1HAU

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: 1.90 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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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 D Biol Crystallogr 57: 1110

  • DOI: 10.1107/s0907444901008654
  • Primary Citation of Related Structures:  
    1HAW, 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 optimum activity at pH 5 ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASEA336Achromobacter xylosoxidansMutation(s): 0 
Gene Names: nir, nirK, ERS451415_02178
EC: 1.7.99.3 (PDB Primary Data), 1.7.2.1 (PDB Primary Data)
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans)
Explore O68601 
Go to UniProtKB:  O68601
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU
Download Ideal Coordinates CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.978α = 90
b = 80.978β = 90
c = 99.781γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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