4M06

Crystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W145F in Complex with Cyanide

Summary for 4M06

• Entry DOI: 10.2210/pdb4m06/pdb
• Related: 4M05 4M07 4M08 4M09
• Descriptor: Chlorite dismutase, PROTOPORPHYRIN IX CONTAINING FE, GLYCEROL, ... (6 entities in total)
• Functional Keywords: ferredoxin-like fold, oxidoreductase
• Biological source: Candidatus Nitrospira defluvii
• Total number of polymer chains: 5
• Total formula weight: 152192.54

Authors

Hagmueller, A.,Gysel, K.,Djinovic-Carugo, K. (deposition date: 2013-08-01, release date: 2014-01-15, Last modification date: 2024-02-28)

Primary citation

Hofbauer, S.,Gysel, K.,Bellei, M.,Hagmuller, A.,Schaffner, I.,Mlynek, G.,Kostan, J.,Pirker, K.F.,Daims, H.,Furtmuller, P.G.,Battistuzzi, G.,Djinovic-Carugo, K.,Obinger, C.
Manipulating conserved heme cavity residues of chlorite dismutase: effect on structure, redox chemistry, and reactivity.
Biochemistry, 53:77-89, 2014

PubMed Abstract: Chlorite dismutases (Clds) are heme b containing oxidoreductases that convert chlorite to chloride and molecular oxygen. In order to elucidate the role of conserved heme cavity residues in the catalysis of this reaction comprehensive mutational and biochemical analyses of Cld from "Candidatus Nitrospira defluvii" (NdCld) were performed. Particularly, point mutations of the cavity-forming residues R173, K141, W145, W146, and E210 were performed. The effect of manipulation in 12 single and double mutants was probed by UV-vis spectroscopy, spectroelectrochemistry, pre-steady-state and steady-state kinetics, and X-ray crystallography. Resulting biochemical data are discussed with respect to the known crystal structure of wild-type NdCld and the variants R173A and R173K as well as the structures of R173E, W145V, W145F, and the R173Q/W146Y solved in this work. The findings allow a critical analysis of the role of these heme cavity residues in the reaction mechanism of chlorite degradation that is proposed to involve hypohalous acid as transient intermediate and formation of an O═O bond. The distal R173 is shown to be important (but not fully essential) for the reaction with chlorite, and, upon addition of cyanide, it acts as a proton acceptor in the formation of the resulting low-spin complex. The proximal H-bonding network including K141-E210-H160 keeps the enzyme in its ferric (E°' = -113 mV) and mainly five-coordinated high-spin state and is very susceptible to perturbation.

PubMed: 24364531
DOI: 10.1021/bi401042z

Experimental method

X-RAY DIFFRACTION (2.6 Å)