1H9Y

Cytochrome cd1 Nitrite Reductase, reduced form complexed to CN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Structure of an Alternative Form of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase

Sjogren, T.Hajdu, J.

(2001) J Biol Chem 276: 29450

  • DOI: 10.1074/jbc.M103657200
  • Primary Citation of Related Structures:  
    1H9Y, 1H9X, 1HCM

  • PubMed Abstract: 
  • Cytochrome cd(1) nitrite reductase is a bifunctional enzyme, which can catalyze the 1-electron reduction of nitrite to nitric oxide and the 4-electron reduction of dioxygen to water. Here we describe the structure of reduced nitrite reductase, crystallized under anaerobic conditions ...

    Cytochrome cd(1) nitrite reductase is a bifunctional enzyme, which can catalyze the 1-electron reduction of nitrite to nitric oxide and the 4-electron reduction of dioxygen to water. Here we describe the structure of reduced nitrite reductase, crystallized under anaerobic conditions. The structure reveals substantial domain rearrangements with the c domain rotated by 60 degrees and shifted by approximately 20 A compared with previously known structures from crystals grown under oxidizing conditions. This alternative conformation gives rise to different electron transfer routes between the c and d(1) domains and points to the involvement of elements of very large structural changes in the function in this enzyme. In the present structure, the c heme has a His-69/Met-106 ligation, and this ligation does not change upon oxidation in the crystal. The d(1) heme is penta-coordinated, and the d(1) iron is displaced from the heme plane by 0.5 A toward the proximal ligand, His-200. After oxidation, the iron moves into the d(1) heme plane. A surprising finding is that although reduced nitrite reductase can be readily oxidized by dioxygen in the new crystal, it cannot turnover with its other substrate, nitrite. The results suggest that the rearrangement of the domains affects catalysis and substrate selectivity.


    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, Box 576, S-751 23 Uppsala, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME CD1 NITRITE REDUCTASEA, B567Paracoccus pantotrophusMutation(s): 0 
Gene Names: nirS
EC: 1.7.2.1 (UniProt), 1.7.99.1 (UniProt)
UniProt
Find proteins for P72181 (Paracoccus pantotrophus)
Explore P72181 
Go to UniProtKB:  P72181
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.238 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.573α = 90
b = 127.573β = 90
c = 263.201γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2001-03-23 
  • Released Date: 2001-08-09 
  • Deposition Author(s): Sjogren, T., Hajdu, J.

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-09
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation