1NDS

CRYSTALLOGRAPHIC STRUCTURE OF A SUBSTRATE BOUND BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of a blue-copper nitrite reductase and its substrate-bound complex.

Dodd, F.E.Hasnain, S.S.Abraham, Z.H.Eady, R.R.Smith, B.E.

(1997) Acta Crystallogr.,Sect.D 53: 406-418

  • DOI: 10.1107/S0907444997002667
  • Primary Citation of Related Structures:  1NDR

  • PubMed Abstract: 
  • Copper-containing nitrite reductases (NiR's) have been conveniently subdivided into blue and green NiR's which are thought to be redox partners of azurins and pseudo-azurins, respectively. Crystal structures of two green NiR's have recently been dete ...

    Copper-containing nitrite reductases (NiR's) have been conveniently subdivided into blue and green NiR's which are thought to be redox partners of azurins and pseudo-azurins, respectively. Crystal structures of two green NiR's have recently been determined. Alcaligenes xylosoxidans has been shown to have a blue-copper nitrite reductase (AxNiR) and two azurins with 67% homology both of which donate electrons to it effectively. The first crystal structure of a blue NiR (AxNiR) in its oxidized and nitrite-bound forms, with particular emphasis to the Cu sites, is presented. The Cu-Smet distance is the same as those in the green NiR's. Thus, the length of this interaction is unlikely to be responsible for differences in colour. Crystallographic data presented here taken together with structural data of other single Cu type-1 proteins and their mutants suggest that the displacement of Cu from the strong ligand plane is perhaps the cause for the differences in colour observed for otherwise 'classical' blue Cu centre. Nitrite is observed binding to the catalytic Cu in a bidentate fashion displacing the water molecule, offering a neat rationalization for the XAFS observation that the type-2 Cu-ligand distances increase on nitrite binding as a result of increased coordination. These results are discussed in terms of enzyme mechanism.


    Related Citations: 
    • Purification and Characterization of the Dissimilatory Nitrite Reductase from Alcaligenes Xylosoxidans Subsp. Xylosoxidans (N.C.I.M.B. 11015): Evidence for the Presence of Both Type 1 and Type 2 Copper Centers
      Abraham, Z.H.,Lowe, D.J.,Smith, B.E.
      (1993) Biochem.J. 295: 587


    Organizational Affiliation

    Molecular Biophysics Group, Synchrotron Radiation Department, CCLRC Daresbury Laboratory, Warrington, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRITE REDUCTASE
A, B, C
330Alcaligenes xylosoxydans xylosoxydansGene Names: nirK
EC: 1.7.2.1
Find proteins for P81445 (Alcaligenes xylosoxydans xylosoxydans)
Go to UniProtKB:  P81445
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO2
Query on NO2

Download SDF File 
Download CCD File 
A, B, C
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.890α = 90.00
b = 102.200β = 90.00
c = 151.880γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
X-PLORphasing
CCP4data scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance