1AS7

STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

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

  • 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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NITRITE REDUCTASEABC343Alcaligenes faecalisMutation(s): 0 
Gene Names: nirKnir
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
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.86α = 90
b = 102.8β = 90
c = 146.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
RIGAKUdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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