X-ray crystallographic study of cyanide binding provides insights into thestructure-function relationship for cytochrome cd(1) nitrite reductase from Paracoccus pantotrophus

We present a 1.59-Angstrom resolution crystal structure of reduced Paracocc us pantotrophus cytochrome ed, 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(3 88) and either a water molecule in subunit A or Tyr(25), subunit B. The fer rous heme-cyanide complex is unusually stable (K-d similar to 10-(6) M); we propose that this reflects both the design of the specialized d(1) heme ri ng and a general feature of anion reductases with active site heme, Oxidati on 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 t he 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 c helate-based effect drives displacement by tyrosine of cyanide or a weaker ligand, like reaction product nitric oxide, from the ferric d(1) heme.