2BWD

Atomic Resolution Structure of Achromobacter cycloclastes Cu Nitrite Reductase with Endogenously bound Nitrite and NO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.114 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Atomic Resolution Structures of Resting-State, Substrate- and Product-Complexed Cu-Nitrite Reductase Provide Insight Into Catalytic Mechanism

Antonyuk, S.V.Strange, R.W.Sawers, G.Eady, R.R.Hasnain, S.S.

(2005) Proc Natl Acad Sci U S A 102: 12041

  • DOI: https://doi.org/10.1073/pnas.0504207102
  • Primary Citation of Related Structures:  
    2BW4, 2BW5, 2BWD, 2BWI

  • PubMed Abstract: 

    Copper-containing nitrite reductases catalyze the reduction of nitrite to nitric oxide (NO), a key step in denitrification that results in the loss of terrestrial nitrogen to the atmosphere. They are found in a wide variety of denitrifying bacteria and fungi of different physiology from a range of soil and aquatic ecosystems. Structural analysis of potential intermediates in the catalytic cycle is an important goal in understanding enzyme mechanism. Using "crystal harvesting" and substrate-soaking techniques, we have determined atomic resolution structures of four forms of the green Cu-nitrite reductase, from the soil bacterium Achromobacter cycloclastes. These structures are the resting state of the enzyme at 0.9 A, two species exhibiting different conformations of nitrite bound at the catalytic type 2 Cu, one of which is stable and also has NO present, at 1.10 A and 1.15 A, and a stable form with the product NO bound side-on to the catalytic type 2 Cu, at 1.12 A resolution. These structures provide incisive insights into the initial binding of substrate, its repositioning before catalysis, bond breakage (O-NO), and the formation of a stable NO adduct.


  • Organizational Affiliation

    Molecular Biophysics Group, Council for the Central Laboratory of the Research Councils Daresbury Laboratory, Warrington WA4 4AD, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COPPER-CONTAINING NITRITE REDUCTASE340Achromobacter cycloclastesMutation(s): 0 
EC: 1.7.2.1
UniProt
Find proteins for P25006 (Achromobacter cycloclastes)
Explore P25006 
Go to UniProtKB:  P25006
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25006
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download Ideal Coordinates CCD File 
D [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
CU
Query on CU

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
ACT
Query on ACT

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E [auth A],
F [auth A],
I [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NO2
Query on NO2

Download Ideal Coordinates CCD File 
H [auth A]NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
HOA
Query on HOA

Download Ideal Coordinates CCD File 
G [auth A]HYDROXYAMINE
H3 N O
AVXURJPOCDRRFD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.114 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.237α = 90
b = 96.237β = 90
c = 96.237γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description