1NID

THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted.

Adman, E.T.Godden, J.W.Turley, S.

(1995) J.Biol.Chem. 270: 27458-27474

  • Primary Citation of Related Structures:  1NIA, 1NIB, 1NIC, 1NIE, 1NIF, 2NRD

  • PubMed Abstract: 
  • High resolution x-ray crystallographic structures of nitrite reductase from Achromobacter cycloclastes, undertaken in order to understand the pH optimum of the reaction with nitrite, show that at pH 5.0, 5.4, 6.0, 6.2, and 6.8, no significant changes ...

    High resolution x-ray crystallographic structures of nitrite reductase from Achromobacter cycloclastes, undertaken in order to understand the pH optimum of the reaction with nitrite, show that at pH 5.0, 5.4, 6.0, 6.2, and 6.8, no significant changes occur, other than in the occupancy of the type II copper at the active site. An extensive network of hydrogen bonds, both within and between subunits of the trimer, maintains the rigidity of the protein structure. A water occupies a site approximately 1.5 A from the site of the type II copper in the structure of the type II copper-depleted structure (at pH 5.4), again with no other significant changes in structure. In nitrite-soaked crystals, nitrite binds via its oxygens to the type II copper and replaces the water normally bound to the type II copper. The active-site cavity of the protein is distinctly hydrophobic on one side and hydrophilic on the other, providing a possible path for diffusion of the product NO. Asp-98 exhibits thermal parameter values higher than its surroundings, suggesting a role in shuttling the two protons necessary for the overall reaction. The strong structural homology with cupredoxins is described.


    Related Citations: 
    • Amino Acid Sequence of Nitrite Reductase: A Copper Protein from Achromobacter Cycloclastes
      Fenderson, F.F.,Kumar, S.,Adman, E.T.,Liu, M.-Y.,Payne, W.J.,Legall, J.
      (1991) Biochemistry 30: 7180
    • Crystallization of Nitrite Reductase from Achromobacter Cycloclastes
      Turley, S.,Adman, E.T.,Sieker, L.C.,Liu, M.-Y.,Payne, W.J.,Legall, J.
      (1988) J.Mol.Biol. 200: 417
    • 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, University of Washington, Seattle 98195-7420, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRITE REDUCTASE
A
340Achromobacter cycloclastesGene Names: nirK
EC: 1.7.2.1
Find proteins for P25006 (Achromobacter cycloclastes)
Go to UniProtKB:  P25006
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO2
Query on NO2

Download SDF File 
Download CCD File 
A
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
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: 2.2 Å
  • R-Value Work: 0.149 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 97.600α = 90.00
b = 97.600β = 90.00
c = 97.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance