1G8K | pdb_00001g8k

CRYSTAL STRUCTURE ANALYSIS OF ARSENITE OXIDASE FROM ALCALIGENES FAECALIS

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1g8ka1	All beta proteins	Double psi beta-barrel	ADC-like	Formate dehydrogenase/DMSO reductase, C-terminal domain	Arsenite oxidase large subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
A	d1g8ka2	Alpha and beta proteins (a/b)	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Arsenite oxidase large subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
C	d1g8kc1	All beta proteins	Double psi beta-barrel	ADC-like	Formate dehydrogenase/DMSO reductase, C-terminal domain	Arsenite oxidase large subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
C	d1g8kc2	Alpha and beta proteins (a/b)	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Arsenite oxidase large subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
E	d1g8ke1	All beta proteins	Double psi beta-barrel	ADC-like	Formate dehydrogenase/DMSO reductase, C-terminal domain	Arsenite oxidase large subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
E	d1g8ke2	Alpha and beta proteins (a/b)	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Arsenite oxidase large subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
G	d1g8kg1	All beta proteins	Double psi beta-barrel	ADC-like	Formate dehydrogenase/DMSO reductase, C-terminal domain	Arsenite oxidase large subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
G	d1g8kg2	Alpha and beta proteins (a/b)	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Arsenite oxidase large subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
B	d1g8kb_	All beta proteins	ISP domain	ISP domain	Rieske iron-sulfur protein (ISP)	Arsenite oxidase Rieske subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
D	d1g8kd_	All beta proteins	ISP domain	ISP domain	Rieske iron-sulfur protein (ISP)	Arsenite oxidase Rieske subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
F	d1g8kf_	All beta proteins	ISP domain	ISP domain	Rieske iron-sulfur protein (ISP)	Arsenite oxidase Rieske subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)
H	d1g8kh_	All beta proteins	ISP domain	ISP domain	Rieske iron-sulfur protein (ISP)	Arsenite oxidase Rieske subunit	(Alcaligenes faecalis ) [TaxId: 511 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Formate dehydrogenase/DMSO reductase, domains 1-3	8020632	4000801	SCOP2 (2022-06-29)
A	SCOP2 Family	Formate dehydrogenase/DMSO reductase, C-terminal domain	8030139	4002360	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Formate dehydrogenase/DMSO reductase, domains 1-3	8033012	3001453	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ADC-like	8042518	3001132	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Formate dehydrogenase/DMSO reductase, domains 1-3	8033012	3001453	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ADC-like	8042518	3001132	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Formate dehydrogenase/DMSO reductase, domains 1-3	8033012	3001453	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ADC-like	8042518	3001132	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Formate dehydrogenase/DMSO reductase, domains 1-3	8033012	3001453	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	ADC-like	8042518	3001132	SCOP2B (2022-06-29)
B	SCOP2 Family	Rieske iron-sulfur protein (ISP)	8029170	4001667	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	ISP domain	8041549	3000233	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	ISP domain	8041549	3000233	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	ISP domain	8041549	3000233	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	ISP domain	8041549	3000233	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Molydop_binding	e1g8kA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
A	Molybdop_Fe4S4,arsenite_ox_L	e1g8kA2	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4,arsenite_ox_L	ECOD (1.6)
A	Molybdopterin_2nd	e1g8kA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
A	Molybdopterin_1st_1	e1g8kA4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
C	Molydop_binding	e1g8kC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
C	Molybdop_Fe4S4,arsenite_ox_L	e1g8kC4	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4,arsenite_ox_L	ECOD (1.6)
C	Molybdopterin_2nd	e1g8kC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
C	Molybdopterin_1st_1	e1g8kC3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
E	Molydop_binding	e1g8kE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
E	Molybdop_Fe4S4,arsenite_ox_L	e1g8kE4	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4,arsenite_ox_L	ECOD (1.6)
E	Molybdopterin_2nd	e1g8kE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
E	Molybdopterin_1st_1	e1g8kE3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
G	Molydop_binding	e1g8kG1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
G	Molybdop_Fe4S4,arsenite_ox_L	e1g8kG4	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4,arsenite_ox_L	ECOD (1.6)
G	Molybdopterin_2nd	e1g8kG2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
G	Molybdopterin_1st_1	e1g8kG3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
B	arsenite_ox_S	e1g8kB1	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: arsenite_ox_S	ECOD (1.6)
B	Rieske_4	e1g8kB2	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_4	ECOD (1.6)
D	arsenite_ox_S	e1g8kD1	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: arsenite_ox_S	ECOD (1.6)
D	Rieske_4	e1g8kD2	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_4	ECOD (1.6)
F	arsenite_ox_S	e1g8kF1	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: arsenite_ox_S	ECOD (1.6)
F	Rieske_4	e1g8kF2	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_4	ECOD (1.6)
H	arsenite_ox_S	e1g8kH1	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: arsenite_ox_S	ECOD (1.6)
H	Rieske_4	e1g8kH2	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.200.200	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
A	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
C	2.60.40.4210	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
C	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
C	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
E	3.30.200.200	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
E	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
E	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
E	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
G	3.30.200.200	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
G	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
G	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
G	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
B	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
D	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
F	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
H	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF01568	Molydopterin dinucleotide binding domain (Molydop_binding)	Molydopterin dinucleotide binding domain	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire s ...	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2].	Domain
A, C, E, G	PF18465	Rieske 3Fe-4S (Rieske_3)	Rieske 3Fe-4S	This domain is comprised of the iron-sulphur cluster and Rieske subunit found in the large subunit of arsenite oxidase. Arsenite oxidase is a 100 kDa molybdenum- and iron-sulfur-containing protein located on the outer surface of the inner membrane of ...	This domain is comprised of the iron-sulphur cluster and Rieske subunit found in the large subunit of arsenite oxidase. Arsenite oxidase is a 100 kDa molybdenum- and iron-sulfur-containing protein located on the outer surface of the inner membrane of Gram-negative organisms. The large subunit of arsenite oxidase is similar to other members of the dimethylsulfoxide (DMSO) reductase family of molybdenum enzymes. The large subunit of arsenite oxidase is divided into four domains, with domain I binding the [3Fe-4S] cluster . Domain I, consists of three antiparallel beta sheets and six helices. The [3Fe-4S] cluster is coordinated by the motif Cys21-X2-Cys24-X3-Cys28 near the interface with domains III and IV. A large, flattened funnel-like cavity bounded by domains I, II, and III leads to the molybdenum center Pfam:PF00384 located near the center of the molecule [1].	Domain
A, C, E, G	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase		Domain
B, D, F, H	PF00355	Rieske [2Fe-2S] domain (Rieske)	Rieske [2Fe-2S] domain	The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in ...	The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilises the protein [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	ARSENITE OXIDASE	oxidoreductase activity, acting on phosphorus or arsenic in donors, with a copper protein as acceptor arsenate reductase (azurin) activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on phosphorus or arsenic in donors oxidoreductase activity, acting on NAD(P)H NADH dehydrogenase activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding molybdopterin cofactor binding cation binding oxidoreductase activity, acting on phosphorus or arsenic in donors, with a copper protein as acceptor arsenate reductase (azurin) activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on phosphorus or arsenic in donors oxidoreductase activity, acting on NAD(P)H NADH dehydrogenase activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding molybdopterin cofactor binding cation binding ion binding metal ion binding	cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	protein-containing complex catalytic complex oxidoreductase complex cellular anatomical structure membrane
B, D, F, H	ARSENITE OXIDASE	oxidoreductase activity, acting on phosphorus or arsenic in donors, with a copper protein as acceptor arsenate reductase (azurin) activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on phosphorus or arsenic in donors iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A, C, E, G	IPR006656	Molybdopterin oxidoreductase	Domain
A, C, E, G	IPR014066	Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, large subunit	Family
A, C, E, G	IPR041632	Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, 3Fe-4S cluster	Domain
A, C, E, G	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR050123	Prokaryotic molybdopterin-containing oxidoreductase	Family
B, D, F, H	IPR017941	Rieske [2Fe-2S] iron-sulphur domain	Domain
B, D, F, H	IPR005805	Rieske iron-sulphur protein, C-terminal	Domain
B, D, F, H	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily
B, D, F, H	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
B, D, F, H	IPR014349	Rieske iron-sulphur protein	Family
B, D, F, H	IPR014067	Arsenite oxidase subunit AioB/Iodate reductase subunit IdrB, small subunit	Family
B, D, F, H	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
E, F	arsenite oxidase M-CSA #144	Arsenite oxidase oxidises arsenite (As(III)O₃^3-)to the less toxic arsenate (As(V)O₄^3-). The electrons produced are transferred towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin. Arsenite oxidase is a heterodimeric enzyme containing a large and a small subunit. The large catalytic subunit harbours the molybdopterin cofactor (comprising two molybdopterin guanosine dinucleotide cofactors bound to molybdenum), and a [3Fe-4S] cluster; the small subunit belongs to the structural class of the Rieske proteins and contains a Rieske-type [2Fe-2S] clusters.	Defined by 6 residues: CYS:E-24SER:E-98SER:E-99SER:E-238HIS:F-62HIS:F-81 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.20.9.1 (UniProt) Search M-CSA Motif + EC 1.20.9.1