2BW4

Atomic Resolution Structure of Resting State of the Achromobacter cycloclastes Cu Nitrite Reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.9 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.117 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 102: 12041

  • DOI: 10.1073/pnas.0504207102
  • Primary Citation of Related Structures:  

  • 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 a ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COPPER-CONTAINING NITRITE REDUCTASE
A
340Achromobacter cycloclastesMutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
Find proteins for P25006 (Achromobacter cycloclastes)
Go to UniProtKB:  P25006
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MLI
Query on MLI

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A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
CU
Query on CU

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.9 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.117 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 95.414α = 90.00
b = 95.414β = 90.00
c = 95.414γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance