5AA5

Actinobacterial-type NiFe-hydrogenase from Ralstonia eutropha H16 at 2.85 Angstrom resolution

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)
C	d5aa5c_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
E	d5aa5e_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
G	d5aa5g_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
I	d5aa5i_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
J [auth K]	d5aa5k_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
K [auth L]	d5aa5l_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Oxidored_q6	e5aa5F2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
F	NiFe_hyd_SSU_C	e5aa5F1	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	e5aa5A1	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	e5aa5A2	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)
B	Oxidored_q6	e5aa5B1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
B	NiFe_hyd_SSU_C	e5aa5B2	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)
D	Oxidored_q6	e5aa5D2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
D	NiFe_hyd_SSU_C	e5aa5D1	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)
H	Oxidored_q6	e5aa5H2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
H	NiFe_hyd_SSU_C	e5aa5H1	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)
L [auth M]	Oxidored_q6	e5aa5M2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
L [auth M]	NiFe_hyd_SSU_C	e5aa5M1	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	NiFeSe_Hases_2nd_1	e5aa5C1	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_1	ECOD (1.6)
C	NiFeSe_Hases_1st	e5aa5C4	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)
C	NiFeSe_Hases_3rd	e5aa5C2	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)
C	NiFeSe_Hases_3rd_1	e5aa5C3	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)
E	NiFeSe_Hases_2nd_1	e5aa5E4	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_1	ECOD (1.6)
E	NiFeSe_Hases_1st	e5aa5E1	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)
E	NiFeSe_Hases_3rd	e5aa5E3	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)
E	NiFeSe_Hases_3rd_1	e5aa5E2	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	NiFeSe_Hases_2nd_1	e5aa5G4	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_1	ECOD (1.6)
G	NiFeSe_Hases_1st	e5aa5G1	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)
G	NiFeSe_Hases_3rd	e5aa5G3	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)
G	NiFeSe_Hases_3rd_1	e5aa5G2	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)
I	NiFeSe_Hases_2nd_1	e5aa5I2	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_1	ECOD (1.6)
I	NiFeSe_Hases_1st	e5aa5I1	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)
I	NiFeSe_Hases_3rd	e5aa5I3	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)
I	NiFeSe_Hases_3rd_1	e5aa5I4	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)
J [auth K]	NiFeSe_Hases_2nd_1	e5aa5K4	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_1	ECOD (1.6)
J [auth K]	NiFeSe_Hases_1st	e5aa5K3	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)
J [auth K]	NiFeSe_Hases_3rd	e5aa5K2	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)
J [auth K]	NiFeSe_Hases_3rd_1	e5aa5K1	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)
K [auth L]	NiFeSe_Hases_2nd_1	e5aa5L2	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_1	ECOD (1.6)
K [auth L]	NiFeSe_Hases_1st	e5aa5L3	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)
K [auth L]	NiFeSe_Hases_3rd	e5aa5L1	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)
K [auth L]	NiFeSe_Hases_3rd_1	e5aa5L4	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
A	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
B	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
D	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
H	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
L [auth M]	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
C	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
E	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
G	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
I	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
J [auth K]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
K [auth L]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, D, F, H, A, B, D, F, H, L [auth M]	NIFE-HYDROGENASE SMALL SUBUNIT, HOFK	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 4 iron, 4 sulfur cluster binding electron transfer activity cation binding ion 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 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 cellular metabolic process metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	membrane cellular anatomical entity protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex [Ni-Fe] hydrogenase complex
C, E, G, I, J [auth K], C, E, G, I, J [auth K], K [auth L]	NIFE-HYDROGENASE LARGE SUBUNIT, HOFG	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, D, F, H, A, B, D, F, H, L [auth M]	IPR001821	[NiFe]-hydrogenase, small subunit	Family
A, B, D, F, H, A, B, D, F, H, L [auth M]	IPR027394	Cytochrome-c3 hydrogenase, C-terminal	Domain
A, B, D, F, H, A, B, D, F, H, L [auth M]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
A, B, D, F, H, A, B, D, F, H, L [auth M]	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
A, B, D, F, H, A, B, D, F, H, L [auth M]	IPR037148	[NiFe]-hydrogenase, small subunit, C-terminal domain superfamily	Homologous Superfamily
C, E, G, I, J [auth K], C, E, G, I, J [auth K], K [auth L]	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
C, E, G, I, J [auth K], C, E, G, I, J [auth K], K [auth L]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
C, E, G, I, J [auth K], C, E, G, I, J [auth K], K [auth L]	IPR050867	[NiFe]/[NiFeSe] hydrogenase large subunit	Family