4AAY

Crystal Structure of the arsenite oxidase protein complex from Rhizobium species strain NT-26


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Respiratory Arsenite Oxidase: Structure and the Role of Residues Surrounding the Rieske Cluster.

Warelow, T.P.Oke, M.Schoepp-Cothenet, B.Dahl, J.U.Bruselat, N.Sivalingam, G.N.Leimkuhler, S.Thalassinos, K.Kappler, U.Naismith, J.H.Santini, J.M.

(2013) Plos One 8: 72535

  • DOI: 10.1371/journal.pone.0072535

  • PubMed Abstract: 
  • The arsenite oxidase (Aio) from the facultative autotrophic Alphaproteobacterium Rhizobium sp. NT-26 is a bioenergetic enzyme involved in the oxidation of arsenite to arsenate. The enzyme from the distantly related heterotroph, Alcaligenes faecalis, ...

    The arsenite oxidase (Aio) from the facultative autotrophic Alphaproteobacterium Rhizobium sp. NT-26 is a bioenergetic enzyme involved in the oxidation of arsenite to arsenate. The enzyme from the distantly related heterotroph, Alcaligenes faecalis, which is thought to oxidise arsenite for detoxification, consists of a large α subunit (AioA) with bis-molybdopterin guanine dinucleotide at its active site and a 3Fe-4S cluster, and a small β subunit (AioB) which contains a Rieske 2Fe-2S cluster. The successful heterologous expression of the NT-26 Aio in Escherichia coli has resulted in the solution of its crystal structure. The NT-26 Aio, a heterotetramer, shares high overall similarity to the heterodimeric arsenite oxidase from A. faecalis but there are striking differences in the structure surrounding the Rieske 2Fe-2S cluster which we demonstrate explains the difference in the observed redox potentials (+225 mV vs. +130/160 mV, respectively). A combination of site-directed mutagenesis and electron paramagnetic resonance was used to explore the differences observed in the structure and redox properties of the Rieske cluster. In the NT-26 AioB the substitution of a serine (S126 in NT-26) for a threonine as in the A. faecalis AioB explains a -20 mV decrease in redox potential. The disulphide bridge in the A. faecalis AioB which is conserved in other betaproteobacterial AioB subunits and the Rieske subunit of the cytochrome bc 1 complex is absent in the NT-26 AioB subunit. The introduction of a disulphide bridge had no effect on Aio activity or protein stability but resulted in a decrease in the redox potential of the cluster. These results are in conflict with previous data on the betaproteobacterial AioB subunit and the Rieske of the bc 1 complex where removal of the disulphide bridge had no effect on the redox potential of the former but a decrease in cluster stability was observed in the latter.


    Organizational Affiliation

    Institute of Structural and Molecular Biology, University College London, London, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AROA
A, C, E, G
845arsenite-oxidising bacterium NT-26Gene Names: aroA
Find proteins for Q6VAL8 (arsenite-oxidising bacterium NT-26)
Go to UniProtKB:  Q6VAL8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AROB
B, D, F, H
175arsenite-oxidising bacterium NT-26Gene Names: aroB
Find proteins for Q6VAL9 (arsenite-oxidising bacterium NT-26)
Go to UniProtKB:  Q6VAL9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F3S
Query on F3S

Download SDF File 
Download CCD File 
A, C, E, G
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
4MO
Query on 4MO

Download SDF File 
Download CCD File 
A, C, E, G
MOLYBDENUM(IV) ION
Mo
ZIKKVZAYJJZBGE-UHFFFAOYSA-N
 Ligand Interaction
O
Query on O

Download SDF File 
Download CCD File 
A, C, E, G
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
B, D, F, H
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MGD
Query on MGD

Download SDF File 
Download CCD File 
A, C, E, G
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 149.130α = 90.00
b = 232.960β = 90.00
c = 141.870γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-09-25
    Type: Database references
  • Version 1.2: 2013-11-20
    Type: Derived calculations, Refinement description
  • Version 1.3: 2014-03-12
    Type: Source and taxonomy