8CCQ

Crystal structure of arsenite oxidase from Pseudorhizobium banfieldiae str. NT-26 (NT-26 Aio) bound to antimony trioxide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Arsenite oxidase in complex with antimonite and arsenite oxyanions: Insights into the catalytic mechanism.

Engrola, F.Correia, M.A.S.Watson, C.Romao, C.C.Veiros, L.F.Romao, M.J.Santos-Silva, T.Santini, J.M.

(2023) J Biol Chem 299: 105036-105036

  • DOI: https://doi.org/10.1016/j.jbc.2023.105036
  • Primary Citation of Related Structures:  
    8CCQ, 8CFF, 8CGS

  • PubMed Abstract: 

    Arsenic contamination of groundwater is among one of the biggest health threats affecting millions of people in the world. There is an urgent need for efficient arsenic biosensors where the use of arsenic metabolizing enzymes can be explored. In this work, we have solved four crystal structures of arsenite oxidase (Aio) in complex with arsenic and antimony oxyanions and the structures determined correspond to intermediate states of the enzymatic mechanism. These structural data were complemented with density-functional theory calculations providing a unique view of the molybdenum active site at different time points that, together with mutagenesis data, enabled to clarify the enzymatic mechanism and the molecular determinants for the oxidation of As(III) to the less toxic As(V) species.


  • Organizational Affiliation

    UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AroA
A, C, E, G
845Pseudorhizobium banfieldiaeMutation(s): 0 
Gene Names: aroA
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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AroB
B, D, F, H
175Pseudorhizobium 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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD (Subject of Investigation/LOI)
Query on MGD

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
JA [auth E]
KA [auth E]
W [auth C]
I [auth A],
J [auth A],
JA [auth E],
KA [auth E],
W [auth C],
WA [auth G],
X [auth C],
XA [auth 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
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
P33
Query on P33

Download Ideal Coordinates CCD File 
EB [auth G],
FB [auth G],
HA [auth C],
U [auth A],
UA [auth E]
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
F3S (Subject of Investigation/LOI)
Query on F3S

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BA [auth C],
BB [auth G],
N [auth A],
OA [auth E]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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IA [auth D],
JB [auth H],
V [auth B],
VA [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SBO (Subject of Investigation/LOI)
Query on SBO

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GA [auth C],
IB [auth G],
T [auth A],
TA [auth E]
TRIHYDROXYANTIMONITE(III)
H3 O3 Sb
SZOADBKOANDULT-UHFFFAOYSA-K
PGE
Query on PGE

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R [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4
Query on SO4

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CA [auth C]
CB [auth G]
DA [auth C]
DB [auth G]
EA [auth C]
CA [auth C],
CB [auth G],
DA [auth C],
DB [auth G],
EA [auth C],
O [auth A],
P [auth A],
PA [auth E],
Q [auth A],
QA [auth E],
RA [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
4MO (Subject of Investigation/LOI)
Query on 4MO

Download Ideal Coordinates CCD File 
AA [auth C],
AB [auth G],
M [auth A],
NA [auth E]
MOLYBDENUM(IV) ION
Mo
ZIKKVZAYJJZBGE-UHFFFAOYSA-N
GOL
Query on GOL

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FA [auth C],
GB [auth G],
HB [auth G],
S [auth A],
SA [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
O (Subject of Investigation/LOI)
Query on O

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
LA [auth E]
MA [auth E]
Y [auth C]
K [auth A],
L [auth A],
LA [auth E],
MA [auth E],
Y [auth C],
YA [auth G],
Z [auth C],
ZA [auth G]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.533α = 90
b = 148.395β = 90
c = 232.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugal--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Data collection, Database references
  • Version 1.2: 2023-08-23
    Changes: Data collection, Database references
  • Version 2.0: 2023-09-06
    Changes: Atomic model, Data collection