1KQF

FORMATE DEHYDROGENASE N FROM E. COLI

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1kqfb1	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Formate dehydrogenase N, iron-sulfur (beta) subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1kqfb2	Membrane and cell surface proteins and peptides	Single transmembrane helix	Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor	Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor	Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1kqfa1	All beta proteins	Double psi beta-barrel	ADC-like	Formate dehydrogenase/DMSO reductase, C-terminal domain	Formate dehydrogenase N, alpha subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1kqfa2	Alpha and beta proteins (a/b)	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase N, alpha subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1kqfc_	Membrane and cell surface proteins and peptides	Heme-binding four-helical bundle	Transmembrane di-heme cytochromes	Formate dehydrogenase N, cytochrome (gamma) subunit	Formate dehydrogenase N, cytochrome (gamma) subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Ferredoxin domains from multidomain proteins	8029753	4000021	SCOP2 (2022-06-29)
B	SCOP2 Family	Iron-sulfur subunit of formate dehydrogenase N transmembrane anchor	8029754	4002174	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	4Fe-4S ferredoxins	8042132	3000020	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Iron-sulfur subunit of formate dehydrogenase N transmembrane anchor	8042133	3000911	SCOP2 (2022-06-29)
A	SCOP2 Family	Formate dehydrogenase/DMSO reductase domains 1-3	8028191	4000801	SCOP2 (2022-06-29)
A	SCOP2 Family	Formate dehydrogenase/DMSO reductase C-terminal domain	8028188	4002360	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Formate dehydrogenase/DMSO reductase domains 1-3	8040570	3001453	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ADC-like	8040567	3001132	SCOP2 (2022-06-29)
C	SCOP2 Family	Formate dehydrogenase N cytochrome (gamma) subunit	8028193	4002897	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Transmembrane di-heme cytochromes	8040572	3000517	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)
B	Fer4_11	e1kqfB3	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11	ECOD (1.6)
B	Fer4_11_1	e1kqfB4	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11_1	ECOD (1.6)
B	Form-deh_trans	e1kqfB1	A: extended segments	X: Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor (From Topology)	H: Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor (From Topology)	T: Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor	F: Form-deh_trans	ECOD (1.6)
A	Molydop_binding	e1kqfA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
A	Molybdop_Fe4S4	e1kqfA3	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	Molybdopterin_2nd	e1kqfA4	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	Molybdopterin_1st_1	e1kqfA5	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_1st_1	ECOD (1.6)
C	Ni_hydr_CYTB	e1kqfC1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: Ni_hydr_CYTB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	1.20.5.480	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
A	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
A	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
C	1.20.950.20	Mainly Alpha	Up-down Bundle	Fumarate Reductase Cytochrome B subunit	Transmembrane di-heme cytochromes, Chain C	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	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	PF09163	Formate dehydrogenase N, transmembrane (Form-deh_trans)	Formate dehydrogenase N, transmembrane	Members of this family are predominantly found in the beta subunit of formate dehydrogenase, and consist of a single transmembrane helix. They act as a transmembrane anchor, and allow for conduction of electrons within the protein [1].	Domain
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
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
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
A	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase	-	Family
C	PF01292	Prokaryotic cytochrome b561 (Ni_hydr_CYTB)	Prokaryotic cytochrome b561	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT	oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion binding metal ion binding	organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process tetrapyrrole 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 cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process formate metabolic process	membrane cellular anatomical entity cell periphery plasma membrane protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex
A	FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT	oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity cation binding transition metal ion binding molybdenum ion binding ion binding binding metal ion binding small molecule binding organic cyclic compound binding molybdopterin cofactor binding oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity cation binding transition metal ion binding molybdenum ion binding ion binding binding metal ion binding small molecule binding organic cyclic compound binding molybdopterin cofactor binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, cytochrome as acceptor formate dehydrogenase (cytochrome-c-553) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding formate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor electron transfer activity selenium binding	organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process tetrapyrrole 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 cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process formate metabolic process	membrane cellular anatomical entity protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex outer membrane-bounded periplasmic space cell envelope periplasmic space
C	FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT	oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme 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 electron transfer activity cation binding oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme 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 electron transfer activity cation binding ion binding metal ion binding small molecule binding	organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process tetrapyrrole 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 cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process formate metabolic process	membrane cellular anatomical entity cell periphery plasma membrane protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR015246	Formate dehydrogenase, transmembrane	Domain
B	IPR038384	Formate dehydrogenase, C-terminal domain superfamily	Homologous Superfamily
B	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B	IPR006470	Formate dehydrogenase iron-sulphur subunit, Proteobacteria	Family
B	IPR014603	Formate dehydrogenase iron-sulphur subunit	Family
A	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A	IPR006656	Molybdopterin oxidoreductase	Domain
A	IPR006443	Formate dehydrogenase-N, alpha subunit	Family
A	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site	Conserved Site
A	IPR027467	Molybdopterin oxidoreductase, molybdopterin cofactor binding site	Binding Site
C	IPR011577	Cytochrome b561, bacterial/Ni-hydrogenase	Domain
C	IPR006471	Formate dehydrogenase, gamma subunit	Family
C	IPR016174	Di-haem cytochrome, transmembrane	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex II superfamily	Formate dehydrogenase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex II	Formate dehydrogenase-N

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, C	formate dehydrogenase (nitrate-inducible) M-CSA #563	Formate dehydrogenase-N (Fdn-N) isolated from Escherichia coli catalyses the oxidation of formate to carbon dioxide and a proton, coupled to the reduction of menaquinone to menaquinol. Fdn-N is involved in nitrate respiration and forms a redox loop with dissimilatory nitrate reductase (Nar). Together they pump protons across the membrane by reducing menaquinone at Fdn-N (taking up protons from the cytoplasm) and oxidising menaquinol at Nar, (releasing protons into the periplasm). They also generate a membrane potential by moving electrons from Fdn-N to Nar. Fdn-N contains an active site for formate oxidation (alpha subunit) and an active site for menaquinone reduction (gamma subunit). They are linked by a redox chain containing two haem groups (gamma), five [4Fe-4S] clusters (FeS-0 in alpha and FeS-1 to FeS-4 in beta) and a molybdenum(VI) ion coordinated to two molybdopterin-guanine dinucleotides, the selenate group from Se-Cys196(alpha) and a hydroxide ion (alpha).	Defined by 3 residues: SEC:A-196HIS:A-197HIS:C_2-169 \| Explore in 3D: M-CSA Motif Definition Extent of motif is too large to support Structure Motif searching. EC: 1.2.1.2 (PDB Primary Data)

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.