1E2R

CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND

Summary for 1E2R

• Entry DOI: 10.2210/pdb1e2r/pdb
• Related: 1AOF 1AOM 1AOQ 1QKS
• Descriptor: NITRITE REDUCTASE, HEME C, HEME D, ... (6 entities in total)
• Functional Keywords: oxidoreductase, denitrification, electron transport, periplasmic, cyanide
• Biological source: PARACOCCUS DENITRIFICANS
• Total number of polymer chains: 2
• Total formula weight: 128105.46

Authors

Fulop, V. (deposition date: 2000-05-24, release date: 2000-05-30, Last modification date: 2024-10-09)

Primary citation

Jafferji, A.,Allen, J.W.,Ferguson, S.J.,Fulop, V.
X-Ray Crystallographic Study of Cyanide Binding Provides Insights Into the Structure-Function Relationship for Cytochrome Cd1 Nitrite Reductase from Paracoccus Pantotrophus.
J.Biol.Chem., 275:25089-, 2000

PubMed Abstract: 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.

PubMed: 10827177
DOI: 10.1074/JBC.M001377200

Experimental method

X-RAY DIFFRACTION (1.59 Å)