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 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.
Jafferji
A
A
Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, United Kingdom.
Allen
J W
JW
Ferguson
S J
SJ
Fulop
V
V
D000838:Anions / Q000737:chemistry; D001665:Binding Sites; D018360:Crystallography, X-Ray; D003486:Cyanides / Q000737:chemistry / Q000378:metabolism*; D003580:Cytochromes; D003576:Electron Transport Complex IV / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology*; D006418:Heme / Q000737:chemistry; D006860:Hydrogen Bonding; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D009572:Nitrite Reductases / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology*; D010084:Oxidation-Reduction; D010230:Paracoccus / Q000201:enzymology*; D011485:Protein Binding; D011487:Protein Conformation; D013329:Structure-Activity Relationship
D000838:Anions; D003486:Cyanides; D003580:Cytochromes; D008024:Ligands; D006418:Heme; D009572:Nitrite Reductases; C028123:nitrite reductase (NO-forming); D003576:Electron Transport Complex IV