3W08

Crystal structure of aldoxime dehydratase

Summary for 3W08

• Entry DOI: 10.2210/pdb3w08/pdb
• Descriptor: Aldoxime dehydratase, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: lyase
• Biological source: Pseudomonas chlororaphis
• Total number of polymer chains: 2
• Total formula weight: 81586.79

Authors

Hashimoto, H.,Nomura, J.,Hashimoto, Y.,Oinuma, K.I.,Wada, K.,Hishiki, A.,Hara, K.,Kobayashi, M. (deposition date: 2012-10-24, release date: 2013-02-20, Last modification date: 2023-11-08)

Primary citation

Nomura, J.,Hashimoto, H.,Ohta, T.,Hashimoto, Y.,Wada, K.,Naruta, Y.,Oinuma, K.,Kobayashi, M.
Crystal structure of aldoxime dehydratase and its catalytic mechanism involved in carbon-nitrogen triple-bond synthesis.
Proc.Natl.Acad.Sci.USA, 110:2810-2815, 2013

PubMed Abstract: 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 ∼6 Å 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.

PubMed: 23382199
DOI: 10.1073/pnas.1200338110

Experimental method

X-RAY DIFFRACTION (1.8 Å)