1NTD

STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE MUTANT M150E THAT CONTAINS ZINC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • Primary Citation of Related Structures:  

  • 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 s ...

    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.


    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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRITE REDUCTASE
A
343Alcaligenes faecalisMutation(s): 1 
Gene Names: nirK (nir)
EC: 1.7.2.1
Find proteins for P38501 (Alcaligenes faecalis)
Go to UniProtKB:  P38501
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.172 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 127.760α = 90.00
b = 127.760β = 90.00
c = 67.020γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
XENGENdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-03-21
    Type: Data collection, Other