7T30

Structure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN/NAD(H) bound state

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	Nickel-iron hydrogenase large subunit	8106923	4002888	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	HydB/Nqo4-like	8106924	3001849	SCOP2 (2022-06-29)
I	SCOP2B Superfamily	HydB/Nqo4-like	8106924	3001849	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	PF12838	e7t30A5	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: PF12838	ECOD (1.6)
A	PF13510	e7t30A4	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF13510	ECOD (1.6)
A	PF04879	e7t30A1	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: PF04879	ECOD (1.6)
A	F_UNCLASSIFIED	e7t30A6	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: F_UNCLASSIFIED	ECOD (1.6)
A	PF00384	e7t30A2	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: PF00384	ECOD (1.6)
A	PF10588	e7t30A3	A: extended segments	X: iron-sulfur center-binding helical hairpin (From Topology)	H: iron-sulfur center-binding helical hairpin (From Topology)	T: iron-sulfur center-binding helical hairpin	F: PF10588	ECOD (1.6)
F	PF12838	e7t30F4	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: PF12838	ECOD (1.6)
F	PF13510	e7t30F5	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF13510	ECOD (1.6)
F	PF04879	e7t30F1	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: PF04879	ECOD (1.6)
F	F_UNCLASSIFIED	e7t30F6	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: F_UNCLASSIFIED	ECOD (1.6)
F	PF00384	e7t30F2	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: PF00384	ECOD (1.6)
F	PF10588	e7t30F3	A: extended segments	X: iron-sulfur center-binding helical hairpin (From Topology)	H: iron-sulfur center-binding helical hairpin (From Topology)	T: iron-sulfur center-binding helical hairpin	F: PF10588	ECOD (1.6)
B	PF10589	e7t30B2	A: alpha bundles	X: Bromodomain-like	H: Nqo1C-terminal domain-like (From Topology)	T: Nqo1C-terminal domain-like	F: PF10589	ECOD (1.6)
B	PF10531	e7t30B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Nqo1 middle domain-like	F: PF10531	ECOD (1.6)
B	PF01512	e7t30B3	A: a/b three-layered sandwiches	X: Nqo1 FMN-binding domain-like (From Topology)	H: Nqo1 FMN-binding domain-like (From Topology)	T: Nqo1 FMN-binding domain-like	F: PF01512	ECOD (1.6)
G	PF10589	e7t30G3	A: alpha bundles	X: Bromodomain-like	H: Nqo1C-terminal domain-like (From Topology)	T: Nqo1C-terminal domain-like	F: PF10589	ECOD (1.6)
G	PF10531	e7t30G1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Nqo1 middle domain-like	F: PF10531	ECOD (1.6)
G	PF01512	e7t30G2	A: a/b three-layered sandwiches	X: Nqo1 FMN-binding domain-like (From Topology)	H: Nqo1 FMN-binding domain-like (From Topology)	T: Nqo1 FMN-binding domain-like	F: PF01512	ECOD (1.6)
C	PF01257	e7t30C1	A: alpha bundles	X: NQO2 helical bundle domain (From Topology)	H: NQO2 helical bundle domain (From Topology)	T: NQO2 helical bundle domain	F: PF01257	ECOD (1.6)
H	PF01257	e7t30H1	A: alpha bundles	X: NQO2 helical bundle domain (From Topology)	H: NQO2 helical bundle domain (From Topology)	T: NQO2 helical bundle domain	F: PF01257	ECOD (1.6)
D	F_UNCLASSIFIED	e7t30D3	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: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e7t30D4	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: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e7t30D1	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: F_UNCLASSIFIED	ECOD (1.6)
D	PF00374	e7t30D2	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: PF00374	ECOD (1.6)
I	F_UNCLASSIFIED	e7t30I4	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: F_UNCLASSIFIED	ECOD (1.6)
I	F_UNCLASSIFIED	e7t30I2	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: F_UNCLASSIFIED	ECOD (1.6)
I	F_UNCLASSIFIED	e7t30I3	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: F_UNCLASSIFIED	ECOD (1.6)
I	PF00374	e7t30I1	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: PF00374	ECOD (1.6)
E	PF01058	e7t30E1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: PF01058	ECOD (1.6)
J	PF01058	e7t30J1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: PF01058	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, F	PF04879	Molybdopterin oxidoreductase Fe4S4 domain (Molybdop_Fe4S4)	Molybdopterin oxidoreductase Fe4S4 domain	This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1].	Domain
A, F	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase	-	Family
A, F	PF13510	2Fe-2S iron-sulfur cluster binding domain (Fer2_4)	2Fe-2S iron-sulfur cluster binding domain	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. Th ...	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins.	Domain
A, F	PF00037	4Fe-4S binding domain (Fer4)	4Fe-4S binding domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich.	Domain
A, F	PF10588	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region	-	Domain
B, G	PF10531	SLBB domain (SLBB)	SLBB domain	-	Domain
B, G	PF01512	Respiratory-chain NADH dehydrogenase 51 Kd subunit (Complex1_51K)	Respiratory-chain NADH dehydrogenase 51 Kd subunit	-	Family
B, G	PF10589	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region	-	Domain
C, H	PF01257	Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx)	Thioredoxin-like [2Fe-2S] ferredoxin	-	Family
D, I	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
E, J	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, F	NiFe hydrogenase subunit A	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds cellular metabolic process ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy respiratory electron transport chain metabolic process cellular process	membrane cellular anatomical entity
B, G	NiFe hydrogenase subunit B	binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding	-	-
C, H	NiFe hydrogenase subunit C	oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-
D, I	NiFe 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	-	-
E, J	NiFe hydrogenase small subunit	oxidoreductase activity catalytic activity iron-sulfur cluster binding binding metal cluster binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, F	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A, F	IPR006656	Molybdopterin oxidoreductase	Domain
A, F	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
A, F	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
A, F	IPR000283	NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site	Conserved Site
A, F	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, F	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, F	IPR019574	NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding	Domain
B, G	IPR019575	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	Domain
B, G	IPR019554	Soluble ligand binding domain	Domain
B, G	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B, G	IPR001949	NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site	Conserved Site
B, G	IPR037225	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily	Homologous Superfamily
B, G	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, G	IPR037207	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily	Homologous Superfamily
B, G	IPR011538	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain	Domain
B, G	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
C, H	IPR028431	NADP-reducing hydrogenase subunit HndA-like	Family
C, H	IPR042128	NuoE domain	Domain
C, H	IPR002023	NADH-quinone oxidoreductase subunit E-like	Family
C, H	IPR041921	NADH-quinone oxidoreductase subunit E, N-terminal	Homologous Superfamily
C, H	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
D, I	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
D, I	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
D, I	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
E, J	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
E, J	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain