4AAY | pdb_00004aay

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 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1371/journal.pone.0072535
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 455.26 kDa 
  • Atom Count: 30,609 
  • Modeled Residue Count: 3,900 
  • Deposited Residue Count: 4,080 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AROA
A, C, E, G
845Pseudorhizobium banfieldiaeMutation(s): 0 
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
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AROB
B, D, F, H
175Pseudorhizobium banfieldiaeMutation(s): 0 
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
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / 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
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-UHFFFAOYSA-N
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
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
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
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
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description