3Q08 image
Entry Detail
PDB ID:
3Q08
Keywords:
Title:
Crystal Structure of Chlorite Dismutase from D. Aromatica at pH 6.5
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2010-12-15
Release Date:
2011-01-05
Method Details:
Experimental Method:
Resolution:
3.05 Å
R-Value Free:
0.22
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Chlorite dismutase
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Chain Length:248
Number of Molecules:20
Biological Source:Dechloromonas aromatica
Primary Citation
Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase.
J.Biol.Inorg.Chem. 15 879 888 (2010)
PMID: 20386942 DOI: 10.1007/s00775-010-0651-0

Abstact

Chlorite dismutase (Cld) is a heme enzyme capable of rapidly and selectively decomposing chlorite (ClO(2) (-)) to Cl(-) and O(2). The ability of Cld to promote O(2) formation from ClO(2) (-) is unusual. Heme enzymes generally utilize ClO(2) (-) as an oxidant for reactions such as oxygen atom transfer to, or halogenation of, a second substrate. The X-ray crystal structure of Dechloromonas aromatica Cld co-crystallized with the substrate analogue nitrite (NO(2) (-)) was determined to investigate features responsible for this novel reactivity. The enzyme active site contains a single b-type heme coordinated by a proximal histidine residue. Structural analysis identified a glutamate residue hydrogen-bonded to the heme proximal histidine that may stabilize reactive heme species. A solvent-exposed arginine residue likely gates substrate entry to a tightly confined distal pocket. On the basis of the proposed mechanism of Cld, initial reaction of ClO(2) (-) within the distal pocket generates hypochlorite (ClO(-)) and a compound I intermediate. The sterically restrictive distal pocket probably facilitates the rapid rebound of ClO(-) with compound I forming the Cl(-) and O(2) products. Common to other heme enzymes, Cld is inactivated after a finite number of turnovers, potentially via the observed formation of an off-pathway tryptophanyl radical species through electron migration to compound I. Three tryptophan residues of Cld have been identified as candidates for this off-pathway radical. Finally, a juxtaposition of hydrophobic residues between the distal pocket and the enzyme surface suggests O(2) may have a preferential direction for exiting the active site.

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