1HJ5

Cytochrome cd1 Nitrite Reductase, reoxidised enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the bound dioxygen species in the cytochrome oxidase reaction of cytochrome cd1 nitrite reductase.

Sjogren, T.Hajdu, J.

(2001) J Biol Chem 276: 13072-13076

  • DOI: 10.1074/jbc.M011312200
  • Primary Citation of Related Structures:  
    1HJ5, 1HJ4, 1HJ3

  • PubMed Abstract: 
  • Reduction of dioxygen to water is a key process in aerobic life, but atomic details of this reaction have been elusive because of difficulties in observing active oxygen intermediates by crystallography. Cytochrome cd(1) is a bifunctional enzyme, capable of catalyzing the one-electron reduction of nitrite to nitric oxide, and the four-electron reduction of dioxygen to water ...

    Reduction of dioxygen to water is a key process in aerobic life, but atomic details of this reaction have been elusive because of difficulties in observing active oxygen intermediates by crystallography. Cytochrome cd(1) is a bifunctional enzyme, capable of catalyzing the one-electron reduction of nitrite to nitric oxide, and the four-electron reduction of dioxygen to water. The latter is a cytochrome oxidase reaction. Here we describe the structure of an active dioxygen species in the enzyme captured by cryo-trapping. The productive binding mode of dioxygen in the active site is very similar to that of nitrite and suggests that the catalytic mechanisms of oxygen reduction and nitrite reduction are closely related. This finding has implications to the understanding of the evolution of oxygen-reducing enzymes. Comparison of the dioxygen complex to complexes of cytochrome cd(1) with stable diatomic ligands shows that nitric oxide and cyanide bind in a similar bent conformation to the iron as dioxygen whereas carbon monoxide forms a linear complex. The significance of these differences is discussed.


    Related Citations: 
    • 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
    • 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.B., Saunders, N.F.W., Ferguson, S.J., Hajdu, J.
      (1995) Cell 81: 369

    Organizational Affiliation

    Department of Biochemistry, Uppsala University, Biomedical Center, Box 576, S-751 23 Uppsala, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrite reductaseA, B567Paracoccus pantotrophusMutation(s): 0 
Gene Names: nirS
EC: 1.7.2.1 (PDB Primary Data), 1.7.99.1 (PDB Primary Data)
UniProt
Find proteins for P72181 (Paracoccus pantotrophus)
Explore P72181 
Go to UniProtKB:  P72181
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHE
Query on DHE

Download Ideal Coordinates CCD File 
D [auth A], K [auth B]HEME D
C34 H32 Fe N4 O10
XLQCGNUTSJTZNF-SOFPVUHFDM
 Ligand Interaction
HEC
Query on HEC

Download Ideal Coordinates CCD File 
C [auth A], J [auth B]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], M [auth B], N [auth B], O [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], L [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.821α = 90
b = 60.968β = 112.24
c = 100.326γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2001-01-08 
  • Released Date: 2001-01-16 
  • Deposition Author(s): Sjogren, T., Hajdu, J.

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-06-20
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation