Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.37 kDa 
• Atom Count: 8922 
• Residue Count: 1008 
• Unique protein chains: 1

1NPJ

Crystal structure of H145A mutant of nitrite reductase from Alcaligenes faecalis

• DOI: 10.2210/pdb1NPJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Alcaligenes faecalis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-01-18 Released: 2003-04-29 
• Deposition Author(s): Wijma, H.J., Boulanger, M.J., Molon, A., Fittipaldi, M., Huber, M., Murphy, M.E., Verbeet, M.P., Canters, G.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.177 

Literature

Reconstitution of the type-1 active site of the H145G/A variants of nitrite reductase by ligand insertion

Wijma, H.J., Boulanger, M.J., Molon, A., Fittipaldi, M., Huber, M., Murphy, M.E., Verbeet, M.P., Canters, G.W.

(2003) Biochemistry 42: 4075-4083

• PubMed: 12680761 
• DOI: 10.1021/bi027270+
• Primary Citation of Related Structures:  
  1NPJ, 1NPN


• PubMed Abstract: 
  

Variants of the copper-containing nitrite reductase (NiR) of Alcaligenes faecalis S6 were constructed by site-directed mutagenesis, by which the C-terminal histidine ligand (His145) of the Cu in the type-1 site was replaced by an alanine or a glycine. The type-1 sites in the NiR variants as isolated, are in the reduced form, but can be oxidized in the presence of external ligands, like (substituted) imidazoles and chloride. The reduction potential of the type-1 site of NiR-H145A reconstituted with imidazole amounts to 505 mV vs NHE (20 degrees C, pH 7, 10 mM imidazole), while for the native type-1 site it amounts to 260 mV. XRD data on crystals of the reduced and oxidized NiR-H145A variant show that in the reduced type-1 site the metal is 3-coordinated, but in the oxidized form takes up a ligand from the solution. With the fourth (exogenous) ligand in place the type-1 site is able to accept electrons at about the same rate as the wt NiR, but it is unable to pass the electron onto the type-2 site, leading to loss of enzymatic activity. It is argued that the uptake of an electron by the mutated type-1 site is accompanied by a loss of the exogenous ligand and a concomitant rise of the redox potential. This rise effectively traps the electron in the type-1 site.

---

Organizational Affiliation: 

Gorlaeus Laboratories, Metallo Protein Group, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A, B, C	343	Alcaligenes faecalis	Mutation(s): 1  Gene Names: NIRK OR NIR, nirK, nir EC: 1.7.99.3 (PDB Primary Data), 1.7.2.1 (UniProt)
Find proteins for P38501 (Alcaligenes faecalis) Explore P38501  Go to UniProtKB:  P38501

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	A, B, C	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.6	α = 90
b = 102.52	β = 90
c = 146.07	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-18 
• Released Date: 2003-04-29 
Deposition Author(s): Wijma, H.J., Boulanger, M.J., Molon, A., Fittipaldi, M., Huber, M., Murphy, M.E., Verbeet, M.P., Canters, G.W.

Revision History 

• Version 1.0: 2003-04-29
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-10-03
  Changes: Advisory, Data collection