2DWS

Cu-containing nitrite reductase at pH 8.4 with bound nitrite

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

Jacobson, F., Pistorius, A., Farkas, D., De Grip, W., Hansson, O., Sjolin, L., Neutze, R.

(2007) J.Biol.Chem. 282: 6347-6355

  • DOI: 10.1074/jbc.M605746200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite ...

    Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.

    Organizational Affiliation: 

    Department of Chemical and Biological Engineering, Chalmers University of Technology, Box 462, SE-40530 Göteborg, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Copper-containing nitrite reductase
A
328Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)Mutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
Find proteins for Q53239 (Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3))
Go to UniProtKB:  Q53239
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO2
Query on NO2
Download SDF File 
Download CCD File 
A
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
CU
Query on CU
Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 82.204α = 90.00
b = 82.204β = 90.00
c = 146.152γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-08-16 
  • Released Date: 2006-12-05 
  • Deposition Author(s): Jacobson, F.

Revision History 

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Data collection, Refinement description