2IWF

Resting form of pink nitrous oxide reductase from Achromobacter Cycloclastes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insight Into Catalysis of Nitrous Oxide Reductase from High-Resolution Structures of Resting and Inhibitor-Bound Enzyme from Achromobacter Cycloclastes.

Paraskevopoulos, K.Antonyuk, S.V.Sawers, R.G.Eady, R.R.Hasnain, S.S.

(2006) J Mol Biol 362: 55

  • DOI: 10.1016/j.jmb.2006.06.064
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The difficult chemistry of nitrous oxide (N2O) reduction to gaseous nitrogen (N2) in biology is catalysed by the novel micro4-sulphide-bridged tetranuclear Cuz cluster of the N2O reductases (N2OR). Two spectroscopically distinct forms of this cluster ...

    The difficult chemistry of nitrous oxide (N2O) reduction to gaseous nitrogen (N2) in biology is catalysed by the novel micro4-sulphide-bridged tetranuclear Cuz cluster of the N2O reductases (N2OR). Two spectroscopically distinct forms of this cluster have been identified as CuZ and CuZ*. We have obtained a 1.86 A resolution crystal structure of the pink-purple species of N2OR from Achromobacter cycloclastes (AcN2OR) isolated under aerobic conditions. This structure reveals a previously unobserved ligation with two oxygen atoms from H2O/OH- coordinated to Cu1 and Cu4 of the catalytic centre. We ascribe this structure to be that of the CuZ form of the cluster, since the previously reported structures of two blue species of N2ORs, also isolated aerobically, have characterised the redox inactive CuZ* form, revealing a single water molecule at Cu4. Exposure of the as-isolated AcN2OR to sodium iodide led to reduction of the electron-donating CuA site and the formation of a blue species. Structure determination of this adduct at 1.7 A resolution showed that iodide was bound at the CuZ site bridging the Cu1 and Cu4 ions. This structure represents the first observation of an inhibitor bound to the Cu1-Cu4 edge of the catalytic cluster, providing clear evidence for this being the catalytic edge in N2ORs. These structures, together with the published structural and spectroscopic data, give fresh insight into the mode of substrate binding, reduction and catalysis.


    Organizational Affiliation

    School of Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 5AF, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITROUS-OXIDE REDUCTASEA, B642Achromobacter cycloclastesMutation(s): 0 
Gene Names: nosZ
EC: 1.7.99.6 (PDB Primary Data), 1.7.2.4 (UniProt)
Find proteins for P94127 (Achromobacter cycloclastes)
Explore P94127 
Go to UniProtKB:  P94127
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CUZ
Query on CUZ

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A, B
(MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION
Cu4 S
IGIWMDIIFLPFOP-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.292α = 90
b = 118.18β = 90
c = 131.135γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance