8BEW | pdb_00008bew

Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	NADH_4Fe-4S	e8bewB2	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	Fer4_21_1	e8bewB5	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
B	SLBB	e8bewB3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Nqo1 middle domain-like	F: SLBB	ECOD (1.6)
B	2Fe-2S_thioredx_C_1	e8bewB4	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: 2Fe-2S_thioredx_C_1	ECOD (1.6)
B	Complex1_51K	e8bewB1	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)
E	NADH_4Fe-4S	e8bewE2	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)
E	Fer4_21_1	e8bewE5	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
E	SLBB	e8bewE3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Nqo1 middle domain-like	F: SLBB	ECOD (1.6)
E	2Fe-2S_thioredx_C_1	e8bewE4	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: 2Fe-2S_thioredx_C_1	ECOD (1.6)
E	Complex1_51K	e8bewE1	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)
C	2Fe-2S_thioredx_N	e8bewC2	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	e8bewC1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: 2Fe-2S_thioredx_C	ECOD (1.6)
F	2Fe-2S_thioredx_N	e8bewF1	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)
F	2Fe-2S_thioredx_C	e8bewF2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: 2Fe-2S_thioredx_C	ECOD (1.6)
A	Fer4_7_1	e8bewA2	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	e8bewA4	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_4	ECOD (1.6)
A	Fe_hyd_lg_C	e8bewA1	A: a/b three-layered sandwiches	X: Fe-only hydrogenase (From Topology)	H: Fe-only hydrogenase (From Topology)	T: Fe-only hydrogenase	F: Fe_hyd_lg_C	ECOD (1.6)
A	NADH-G_4Fe-4S_3	e8bewA3	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)
A	Fe_hyd_SSU	e8bewA5	A: extended segments	X: Fe-only hydrogenase smaller subunit (From Topology)	H: Fe-only hydrogenase smaller subunit (From Topology)	T: Fe-only hydrogenase smaller subunit	F: Fe_hyd_SSU	ECOD (1.6)
D	Fer4_7_1	e8bewD2	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)
D	Fer2_4	e8bewD4	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_4	ECOD (1.6)
D	Fe_hyd_lg_C	e8bewD1	A: a/b three-layered sandwiches	X: Fe-only hydrogenase (From Topology)	H: Fe-only hydrogenase (From Topology)	T: Fe-only hydrogenase	F: Fe_hyd_lg_C	ECOD (1.6)
D	NADH-G_4Fe-4S_3	e8bewD3	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)
D	Fe_hyd_SSU	e8bewD5	A: extended segments	X: Fe-only hydrogenase smaller subunit (From Topology)	H: Fe-only hydrogenase smaller subunit (From Topology)	T: Fe-only hydrogenase smaller subunit	F: Fe_hyd_SSU	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
B	3.40.50.11540	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH-ubiquinone oxidoreductase 51kDa subunit	CATH (utative)
B	3.10.20.600	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
B	1.20.1440.230	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	CATH (utative)
E	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
E	3.40.50.11540	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH-ubiquinone oxidoreductase 51kDa subunit	CATH (utative)
E	3.10.20.600	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
E	1.20.1440.230	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	CATH (utative)
C	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
F	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E	PF12838	4Fe-4S dicluster domain (Fer4_7)	4Fe-4S dicluster 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 contai ...	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 contains two 4Fe4S clusters.	Domain
B, E	PF01257	Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx)	Thioredoxin-like [2Fe-2S] ferredoxin	-	Family
B, E	PF01512	Nuo51 FMN-binding domain (Complex1_51K)	Nuo51 FMN-binding domain	This entry represents the FMN-binding domain of NADH-ubiquinone oxidoreductase 51kDa subunit from NADH:ubiquinone oxidoreductase.	Domain
B, E	PF10589	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region		Domain
C, F	PF01257	Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx)	Thioredoxin-like [2Fe-2S] ferredoxin	-	Family
A, D	PF02906	Iron only hydrogenase large subunit, C-terminal domain (Fe_hyd_lg_C)	Iron only hydrogenase large subunit, C-terminal domain		Domain
A, D	PF02256	Iron hydrogenase small subunit (Fe_hyd_SSU)	Iron hydrogenase small subunit	This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold [1].	Domain
A, D	PF22117	NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain (Fer4_Nqo3)	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, D	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, D	PF10588	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, E	Electron bifurcating hydrogenase subunit HydB	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrogen dehydrogenase (NADP+) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor oxidoreductase activity, acting on hydrogen as donor, NAD or NADP as acceptor FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrogen dehydrogenase (NADP+) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor oxidoreductase activity, acting on hydrogen as donor, NAD or NADP as acceptor catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding	-	-
C, F	Electron bifurcating hydrogenase subunit HydC	hydrogen dehydrogenase (NADP+) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor oxidoreductase activity, acting on hydrogen as donor, NAD or NADP as acceptor 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	-	-
A, D	Electron bifurcating hydrogenase subunit HydA1	hydrogen dehydrogenase (NADP+) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor oxidoreductase activity, acting on hydrogen as donor, NAD or NADP as acceptor catalytic activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor ferredoxin hydrogenase activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding transition metal ion binding hydrogen dehydrogenase (NADP+) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor oxidoreductase activity, acting on hydrogen as donor, NAD or NADP as acceptor catalytic activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor ferredoxin hydrogenase activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity 4 iron, 4 sulfur cluster binding	aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain ATP synthesis coupled electron transport electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, E	IPR019575	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	Domain
B, E	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B, E	IPR001949	NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site	Conserved Site
B, E	IPR037225	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily	Homologous Superfamily
B, E	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, E	IPR037207	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily	Homologous Superfamily
B, E	IPR011538	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain	Domain
B, E	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
C, F	IPR028431	NADP-reducing hydrogenase subunit HndA-like	Family
C, F	IPR042128	NuoE domain	Domain
C, F	IPR002023	NADH-quinone oxidoreductase subunit E-like	Family
C, F	IPR041921	NADH-quinone oxidoreductase subunit E, N-terminal	Homologous Superfamily
C, F	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A, D	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
A, D	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
A, D	IPR009016	Iron hydrogenase	Homologous Superfamily
A, D	IPR000283	NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site	Conserved Site
A, D	IPR054351	NADH-ubiquinone oxidoreductase, ferredoxin-like domain	Domain
A, D	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, D	IPR004108	Iron hydrogenase, large subunit, C-terminal	Domain
A, D	IPR036991	Iron hydrogenase, small subunit superfamily	Homologous Superfamily
A, D	IPR050340	Cytosolic Fe-S Cluster Assembly Factor	Family
A, D	IPR049830	NADP-reducing hydrogenase subunit HndD	Family
A, D	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, D	IPR013352	Iron hydrogenase, subset	Domain
A, D	IPR003149	Iron hydrogenase, small subunit	Domain
A, D	IPR019574	NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding	Domain

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Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

8BEW | pdb_00008bew