.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3w08 is a 2 chain structure with sequence from Pseudomonas chlororaphis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.8Å Ligands: HEM Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function OXD_PSECL Catalyzes the dehydration of aldoximes to their corresponding nitrile (PubMed:12773527, PubMed:23382199). Aliphatic aldoximes are more effective substrates than aromatic aldoximes (PubMed:12773527). Shows high activity with butyraldoxime and acetaldoxime, but only weak activity with the aromatic aldoxime pyridine-2-aldoxime (PubMed:12773527). Cannot use benzaldoxime, isonitrosoacetophenone and pyridine-4-aldoxime (PubMed:12773527). Is involved in the metabolism of aldoxime in vivo (PubMed:12773527). Publication Abstract from PubMed Aldoxime dehydratase (OxdA), which is a unique heme protein, catalyzes the dehydration of an aldoxime to a nitrile even in the presence of water in the reaction mixture. Unlike the utilization of H(2)O(2) or O(2) as a mediator of catalysis by other heme-containing enzymes (e.g., P450), OxdA is notable for the direct binding of a substrate to the heme iron. Here, we determined the crystal structure of OxdA. We then constructed OxdA mutants in which each of the polar amino acids lying within approximately 6 A of the iron atom of the heme was converted to alanine. Among the purified mutant OxdAs, S219A had completely lost and R178A exhibited a reduction in the activity. Together with this finding, the crystal structural analysis of OxdA and spectroscopic and electrostatic potential analyses of the wild-type and mutant OxdAs suggest that S219 plays a key role in the catalysis, forming a hydrogen bond with the substrate. Based on the spatial arrangement of the OxdA active site and the results of a series of mutagenesis experiments, we propose the detailed catalytic mechanism of general aldoxime dehydratases: (i) S219 stabilizes the hydroxy group of the substrate to increase its basicity; (ii) H320 acts as an acid-base catalyst; and (iii) R178 stabilizes the heme, and would donate a proton to and accept one from H320. Crystal structure of aldoxime dehydratase and its catalytic mechanism involved in carbon-nitrogen triple-bond synthesis.,Nomura J, Hashimoto H, Ohta T, Hashimoto Y, Wada K, Naruta Y, Oinuma KI, Kobayashi M Proc Natl Acad Sci U S A. 2013 Feb 4. PMID:23382199 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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