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: 111.57 kDa 
• Atom Count: 8070 
• Residue Count: 993 
• Unique protein chains: 1

2AFN

STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE AND A COPPER SITE MUTANT, M150E, THAT CONTAINS ZINC

• DOI: 10.2210/pdb2AFN/pdb
• Entry: 2AFN supersedes: 1AFN

• Classification: OXIDOREDUCTASE (NITRIC OXIDE(A))
• Organism(s): Alcaligenes faecalis
• Mutation(s): No 


• Deposited: 1995-07-03 Released: 1996-08-01 
• Deposition Author(s): Murphy, M.E.P., Adman, E.T., Turley, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.223 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 

Literature

Structure of Alcaligenes faecalis nitrite reductase and a copper site mutant, M150E, that contains zinc.

Murphy, M.E., Turley, S., Kukimoto, M., Nishiyama, M., Horinouchi, S., Sasaki, H., Tanokura, M., Adman, E.T.

(1995) Biochemistry 34: 12107-12117

• PubMed: 7547950 
• DOI: 10.1021/bi00038a003
• Primary Citation of Related Structures:  
  2AFN, 1NTD


• PubMed Abstract: 
  

The structures at 2.0 and 2.25 A resolution of native and recombinant nitrite reductase from Alcaligenes faecalis show that they are identical to each other and very similar to nitrite reductase from Achromobacter cycloclastes. The crystallographic structure of a mutant, M150E, which unlike the wild-type protein cannot be reduced by pseudoazurin, shows that the glutamate replacement for methionine binds to a metal at the type I Cu site via only one oxygen. Anomalous scattering data collected at wavelengths of 1.040 and 1.377 A reveal that the metal at the type I site is a Zn. No significant differences from the native structure other than local perturbations at the type I site are seen. A local pseudo 2-fold axis relates the two domains of different monomers which form the active site. The two residues, Asp98 and His255, believed to be involved in catalysis are related by this 2-fold. An unusual (+)-(+) charge interaction between Lys269, Glu279, and His100 helps to orient the active site Cu ligand, His100. A number of negatively charged surface residues create an electrostatic field whose shape suggests that it may serve to direct incoming negatively charged nitrite as well as to dock the electron donor partner, pseudoazurin.

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Related Citations: 

• X-Ray Structure and Site-Directed Mutagenesis of a Nitrite Reductase from Alcaligenes Faecalis S-6: Roles of Two Copper Atoms in Nitrite Reduction
  Kukimoto, M., Nishiyama, M., Murphy, M.E., Turley, S., Adman, E.T., Horinouchi, S., Beppu, T.
  (1994) Biochemistry 33: 5246

• The 2.3 Angstrom X-Ray Structure of Nitrite Reductase from Achromobacter Cycloclastes
  Godden, J.W., Turley, S., Teller, D.C., Adman, E.T., Liu, M.Y., Payne, W.J., Legall, J.
  (1991) Science 253: 438

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Organizational Affiliation: 

Department of Biological Structure, School of Medicine, University of Washington, Seattle 98195-7420, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NITRITE REDUCTASE	A, B, C	343	Alcaligenes faecalis	Mutation(s): 0  Gene Names: 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: 2.00 Å
• R-Value Free: 0.223 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.035	α = 90
b = 103.61	β = 90
c = 146.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
RIGAKU	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-07-03 
• Released Date: 1996-08-01 
Deposition Author(s): Murphy, M.E.P., Adman, E.T., Turley, S.
• This entry supersedes: 1AFN

Revision History 

• Version 1.0: 1996-08-01
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-21
  Changes: Data collection, Other