2B08

Reduced acetamide-bound M150G Nitrite Reductase from Alcaligenes faecalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Effect of the methionine ligand on the reorganization energy of the type-1 copper site of nitrite reductase.

Wijma, H.J.MacPherson, I.Farver, O.Tocheva, E.I.Pecht, I.Verbeet, M.P.Murphy, M.E.P.Canters, G.W.

(2007) J Am Chem Soc 129: 519-525

  • DOI: 10.1021/ja064763j
  • Primary Citation of Related Structures:  
    2FJS, 2B08

  • PubMed Abstract: 
  • Copper-containing nitrite reductase harbors a type-1 and a type-2 Cu site. The former acts as the electron acceptor site of the enzyme, and the latter is the site of catalytic action. The effect of the methionine ligand on the reorganization energy o ...

    Copper-containing nitrite reductase harbors a type-1 and a type-2 Cu site. The former acts as the electron acceptor site of the enzyme, and the latter is the site of catalytic action. The effect of the methionine ligand on the reorganization energy of the type-1 site was explored by studying the electron-transfer kinetics between NiR (wild type (wt) and the variants Met150Gly and Met150Thr) with Fe(II)EDTA and Fe(II)HEDTA. The mutations increased the reorganization energy by 0.3 eV (30 kJ mol-1). A similar increase was found from pulse radiolysis experiments on the wt NIR and three variants (Met150Gly, Met150His, and Met150Thr). Binding of the nearby Met62 to the type-1 Cu site in Met150Gly (under influence of an allosteric effector) lowered the reorganization energy back to approximately the wt value. According to XRD data the structure of the reduced type-1 site in Met150Gly NiR in the presence of an allosteric effector is similar to that in the reduced wt NiR (solved to 1.85 A), compatible with the similarity in reorganization energy.


    Organizational Affiliation

    Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper-containing nitrite reductaseABC340Alcaligenes faecalisMutation(s): 1 
Gene Names: nirKnir
EC: 1.7.2.1
Find proteins for P38501 (Alcaligenes faecalis)
Explore P38501 
Go to UniProtKB:  P38501
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.972α = 90
b = 102.047β = 90
c = 146.423γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance