1ZV2

Cu-containing nitrite reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

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This is version 1.3 of the entry. See complete history


Literature

Structures of the oxidized and reduced forms of nitrite reductase from Rhodobacter sphaeroides 2.4.3 at high pH: changes in the interactions of the type 2 copper.

Jacobson, F.Guo, H.Olesen, K.Okvist, M.Neutze, R.Sjolin, L.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1190-1198

  • DOI: 10.1107/S0907444905017488
  • Primary Citation of Related Structures:  
    1ZV2, 2A3T

  • PubMed Abstract: 
  • Nitrite reductase is an enzyme operating in the denitrification pathway which catalyses the conversion of nitrite (NO2(-)) to gaseous nitric oxide (NO). Here, crystal structures of the oxidized and reduced forms of the copper-containing nitrite reductase from Rhodobacter sphaeroides 2 ...

    Nitrite reductase is an enzyme operating in the denitrification pathway which catalyses the conversion of nitrite (NO2(-)) to gaseous nitric oxide (NO). Here, crystal structures of the oxidized and reduced forms of the copper-containing nitrite reductase from Rhodobacter sphaeroides 2.4.3 are presented at 1.74 and 1.85 A resolution, respectively. Whereas the structure of the enzyme is very similar to those of other copper-containing nitrite reductases, folding as a trimer and containing two copper sites per monomer, the structures reported here enable conformational differences between the oxidized and reduced forms of the enzyme to be identified. In the type 1 copper site, a rotational perturbation of the side chain of the copper ligand Met182 occurs upon reduction. At the type 2 copper site, a dual conformation of the catalytic residue His287 is observed in the oxidized structure but is lacking in the reduced structure, such that the interactions of the oxidized type 2 copper ion can be regarded as adopting octahedral geometry. These findings shed light on the structural mechanism of the reduction of a copper-bound nitrite to nitric oxide and water.


    Organizational Affiliation

    Department of Chemistry and Bioscience, Chalmers University, Box 462, SE-405 30 Göteborg, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper-containing nitrite reductaseA328Cereibacter sphaeroidesMutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
UniProt
Find proteins for Q53239 (Cereibacter sphaeroides (strain ATCC 17025 / ATH 2.4.3))
Explore Q53239 
Go to UniProtKB:  Q53239
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.381α = 90
b = 72.381β = 90
c = 147.509γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Data collection, Refinement description