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

• Published in: The Journal of biological chemistry Vol. 275; no. 33; pp. 25089 - 25094
• Main Authors: Jafferji, A, Allen, J W, Ferguson, S J, Fulop, V
• Format: Journal Article
• Language: English
• Published: United States 18.08.2000
• 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
• ISSN: 0021-9258
• DOI: 10.1074/jbc.M001377200

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.