7T2R

Structure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN-free apo 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)
C	SCOP2 Family	NQO2-like	8106925	4002945	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Thioredoxin-like	8106926	3000031	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	Thioredoxin-like	8106926	3000031	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HydB/Nqo4-like	8106924	3001849	SCOP2B (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	Fer4_7_1	e7t2rA1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_7_1	ECOD (1.6)
A	Fer2_4	e7t2rA6	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_4	ECOD (1.6)
A	Molybdop_Fe4S4	e7t2rA4	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	ECOD (1.6)
A	F_UNCLASSIFIED	e7t2rA3	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	Molybdopterin_2nd	e7t2rA5	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	NADH-G_4Fe-4S_3	e7t2rA2	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: NADH-G_4Fe-4S_3	ECOD (1.6)
F	Fer4_7_1	e7t2rF4	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_7_1	ECOD (1.6)
F	Fer2_4	e7t2rF2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_4	ECOD (1.6)
F	Molybdop_Fe4S4	e7t2rF3	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	ECOD (1.6)
F	F_UNCLASSIFIED	e7t2rF5	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	Molybdopterin_2nd	e7t2rF6	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)
F	NADH-G_4Fe-4S_3	e7t2rF1	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: NADH-G_4Fe-4S_3	ECOD (1.6)
C	2Fe-2S_thioredx_N	e7t2rC1	A: alpha bundles	X: NQO2 helical bundle domain (From Topology)	H: NQO2 helical bundle domain (From Topology)	T: NQO2 helical bundle domain	F: 2Fe-2S_thioredx_N	ECOD (1.6)
C	2Fe-2S_thioredx_C	e7t2rC2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: 2Fe-2S_thioredx_C	ECOD (1.6)
H	2Fe-2S_thioredx_N	e7t2rH1	A: alpha bundles	X: NQO2 helical bundle domain (From Topology)	H: NQO2 helical bundle domain (From Topology)	T: NQO2 helical bundle domain	F: 2Fe-2S_thioredx_N	ECOD (1.6)
H	2Fe-2S_thioredx_C	e7t2rH2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: 2Fe-2S_thioredx_C	ECOD (1.6)
D	F_UNCLASSIFIED	e7t2rD4	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	NiFeSe_Hases_1st	e7t2rD2	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	e7t2rD1	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	e7t2rD3	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	F_UNCLASSIFIED	e7t2rI3	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	NiFeSe_Hases_1st	e7t2rI4	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	e7t2rI2	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	e7t2rI1	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	Oxidored_q6	e7t2rE1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
J	Oxidored_q6	e7t2rJ1	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	NADH_4Fe-4S	e7t2rG3	A: alpha bundles	X: Bromodomain-like	H: Nqo1C-terminal domain-like (From Topology)	T: Nqo1C-terminal domain-like	F: NADH_4Fe-4S	ECOD (1.6)
G	SLBB	e7t2rG2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Nqo1 middle domain-like	F: SLBB	ECOD (1.6)
G	Complex1_51K	e7t2rG1	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: Complex1_51K	ECOD (1.6)
B	NADH_4Fe-4S	e7t2rB2	A: alpha bundles	X: Bromodomain-like	H: Nqo1C-terminal domain-like (From Topology)	T: Nqo1C-terminal domain-like	F: NADH_4Fe-4S	ECOD (1.6)
B	SLBB	e7t2rB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Nqo1 middle domain-like	F: SLBB	ECOD (1.6)
B	Complex1_51K	e7t2rB3	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: Complex1_51K	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	PF22117	NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain (Nqo3_Fer4)	NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain	NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contain ...	NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contains Fe4-S4 cluster, one of the redox centers of the complex [1-5].	Domain
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	PF10588	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)	NADH-ubiquinone oxidoreductase-G 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
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

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
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	-	-
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	-	-

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	IPR054351	NADH-ubiquinone oxidoreductase, ferredoxin-like domain	Domain
A, F	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, F	IPR050123	Prokaryotic molybdopterin-containing oxidoreductase	Family
A, F	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, F	IPR019574	NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding	Domain
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	IPR051349	Hydrogenase complex-associated protein	Family
E, J	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
E, J	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	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