8CFF | pdb_00008cff

Crystal structure of arsenite oxidase from Alcaligenes faecalis (Af Aio) bound to arsenite

PDB DOI: https://doi.org/10.2210/pdb8CFF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Alcaligenes faecalis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-03 Released: 2023-07-12
Deposition Author(s): Engrola, F., Correia, M.A.S., Romao, M.J., Santos-Silva, T.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.204 (Depositor), 0.213 (DCC)
R-Value Work:
0.168 (Depositor), 0.178 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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 Biological Chem 299: 105036-105036

PubMed: 37442232 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2023.105036
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 437.55 kDa
Atom Count: 34,530
Modeled Residue Count: 3,825
Deposited Residue Count: 3,828
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arsenite oxidase subunit AioA	A, C, E, G	823	Alcaligenes faecalis	Mutation(s): 0 Gene Names: aioA, aoxB, asoA EC: 1.20.9.1
UniProt
Find proteins for Q7SIF4 (Alcaligenes faecalis) Explore Q7SIF4 Go to UniProtKB: Q7SIF4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SIF4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Arsenite oxidase subunit AioB	B, D, F, H	134	Alcaligenes faecalis	Mutation(s): 0 Gene Names: aioB, aoxA, asoB EC: 1.20.9.1
UniProt
Find proteins for Q7SIF3 (Alcaligenes faecalis) Explore Q7SIF3 Go to UniProtKB: Q7SIF3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SIF3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD (Subject of Investigation/LOI) Query on MGD Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain HB [auth G] SDF format, chain I [auth A] SDF format, chain IB [auth G] SDF format, chain J [auth A] SDF format, chain RA [auth E] SDF format, chain TA [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain HB [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth G] MOL2 format, chain J [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain TA [auth E] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain HB [auth G] mmCIF format, chain I [auth A] mmCIF format, chain IB [auth G] mmCIF format, chain J [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain TA [auth E]	BA [auth C] CA [auth C] HB [auth G] I [auth A] IB [auth G] BA [auth C], CA [auth C], HB [auth G], I [auth A], IB [auth G], J [auth A], RA [auth E], TA [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		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HB [auth G] Focus chain I [auth A] Focus chain IB [auth G] Focus chain J [auth A] Focus chain RA [auth E] Focus chain TA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HB [auth G] Focus chain I [auth A] Focus chain IB [auth G] Focus chain J [auth A] Focus chain RA [auth E] Focus chain TA [auth E]
F3S (Subject of Investigation/LOI) Query on F3S Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain JB [auth G] SDF format, chain L [auth A] SDF format, chain UA [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain JB [auth G] MOL2 format, chain L [auth A] MOL2 format, chain UA [auth E] mmCIF format, chain DA [auth C] mmCIF format, chain JB [auth G] mmCIF format, chain L [auth A] mmCIF format, chain UA [auth E]	DA [auth C], JB [auth G], L [auth A], UA [auth E]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain JB [auth G] Focus chain L [auth A] Focus chain UA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain JB [auth G] Focus chain L [auth A] Focus chain UA [auth E]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain FB [auth F] SDF format, chain PA [auth D] SDF format, chain VB [auth H] SDF format, chain Z [auth B] MOL2 format, chain FB [auth F] MOL2 format, chain PA [auth D] MOL2 format, chain VB [auth H] MOL2 format, chain Z [auth B] mmCIF format, chain FB [auth F] mmCIF format, chain PA [auth D] mmCIF format, chain VB [auth H] mmCIF format, chain Z [auth B]	FB [auth F], PA [auth D], VB [auth H], Z [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain FB [auth F] Focus chain PA [auth D] Focus chain VB [auth H] Focus chain Z [auth B] Interactions & Density Focus chain FB [auth F] Focus chain PA [auth D] Focus chain VB [auth H] Focus chain Z [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain MB [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth G] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth G]	M [auth A], MB [auth G]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain MB [auth G] Interactions & Density Focus chain M [auth A] Focus chain MB [auth G]
AST (Subject of Investigation/LOI) Query on AST Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain LB [auth G] SDF format, chain O [auth A] SDF format, chain WA [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain LB [auth G] MOL2 format, chain O [auth A] MOL2 format, chain WA [auth E] mmCIF format, chain EA [auth C] mmCIF format, chain LB [auth G] mmCIF format, chain O [auth A] mmCIF format, chain WA [auth E]	EA [auth C], LB [auth G], O [auth A], WA [auth E]	ARSENITE As O₃ OWTFKEBRIAXSMO-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain LB [auth G] Focus chain O [auth A] Focus chain WA [auth E] Interactions & Density Focus chain EA [auth C] Focus chain LB [auth G] Focus chain O [auth A] Focus chain WA [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain Y [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Y [auth B]	R [auth A], Y [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Focus chain Y [auth B] Interactions & Density Focus chain R [auth A] Focus chain Y [auth B]
MO (Subject of Investigation/LOI) Query on MO Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GB [auth G] SDF format, chain K [auth A] SDF format, chain SA [auth E] MOL2 format, chain AA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain K [auth A] MOL2 format, chain SA [auth E] mmCIF format, chain AA [auth C] mmCIF format, chain GB [auth G] mmCIF format, chain K [auth A] mmCIF format, chain SA [auth E]	AA [auth C], GB [auth G], K [auth A], SA [auth E]	MOLYBDENUM ATOM Mo ZOKXTWBITQBERF-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GB [auth G] Focus chain K [auth A] Focus chain SA [auth E] Interactions & Density Focus chain AA [auth C] Focus chain GB [auth G] Focus chain K [auth A] Focus chain SA [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CB [auth E] SDF format, chain DB [auth E] SDF format, chain EB [auth E] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain KB [auth G] SDF format, chain LA [auth C] SDF format, chain N [auth A] SDF format, chain SB [auth G] MOL2 format, chain CB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain KB [auth G] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain SB [auth G] mmCIF format, chain CB [auth E] mmCIF format, chain DB [auth E] mmCIF format, chain EB [auth E] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain KB [auth G] mmCIF format, chain LA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain SB [auth G]	CB [auth E] DB [auth E] EB [auth E] HA [auth C] IA [auth C] CB [auth E], DB [auth E], EB [auth E], HA [auth C], IA [auth C], KB [auth G], LA [auth C], N [auth A], SB [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain KB [auth G] Focus chain LA [auth C] Focus chain N [auth A] Focus chain SB [auth G] Interactions & Density Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain KB [auth G] Focus chain LA [auth C] Focus chain N [auth A] Focus chain SB [auth G]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain GA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain OB [auth G] SDF format, chain P [auth A] SDF format, chain PB [auth G] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain QB [auth G] SDF format, chain RB [auth G] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TB [auth G] SDF format, chain UB [auth G] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain XA [auth E] SDF format, chain YA [auth E] SDF format, chain ZA [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain GA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain OB [auth G] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain QB [auth G] MOL2 format, chain RB [auth G] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TB [auth G] MOL2 format, chain UB [auth G] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth E] mmCIF format, chain AB [auth E] mmCIF format, chain BB [auth E] mmCIF format, chain GA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain OB [auth G] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain QB [auth G] mmCIF format, chain RB [auth G] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TB [auth G] mmCIF format, chain UB [auth G] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain ZA [auth E]	AB [auth E] BB [auth E] GA [auth C] JA [auth C] KA [auth C] AB [auth E], BB [auth E], GA [auth C], JA [auth C], KA [auth C], MA [auth C], NA [auth C], OA [auth C], OB [auth G], P [auth A], PB [auth G], Q [auth A], QA [auth D], QB [auth G], RB [auth G], S [auth A], T [auth A], TB [auth G], UB [auth G], V [auth A], W [auth A], X [auth A], XA [auth E], YA [auth E], ZA [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain GA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PB [auth G] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain QB [auth G] Focus chain RB [auth G] Focus chain S [auth A] Focus chain T [auth A] Focus chain TB [auth G] Focus chain UB [auth G] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain GA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PB [auth G] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain QB [auth G] Focus chain RB [auth G] Focus chain S [auth A] Focus chain T [auth A] Focus chain TB [auth G] Focus chain UB [auth G] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain NB [auth G] SDF format, chain U [auth A] SDF format, chain VA [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain NB [auth G] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth E] mmCIF format, chain FA [auth C] mmCIF format, chain NB [auth G] mmCIF format, chain U [auth A] mmCIF format, chain VA [auth E]	FA [auth C], NB [auth G], U [auth A], VA [auth E]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain NB [auth G] Focus chain U [auth A] Focus chain VA [auth E] Interactions & Density Focus chain FA [auth C] Focus chain NB [auth G] Focus chain U [auth A] Focus chain VA [auth E]