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: 8260 
• Residue Count: 993 
• Unique protein chains: 1

1AQ8

STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE REDUCED WITH ASCORBATE

• DOI: 10.2210/pdb1AQ8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Alcaligenes faecalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-08-07 Released: 1998-02-25 
• 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 Work: 0.189 
• R-Value Observed: 0.189 

Literature

Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications.

Murphy, M.E., Turley, S., Adman, E.T.

(1997) J Biol Chem 272: 28455-28460

• PubMed: 9353305 
• DOI: 10.1074/jbc.272.45.28455
• Primary Citation of Related Structures:  
  1AQ8, 1AS8, 1AS7, 1AS6


• PubMed Abstract: 
  

The structures of oxidized, reduced, nitrite-soaked oxidized and nitrite-soaked reduced nitrite reductase from Alcaligenes faecalis have been determined at 1.8-2.0 A resolution using data collected at -160 degrees C. The active site at cryogenic temperature, as at room temperature, contains a tetrahedral type II copper site liganded by three histidines and a water molecule. The solvent site is empty when crystals are reduced with ascorbate. A fully occupied oxygen-coordinate nitrite occupies the solvent site in crystals soaked in nitrite. Ascorbate-reduced crystals soaked in a glycerol-methanol solution and nitrite at -40 degrees C remain colorless at -160 degrees C but turn amber-brown when warmed, suggesting that NO is released. Nitrite is found at one-half occupancy. Five new solvent sites in the oxidized nitrite bound form exhibit defined but different occupancies in the other three forms. These results support a previously proposed mechanism by which nitrite is bound primarily by a single oxygen atom that is protonable, and after reduction and cleavage of that N-O bond, NO is released leaving the oxygen atom bound to the Cu site as hydroxide or water.

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Related Citations: 

• 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

• 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, Washington 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 Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.79	α = 90
b = 102.4	β = 90
c = 146.2	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: 1997-08-07 
• Released Date: 1998-02-25 
Deposition Author(s): Murphy, M.E.P., Adman, E.T., Turley, S.

Revision History 

• Version 1.0: 1998-02-25
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance