1NIB

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: 2.70 Å
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 

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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

  • DOI: 10.1074/jbc.270.46.27458
  • Primary Citation of Related Structures:  
    2NRD, 1NIC, 1NIB, 1NIA, 1NIF, 1NIE, 1NID

  • 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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NITRITE REDUCTASEABC340Achromobacter cycloclastesMutation(s): 0 
Gene Names: nirK
EC: 1.7.99.3 (PDB Primary Data), 1.7.2.1 (UniProt)
Find proteins for P25006 (Achromobacter cycloclastes)
Explore P25006 
Go to UniProtKB:  P25006
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.56α = 90
b = 115.36β = 90
c = 115.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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