7Z0T

Structure of the Escherichia coli formate hydrogenlyase complex (aerobic preparation, composite structure)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth A]	SCOP2B Superfamily	ADC-like	8042869	3001132	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	Formate dehydrogenase/DMSO reductase domains 1-3	8042870	3001453	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 [auth C]	PF00361	e7z0tC1	A: alpha complex topology	X: Sodium/proton antiporter subunits-like (From Homology)	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit L (NuoL)-related	F: PF00361	ECOD (1.6)
F [auth D]	PF00146	e7z0tD1	A: alpha complex topology	X: Sodium/proton antiporter subunits-like (From Homology)	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related	F: PF00146	ECOD (1.6)
G [auth A]	PF01568	e7z0tA3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: PF01568	ECOD (1.6)
G [auth A]	PF04879	e7z0tA2	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)
G [auth A]	PF00384	e7z0tA4	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C]	PF00361	Proton-conducting membrane transporter (Proton_antipo_M)	Proton-conducting membrane transporter	-	Family
B [auth E]	PF00329	Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa)	Respiratory-chain NADH dehydrogenase, 30 Kd subunit	-	Family
B [auth E]	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
B [auth E]	PF00346	Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa)	Respiratory-chain NADH dehydrogenase, 49 Kd subunit	-	Family
C [auth B]	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
D [auth G]	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit	-	Family
E [auth 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
F [auth D]	PF00146	NADH dehydrogenase (NADHdh)	NADH dehydrogenase	-	Family
G [auth A]	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
G [auth A]	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
G [auth A]	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	Formate hydrogenlyase subunit 3	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	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 anaerobic electron transport chain anaerobic respiration monosaccharide metabolic process 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 anaerobic electron transport chain anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process carbohydrate catabolic process hexose metabolic process primary metabolic process organic substance metabolic process glucose catabolic process small molecule metabolic process monosaccharide catabolic process small molecule catabolic process organic substance catabolic process glucose metabolic process oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process monocarboxylic acid metabolic process formate metabolic process	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex
B [auth E]	Formate hydrogenlyase subunit 5	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion 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 cation binding transition metal ion binding ion binding binding nickel cation binding metal ion 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 quinone binding NAD binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding	anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process carbohydrate catabolic process hexose metabolic process primary metabolic process organic substance metabolic process glucose catabolic process small molecule metabolic process monosaccharide catabolic process small molecule catabolic process organic substance catabolic process glucose metabolic process oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process monocarboxylic acid metabolic process formate metabolic process	protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex
C [auth B]	Formate hydrogenlyase subunit 2	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process carbohydrate catabolic process hexose metabolic process primary metabolic process organic substance metabolic process glucose catabolic process small molecule metabolic process monosaccharide catabolic process small molecule catabolic process organic substance catabolic process glucose metabolic process oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process monocarboxylic acid metabolic process formate metabolic process	protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex
D [auth G]	Formate hydrogenlyase subunit 7	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion 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 iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion 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 quinone binding	anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process carbohydrate catabolic process hexose metabolic process primary metabolic process organic substance metabolic process glucose catabolic process small molecule metabolic process monosaccharide catabolic process small molecule catabolic process organic substance catabolic process glucose metabolic process oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process monocarboxylic acid metabolic process formate metabolic process	protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex
E [auth F]	Formate hydrogenlyase subunit 6	oxidoreductase activity oxidoreductase activity, acting on NAD(P)H 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	anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process carbohydrate catabolic process hexose metabolic process primary metabolic process organic substance metabolic process glucose catabolic process small molecule metabolic process monosaccharide catabolic process small molecule catabolic process organic substance catabolic process glucose metabolic process aerobic respiration oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process monocarboxylic acid metabolic process formate metabolic process	respiratory chain complex protein-containing complex catalytic complex plasma membrane protein complex plasma membrane respirasome membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex NADH dehydrogenase complex cell periphery transmembrane transporter complex respiratory chain complex I respiratory chain complex protein-containing complex catalytic complex plasma membrane protein complex plasma membrane respirasome membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex NADH dehydrogenase complex cell periphery transmembrane transporter complex respiratory chain complex I respirasome oxidoreductase complex plasma membrane respiratory chain complex I formate dehydrogenase complex
F [auth D]	Formate hydrogenlyase subunit 4	oxidoreductase activity catalytic activity	anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process carbohydrate catabolic process hexose metabolic process primary metabolic process organic substance metabolic process glucose catabolic process small molecule metabolic process monosaccharide catabolic process small molecule catabolic process organic substance catabolic process glucose metabolic process oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process monocarboxylic acid metabolic process formate metabolic process	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex
G [auth A]	Formate dehydrogenase H	oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity binding organic cyclic compound 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, NAD or NADP as acceptor cation binding ion binding oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity binding organic cyclic compound 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, NAD or NADP as acceptor cation binding ion binding metal ion binding	anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process carbohydrate catabolic process hexose metabolic process primary metabolic process organic substance metabolic process glucose catabolic process small molecule metabolic process monosaccharide catabolic process small molecule catabolic process organic substance catabolic process glucose metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process purine-containing compound catabolic process organic cyclic compound catabolic process purine-containing compound metabolic process urate metabolic process organic cyclic compound metabolic process urate catabolic process oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process monocarboxylic acid metabolic process formate metabolic process	membrane cellular anatomical entity respiratory chain complex protein-containing complex catalytic complex plasma membrane protein complex plasma membrane respirasome plasma membrane membrane protein complex transporter complex NADH dehydrogenase complex cell periphery transmembrane transporter complex respiratory chain complex I membrane cellular anatomical entity respiratory chain complex protein-containing complex catalytic complex plasma membrane protein complex plasma membrane respirasome plasma membrane membrane protein complex transporter complex NADH dehydrogenase complex cell periphery transmembrane transporter complex respiratory chain complex I respirasome oxidoreductase complex plasma membrane respiratory chain complex I intracellular anatomical structure cytoplasm cytosol formate dehydrogenase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C]	IPR003918	NADH:ubiquinone oxidoreductase	Family
A [auth C]	IPR001750	NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit	Domain
B [auth E]	IPR037232	NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily	Homologous Superfamily
B [auth E]	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
B [auth E]	IPR014029	NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site	Conserved Site
B [auth E]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
B [auth E]	IPR001268	NADH:ubiquinone oxidoreductase, 30kDa subunit	Domain
B [auth E]	IPR001135	NADH-quinone oxidoreductase, subunit D	Domain
C [auth B]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
C [auth B]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
D [auth G]	IPR006138	NADH-ubiquinone oxidoreductase, 20 Kd subunit	Family
D [auth G]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
E [auth F]	IPR010226	NADH-quinone oxidoreductase, chain I	Family
E [auth F]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
E [auth F]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
F [auth D]	IPR001694	NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H	Family
F [auth D]	IPR018086	NADH:ubiquinone oxidoreductase, subunit 1, conserved site	Conserved Site
G [auth A]	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
G [auth A]	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
G [auth A]	IPR006656	Molybdopterin oxidoreductase	Domain
G [auth A]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
G [auth A]	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site	Conserved Site
G [auth A]	IPR041924	Formate dehydrogenase H, N-terminal	Domain
G [auth A]	IPR027467	Molybdopterin oxidoreductase, molybdopterin cofactor binding site	Binding Site
G [auth A]	IPR041925	Formate dehydrogenase H, molybdopterin-binding domain	Domain
G [auth A]	IPR006478	Formate dehydrogenase, alpha subunit	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth C], F [auth D]	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex I (NADH dehydrogenase) and supercomplexes	H+ or Na+ translocating NADH dehydrogenase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth C], F [auth D]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth C], F [auth D]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex I	Formate hydrogenlyase complex, anaerobic preparation, without formate dehydrogenase H