1HAW

X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-Ray Structure of a Blue Copper Nitrite Reductase at High Ph and in Copper-Free Form at 1.9 A Resolution

Ellis, M.J.Dodd, F.E.Strange, R.W.Prudencio, M.Sawers, G.Eady, R.R.Hasnain, S.S.

(2001) Acta Crystallogr.,Sect.D 57: 1110

  • Primary Citation of Related Structures:  1HAU

  • PubMed Abstract: 
  • Copper-containing nitrite reductases possess a trimeric structure where the catalytic Cu site, located at the monomer-monomer interface, resembles the catalytic sites of a number of Zn enzymes. Nitrite reductase from Alcaligenes xylosoxidans has opti ...

    Copper-containing nitrite reductases possess a trimeric structure where the catalytic Cu site, located at the monomer-monomer interface, resembles the catalytic sites of a number of Zn enzymes. Nitrite reductase from Alcaligenes xylosoxidans has optimum activity at pH 5.2 which decreases to a negligible level at pH 8. The structure of this nitrite reductase has previously been determined at pH 4.6. It has now been crystallized under new conditions at pH 8.5. Its crystallographic structure provides a structural explanation for the greatly reduced activity of the enzyme at high pH. Characterization of overexpressed protein in solution by EXAFS suggested that the protein lacked Cu in the catalytic type 2 Cu site and that the site was most probably occupied by Zn. Using the anomalous signals from Cu and Zn, the crystal structure revealed that the expressed protein was devoid of Cu in the catalytic site and that only a trace amount (<10%) of Zn was present at this site in the crystal. Despite the close structural similarity of the catalytic site to a number of Zn enzymes, these data suggest that Zn, if it binds at the catalytic copper site, binds weakly in nitrite reductase.


    Organizational Affiliation

    Synchrotron Radiation Department, CLRC Daresbury Laboratory, Warrington WA4 4AD, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
A
336Alcaligenes xylosoxydans xylosoxydansGene Names: nir (nirK)
EC: 1.7.2.1
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans)
Go to UniProtKB:  O68601
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU1
Query on CU1

Download SDF File 
Download CCD File 
A
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 106.106α = 90.00
b = 106.106β = 90.00
c = 63.647γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
CCP4data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-02
    Type: Initial release
  • Version 1.1: 2012-05-09
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance