1AS8

STRUCTURE OF NITRITE BOUND TO REDUCED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • Primary Citation of Related Structures:  1AQ8, 1AS6, 1AS7

  • 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 temp ...

    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.


    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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRITE REDUCTASE
A, B, C
343Alcaligenes faecalisGene Names: nirK (nir)
EC: 1.7.2.1
Find proteins for P38501 (Alcaligenes faecalis)
Go to UniProtKB:  P38501
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO2
Query on NO2

Download SDF File 
Download CCD File 
A, B, C
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.100α = 90.00
b = 102.800β = 90.00
c = 146.300γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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