1QKS

CYTOCHROME CD1 NITRITE REDUCTASE, OXIDISED FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The anatomy of a bifunctional enzyme: structural basis for reduction of oxygen to water and synthesis of nitric oxide by cytochrome cd1.

Fulop, V.Moir, J.W.Ferguson, S.J.Hajdu, J.

(1995) Cell 81: 369-377

  • Also Cited By: 1HJ5, 1HJ4, 1HJ3, 1HCM, 1H9Y, 1H9X, 1GQ1, 1E2R

  • PubMed Abstract: 
  • Cytochrome cd1-nitrite reductase is a bifunctional enzyme that catalyzes the one-electron reduction of nitrite to nitric oxide and the four-electron reduction of oxygen to water. The 1.55 A crystal structure of the dimeric enzyme from Thiosphaera pan ...

    Cytochrome cd1-nitrite reductase is a bifunctional enzyme that catalyzes the one-electron reduction of nitrite to nitric oxide and the four-electron reduction of oxygen to water. The 1.55 A crystal structure of the dimeric enzyme from Thiosphaera pantotropha is reported here. The protein was sequenced from the X-ray structure. Each subunit contains a covalent c heme with two axial His ligands (His-17, His-69) and a unique noncovalent d1 heme ligated by Tyr-25 and His-200. The d1 heme is the mononuclear iron center where both oxygen and nitrite reduction take place. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis.


    Related Citations: 
    • 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


    Organizational Affiliation

    Laboratory of Molecular Biophysics, University of Oxford, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME CD1 NITRITE REDUCTASE
A, B
567Paracoccus pantotrophusMutation(s): 0 
Gene Names: nirS
EC: 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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: 1.28 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 106.400α = 90.00
b = 60.600β = 112.30
c = 100.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-08-05 
  • Released Date: 1999-08-18 
  • Deposition Author(s): Fulop, V.

Revision History 

  • Version 1.0: 1999-08-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-01-16
    Type: Data collection, Database references