6TGA

Cryo-EM Structure of as isolated form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus

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 [auth G]	SCOP2B Superfamily	Thioredoxin-like	8101397	3000031	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	Thioredoxin-like	8101397	3000031	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	PF01568	e6tgaA3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: PF01568	ECOD (1.6)
A	PF00037,PF12837	e6tgaA4	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: PF00037,PF12837	ECOD (1.6)
A	PF13510	e6tgaA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF13510	ECOD (1.6)
A	PF04879	e6tgaA7	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	PF00384	e6tgaA5	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	e6tgaA6	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)
E	PF01568	e6tgaE3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: PF01568	ECOD (1.6)
E	PF00037,PF12837	e6tgaE4	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: PF00037,PF12837	ECOD (1.6)
E	PF13510	e6tgaE2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF13510	ECOD (1.6)
E	PF04879	e6tgaE7	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)
E	PF00384	e6tgaE5	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)
E	PF10588	e6tgaE6	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	e6tgaB2	A: alpha bundles	X: Bromodomain-like	H: Nqo1C-terminal domain-like (From Topology)	T: Nqo1C-terminal domain-like	F: PF10589	ECOD (1.6)
B	F_UNCLASSIFIED	e6tgaB4	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Nqo1 middle domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e6tgaB3	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF01512	e6tgaB1	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)
F	PF10589	e6tgaF2	A: alpha bundles	X: Bromodomain-like	H: Nqo1C-terminal domain-like (From Topology)	T: Nqo1C-terminal domain-like	F: PF10589	ECOD (1.6)
F	F_UNCLASSIFIED	e6tgaF4	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Nqo1 middle domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
F	F_UNCLASSIFIED	e6tgaF3	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: F_UNCLASSIFIED	ECOD (1.6)
F	PF01512	e6tgaF1	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 [auth G]	PF01257	e6tgaG2	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)
C [auth G]	PF01257	e6tgaG1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: PF01257	ECOD (1.6)
G [auth C]	PF01257	e6tgaC1	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)
G [auth C]	PF01257	e6tgaC2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: PF01257	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E	PF01568	Molydopterin dinucleotide binding domain (Molydop_binding)	Molydopterin dinucleotide binding domain	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entir ...	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2].	Domain
A, E	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, 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
A, E	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase	-	Family
A, E	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, E	PF10588	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region	-	Domain
B, F	PF01512	Respiratory-chain NADH dehydrogenase 51 Kd subunit (Complex1_51K)	Respiratory-chain NADH dehydrogenase 51 Kd subunit	-	Family
B, F	PF10589	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region	-	Domain
C [auth G], G [auth C]	PF01257	Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx)	Thioredoxin-like [2Fe-2S] ferredoxin	-	Family
D, H	PF11390	NADH-dependant formate dehydrogenase delta subunit FdsD (FdsD)	NADH-dependant formate dehydrogenase delta subunit FdsD	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E	Formate dehydrogenase subunit alpha	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding organic cyclic compound binding molybdopterin cofactor binding 4 iron, 4 sulfur cluster binding oxidoreductase activity formate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor cation binding iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding organic cyclic compound binding molybdopterin cofactor binding 4 iron, 4 sulfur cluster binding oxidoreductase activity formate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor cation binding ion binding metal ion binding	organic substance metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process organic acid metabolic process formate metabolic process cellular respiration energy derivation by oxidation of organic compounds generation of precursor metabolites and energy	protein-containing complex catalytic complex oxidoreductase complex
B, F	Formate dehydrogenase subunit beta	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 iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding 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 iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion 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	-	-
C [auth G], G [auth C]	Formate dehydrogenase subunit gamma	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, H	NAD-dependent formate dehydrogenase subunit delta	oxidoreductase activity catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A, E	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A, E	IPR006656	Molybdopterin oxidoreductase	Domain
A, E	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
A, E	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
A, E	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A, E	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site	Conserved Site
A, E	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, E	IPR041924	Formate dehydrogenase H, N-terminal	Domain
A, E	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, E	IPR006478	Formate dehydrogenase, alpha subunit	Family
A, E	IPR019574	NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding	Domain
B, F	IPR019575	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	Domain
B, F	IPR001949	NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site	Conserved Site
B, F	IPR037225	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily	Homologous Superfamily
B, F	IPR037207	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily	Homologous Superfamily
B, F	IPR011538	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain	Domain
C [auth G], G [auth C]	IPR028431	NADP-reducing hydrogenase subunit HndA-like	Family
C [auth G], G [auth C]	IPR002023	NADH-quinone oxidoreductase subunit E-like	Family
C [auth G], G [auth C]	IPR041921	NADH-quinone oxidoreductase subunit E, N-terminal	Homologous Superfamily
C [auth G], G [auth C]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
D, H	IPR021074	Formate dehydrogenase, delta subunit	Family