3MYR | pdb_00003myr

Crystal structure of [NiFe] hydrogenase from Allochromatium vinosum in its Ni-A state

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d3myrh_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Allochromatium vinosum ) [TaxId: 1049 ],	SCOPe (2.08)
F	d3myrf_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Allochromatium vinosum ) [TaxId: 1049 ],	SCOPe (2.08)
D	d3myrd_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Allochromatium vinosum ) [TaxId: 1049 ],	SCOPe (2.08)
B	d3myrb_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Allochromatium vinosum ) [TaxId: 1049 ],	SCOPe (2.08)
G	d3myrg_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	automated matches	automated matches	(Allochromatium vinosum ) [TaxId: 1049 ],	SCOPe (2.08)
E	d3myre_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	automated matches	automated matches	(Allochromatium vinosum ) [TaxId: 1049 ],	SCOPe (2.08)
C	d3myrc_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	automated matches	automated matches	(Allochromatium vinosum ) [TaxId: 1049 ],	SCOPe (2.08)
A	d3myra_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	automated matches	automated matches	(Allochromatium vinosum ) [TaxId: 1049 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	NiFeSe_Hases_2nd	e3myrH1	A: beta meanders	X: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	T: all-beta domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_2nd	ECOD (1.6)
H	NiFeSe_Hases_1st	e3myrH2	A: alpha complex topology	X: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	T: alpha-helical domain in nickel-iron hydrogenase, large subunit	F: NiFeSe_Hases_1st	ECOD (1.6)
H	NiFeSe_Hases_3rd	e3myrH3	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_3rd	ECOD (1.6)
H	NiFeSe_Hases_3rd_1	e3myrH4	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_3rd_1	ECOD (1.6)
F	NiFeSe_Hases_2nd	e3myrF1	A: beta meanders	X: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	T: all-beta domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_2nd	ECOD (1.6)
F	NiFeSe_Hases_1st	e3myrF2	A: alpha complex topology	X: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	T: alpha-helical domain in nickel-iron hydrogenase, large subunit	F: NiFeSe_Hases_1st	ECOD (1.6)
F	NiFeSe_Hases_3rd	e3myrF3	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_3rd	ECOD (1.6)
F	NiFeSe_Hases_3rd_1	e3myrF4	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_3rd_1	ECOD (1.6)
D	NiFeSe_Hases_2nd	e3myrD1	A: beta meanders	X: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	T: all-beta domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_2nd	ECOD (1.6)
D	NiFeSe_Hases_1st	e3myrD2	A: alpha complex topology	X: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	T: alpha-helical domain in nickel-iron hydrogenase, large subunit	F: NiFeSe_Hases_1st	ECOD (1.6)
D	NiFeSe_Hases_3rd	e3myrD3	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_3rd	ECOD (1.6)
D	NiFeSe_Hases_3rd_1	e3myrD4	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_3rd_1	ECOD (1.6)
B	NiFeSe_Hases_2nd	e3myrB4	A: beta meanders	X: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	T: all-beta domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_2nd	ECOD (1.6)
B	NiFeSe_Hases_1st	e3myrB1	A: alpha complex topology	X: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	T: alpha-helical domain in nickel-iron hydrogenase, large subunit	F: NiFeSe_Hases_1st	ECOD (1.6)
B	NiFeSe_Hases_3rd	e3myrB3	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_3rd	ECOD (1.6)
B	NiFeSe_Hases_3rd_1	e3myrB2	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_3rd_1	ECOD (1.6)
G	Oxidored_q6	e3myrG2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
G	NiFe_hyd_SSU_C	e3myrG1	A: few secondary structure elements	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (1.6)
E	Oxidored_q6	e3myrE2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
E	NiFe_hyd_SSU_C	e3myrE1	A: few secondary structure elements	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (1.6)
C	Oxidored_q6	e3myrC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
C	NiFe_hyd_SSU_C	e3myrC1	A: few secondary structure elements	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (1.6)
A	Oxidored_q6	e3myrA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
A	NiFe_hyd_SSU_C	e3myrA1	A: few secondary structure elements	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
F	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
D	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
B	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
G	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (4.3.0)
G	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
E	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (4.3.0)
E	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
C	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (4.3.0)
C	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
A	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (4.3.0)
A	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
A, C, E, G	PF14720	NiFe/NiFeSe hydrogenase small subunit C-terminal (NiFe_hyd_SSU_C)	NiFe/NiFeSe hydrogenase small subunit C-terminal	-	Family
A, C, E, G	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Nickel-dependent hydrogenase large subunit	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity	-	cell periphery cellular anatomical structure plasma membrane membrane
A, C, E, G	Hydrogenase (NiFe) small subunit HydA	oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding hydrogenase (acceptor) activity 4 iron, 4 sulfur cluster binding electron transfer activity cation binding oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding hydrogenase (acceptor) activity 4 iron, 4 sulfur cluster binding electron transfer activity cation binding ion binding metal ion binding	cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	cellular anatomical structure membrane protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex [Ni-Fe] hydrogenase complex cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
B, D, F, H	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
B, D, F, H	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
B, D, F, H	IPR050867	[NiFe]/[NiFeSe] hydrogenase large subunit	Family
A, C, E, G	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A, C, E, G	IPR001821	[NiFe]-hydrogenase, small subunit	Family
A, C, E, G	IPR027394	Cytochrome-c3 hydrogenase, C-terminal	Domain
A, C, E, G	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
A, C, E, G	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
A, C, E, G	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site
A, C, E, G	IPR037148	[NiFe]-hydrogenase, small subunit, C-terminal domain superfamily	Homologous Superfamily