X-ray crystallographic study of cyanide binding provides insights into the structure-function relationship for cytochrome cd1 nitrite reductase from Paracoccus pantotrophus

We present a 1.59-A resolution crystal structure of reduced Paracoccus pantotrophus cytochrome cd(1) with cyanide bound to the d(1) heme and His/Met coordination of the c heme. Fe-C-N bond angles are 146 degrees for the A subunit and 164 degrees for the B subunit of the dimer. The nitrogen atom of b...

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Bibliographic Details
Published in:The Journal of biological chemistry 2000-08, Vol.275 (33), p.25089-25094
Main Authors: Jafferji, A, Allen, J W, Ferguson, S J, Fulop, V
Format: Article
Language:English
Subjects:
Anions - chemistry
Binding Sites
Crystallography, X-Ray
Cyanides - chemistry
Cyanides - metabolism
Cytochromes
Electron Transport Complex IV - chemistry
Electron Transport Complex IV - metabolism
Electron Transport Complex IV - physiology
Heme - chemistry
Hydrogen Bonding
Kinetics
Ligands
Models, Molecular
Nitrite Reductases - chemistry
Nitrite Reductases - metabolism
Nitrite Reductases - physiology
Oxidation-Reduction
Paracoccus - enzymology
Protein Binding
Protein Conformation
Structure-Activity Relationship
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Summary:We present a 1.59-A resolution crystal structure of reduced Paracoccus pantotrophus cytochrome cd(1) with cyanide bound to the d(1) heme and His/Met coordination of the c heme. Fe-C-N bond angles are 146 degrees for the A subunit and 164 degrees for the B subunit of the dimer. The nitrogen atom of bound cyanide is within hydrogen bonding distance of His(345) and His(388) and either a water molecule in subunit A or Tyr(25) in subunit B. The ferrous heme-cyanide complex is unusually stable (K(d) approximately 10(-6) m); we propose that this reflects both the design of the specialized d(1) heme ring and a general feature of anion reductases with active site heme. Oxidation of crystals of reduced, cyanide-bound, cytochrome cd(1) results in loss of cyanide and return to the native structure with Tyr(25) as a ligand to the d(1) heme iron and switching to His/His coordination at the c-type heme. No reason for unusually weak binding of cyanide to the ferric state can be identified; rather it is argued that the protein is designed such that a chelate-based effect drives displacement by tyrosine of cyanide or a weaker ligand, like reaction product nitric oxide, from the ferric d(1) heme.
ISSN:0021-9258
DOI:10.1074/jbc.M001377200