X-ray Crystallographic Study of Cyanide Binding Provides Insights into the Structure-Function Relationship for Cytochromecd1 Nitrite Reductase from Paracoccus pantotrophus

• Published in: The Journal of biological chemistry 2000-08, Vol.275 (33), p.25089-25094
• Main Authors: Jafferji, Arif, Allen, James W.A., Ferguson, Stuart J., Fülöp, Vilmos
• Format: Article
• Language: English
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M001377200

We present a 1.59-Å resolution crystal structure of reduced Paracoccus pantotrophus cytochromecd1 with cyanide bound to thed1 heme and His/Met coordination of thec heme. Fe–C–N bond angles are 146° for the A subunit and 164° for the B subunit of the dimer. The nitrogen atom of bound cyanide is within hydrogen bonding distance of His345 and His388 and either a water molecule in subunit A or Tyr25 in subunit B. The ferrous heme-cyanide complex is unusually stable (Kd ∼10−6m); we propose that this reflects both the design of the specialized d1 heme ring and a general feature of anion reductases with active site heme. Oxidation of crystals of reduced, cyanide-bound, cytochrome cd1 results in loss of cyanide and return to the native structure with Tyr25 as a ligand to the d1 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 d1 heme.