7BKE | pdb_00007bke

Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (heterodisulfide reductase core and mobile arm in conformational state 2, composite structure)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
I [auth D]	SCOP2 Family	Formate dehydrogenase/DMSO reductase, domains 1-3	8105472	4000801	SCOP2 (2022-06-29)
I [auth D]	SCOP2 Superfamily	Formate dehydrogenase/DMSO reductase, domains 1-3	8105473	3001453	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I [auth D]	Lant_dehydr_C	e7bkeD1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Lant_dehydr_C	ECOD (v294.1)
E [auth F]	Lant_dehydr_C	e7bkeF1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Lant_dehydr_C	ECOD (v294.1)
H [auth b]	Lant_dehydr_C	e7bkeb1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Lant_dehydr_C	ECOD (v294.1)
C [auth B]	Lant_dehydr_C	e7bkeB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Lant_dehydr_C	ECOD (v294.1)
G [auth c]	Lant_dehydr_C	e7bkec1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Lant_dehydr_C	ECOD (v294.1)
B [auth C]	Lant_dehydr_C	e7bkeC1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Lant_dehydr_C	ECOD (v294.1)
D [auth a]	NDUS4	e7bkea1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: NDUS4	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I [auth D]	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (utative)
H [auth b]	1.20.1050.140	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (utative)
C [auth B]	1.20.1050.140	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (utative)
G [auth c]	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (utative)
B [auth C]	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (utative)
D [auth a]	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth D]	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
I [auth D]	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase		Domain
F [auth E]	PF04422	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term (FrhB_FdhB_N)	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term	-	Family
F [auth E]	PF04432	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus (FrhB_FdhB_C)	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus	Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum fo ...	Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2, Swiss:P06130) is also a member of this family [3]. This region is often found in association with the 4Fe-4S binding domain, fer4 (Pfam:PF00037).	Domain
E [auth F]	PF02662	Methyl-viologen-reducing hydrogenase, delta subunit (FlpD)	Methyl-viologen-reducing hydrogenase, delta subunit	-	Family
C [auth B], H [auth b]	PF02754	Cysteine-rich domain (CCG)	Cysteine-rich domain	The key element of this domain is the CX31-38CCX33-34CXXC sequence motif normally found at the C-terminus in archaeal and bacterial Hdr-like proteins [2]. There may be one or two copies, and the motif is probably an iron-sulfur binding cluster. In so ...	The key element of this domain is the CX31-38CCX33-34CXXC sequence motif normally found at the C-terminus in archaeal and bacterial Hdr-like proteins [2]. There may be one or two copies, and the motif is probably an iron-sulfur binding cluster. In some instances one of the cysteines is replaced by an aspartate, and aspartate can in principle also function as a ligand of an iron-sulfur cluster [2]. The entry includes a subunit from heterodisulphide reductase and a subunit from glycolate oxidase (Swiss:P52074) [1] and glycerol-3-phosphate dehydrogenase.	Domain
B [auth C], G [auth c]	PF13183	4Fe-4S dicluster domain (Fer4_8)	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, D [auth a]	PF12831	FAD dependent oxidoreductase (FAD_oxidored)	FAD dependent oxidoreductase	-	Family
A, D [auth a]	PF13187	4Fe-4S dicluster domain (Fer4_9)	4Fe-4S dicluster domain	-	Family
A, D [auth a]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth D]	Formate dehydrogenase	oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity NADH dehydrogenase activity binding molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding formate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor cation binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity NADH dehydrogenase activity binding molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding formate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor cation binding ion binding metal ion binding	oxoacid 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 respiratory electron transport chain electron transport chain generation of precursor metabolites and energy	cellular anatomical structure membrane
F [auth E]	Formate dehydrogenase, beta subunit (F420)	iron-sulfur cluster binding binding metal cluster binding small molecule binding oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups catalytic activity cation binding ion binding metal ion binding	-	-
E [auth F]	F420-non-reducing hydrogenase subunit D	oxidoreductase activity catalytic activity iron-sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-
C [auth B], H [auth b]	CoB--CoM heterodisulfide reductase subunit B	oxidoreductase activity, acting on a sulfur group of donors CoB--CoM heterodisulfide reductase activity oxidoreductase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding	cellular respiration energy derivation by oxidation of organic compounds alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	-
B [auth C], G [auth c]	CoB--CoM heterodisulfide reductase subunit C	oxidoreductase activity, acting on a sulfur group of donors CoB--CoM heterodisulfide reductase activity oxidoreductase 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	cellular respiration energy derivation by oxidation of organic compounds alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	cell periphery cellular anatomical structure plasma membrane membrane
A, D [auth a]	CoB--CoM heterodisulfide reductase iron-sulfur subunit A	oxidoreductase 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	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth D]	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
I [auth D]	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
I [auth D]	IPR006656	Molybdopterin oxidoreductase	Domain
I [auth D]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
I [auth D]	IPR050123	Prok_molybdopt-oxidoreductase	Unknown
I [auth D]	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site	Conserved Site
I [auth D]	IPR041924	Formate dehydrogenase H, N-terminal	Domain
I [auth D]	IPR027467	Molybdopterin oxidoreductase, molybdopterin cofactor binding site	Binding Site
I [auth D]	IPR006478	Formate dehydrogenase, alpha subunit	Family
F [auth E]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
F [auth E]	IPR045220	Oxidoreductase FRHB/FDHB/HCAR-like	Family
F [auth E]	IPR007516	Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal	Domain
F [auth E]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
F [auth E]	IPR007525	Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal	Domain
E [auth F]	IPR003813	F420-non-reducing hydrogenase iron-sulfur subunit D	Domain
C [auth B], H [auth b]	IPR004017	Cysteine-rich domain	Domain
C [auth B], H [auth b]	IPR017678	CoB--CoM heterodisulphide reductase, subunit B	Family
C [auth B], H [auth b]	IPR051278	CoM-S-S-CoB heterodisulfide reductase	Family
B [auth C], G [auth c]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B [auth C], G [auth c]	IPR051460	HdrC_iron-sulfur_subunit	Unknown
B [auth C], G [auth c]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B [auth C], G [auth c]	IPR017680	CoB--CoM heterodisulphide reductase, subunit C	Family
B [auth C], G [auth c]	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
A, D [auth a]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, D [auth a]	IPR039650	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like	Family
A, D [auth a]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, D [auth a]	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily