4AAY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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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
  • Primary Citation of Related Structures:  
    4AAY

  • 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, 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 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AROAA, C, E, G845Pseudorhizobium banfieldiaeMutation(s): 0 
Gene Names: aroAaioANT26_p10030
EC: 1.20.98.1
UniProt
Find proteins for Q6VAL8 (Pseudorhizobium banfieldiae)
Explore Q6VAL8 
Go to UniProtKB:  Q6VAL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6VAL8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AROBB, D, F, H175Pseudorhizobium banfieldiaeMutation(s): 0 
Gene Names: aroB
UniProt
Find proteins for Q6VAL9 (Pseudorhizobium banfieldiae)
Explore Q6VAL9 
Go to UniProtKB:  Q6VAL9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6VAL9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD

Download Ideal Coordinates CCD File 
AA [auth G],
BA [auth G],
I [auth A],
J [auth A],
O [auth C],
AA [auth G],
BA [auth G],
I [auth A],
J [auth A],
O [auth C],
P [auth C],
U [auth E],
V [auth E]
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
EA [auth G],
M [auth A],
S [auth C],
Y [auth E]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
FA [auth H],
N [auth B],
T [auth D],
Z [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
4MO
Query on 4MO

Download Ideal Coordinates CCD File 
DA [auth G],
L [auth A],
R [auth C],
X [auth E]
MOLYBDENUM(IV) ION
Mo
ZIKKVZAYJJZBGE-UHFFFAOYSA-N
 Ligand Interaction
O
Query on O

Download Ideal Coordinates CCD File 
CA [auth G],
K [auth A],
Q [auth C],
W [auth E]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.13α = 90
b = 232.96β = 90
c = 141.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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