1E2R

CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-Ray Crystallographic Study of Cyanide Binding Provides Insights Into the Structure-Function Relationship for Cytochrome Cd1 Nitrite Reductase from Paracoccus Pantotrophus.

Jafferji, A.Allen, J.W.Ferguson, S.J.Fulop, V.

(2000) J.Biol.Chem. 275: 25089

  • DOI: 10.1074/jbc.M001377200

  • 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 ...

    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.


    Related Citations: 
    • The Anatomy of a Bifunctional Enzyme: Structural Basis for Reduction of Oxygen to Water and Synthesys of Nitric Oxide by Cytochrome Cd1
      Fulop, V.,Moir, J.W.B.,Ferguson, S.J.,Hajdu, J.
      (1995) Cell 81: 369
    • Cytochrome Cd1 Structure: Unusual Haem Environments in a Nitrite Reductase and Analysis of Factors Contributing to Beta-Propeller Folds
      Baker, S.C.,Saunders, N.F.W.,Willis, A.C.,Ferguson, S.J.,Hajdu, J.,Fulop, V.
      (1997) J.Mol.Biol. 269: 440
    • Haem Ligand-Switching During Catalysis in Crystals of a Nitrogen Cycle Enzyme
      Williams, P.A.,Fulop, V.,Garman, E.F.,Saunders, N.F.W.,Ferguson, S.J.,Hajdu, J.
      (1997) Nature 389: 406


    Organizational Affiliation

    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRITE REDUCTASE
A, B
567Paracoccus pantotrophusGene Names: nirS
EC: 1.7.99.1, 1.7.2.1
Find proteins for P72181 (Paracoccus pantotrophus)
Go to UniProtKB:  P72181
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYN
Query on CYN

Download SDF File 
Download CCD File 
A, B
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
A, B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
DHE
Query on DHE

Download SDF File 
Download CCD File 
A, B
HEME D
C34 H32 Fe N4 O10
XLQCGNUTSJTZNF-SOFPVUHFDM
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 106.500α = 90.00
b = 60.900β = 111.90
c = 100.100γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CCP4phasing
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
Ophasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-05-24 
  • Released Date: 2000-05-30 
  • Deposition Author(s): Fulop, V.

Revision History 

  • Version 1.0: 2000-05-30
    Type: Initial release
  • Version 1.1: 2011-10-19
    Type: Data collection, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance