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-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2 Family | Formate dehydrogenase/DMSO reductase, C-terminal domain | 8028188 | 4002360 | SCOP2 (2022-06-29) |
A | SCOP2 Family | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8028191 | 4000801 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | ADC-like | 8040567 | 3001132 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8040570 | 3001453 | SCOP2 (2022-06-29) |
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) |
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) |
---|---|---|---|---|---|---|---|---|
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) |
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) |
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) |
---|---|---|---|---|---|---|
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) | |
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) |
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 |
---|---|---|---|---|---|
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 ... | Domain | |
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 | |
PF00384 | Molybdopterin oxidoreductase (Molybdopterin) | Molybdopterin oxidoreductase | - | Family | |
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 ... | Domain | |
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 | |
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 | |
PF01292 | Prokaryotic cytochrome b561 (Ni_hydr_CYTB) | Prokaryotic cytochrome b561 | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Membrane Protein Annotation: OPM OPM Database Homepage
Chains | External Link | Type | Class | Superfamily | Family |
---|---|---|---|---|---|
OPM | Transmembrane | Alpha-helical polytopic | Electron transport chain complex II superfamily | Formate dehydrogenase |
Membrane Protein Annotation: PDBTM PDBTM Database Homepage
Chains | External Link | Comment |
---|---|---|
PDBTM | Annotated as membrane protein by PDBTM |
Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage
Chains | External Link | Comment |
---|---|---|
MemProtMD | Annotated as membrane protein by MemProtMD |
Membrane Protein Annotation: mpstruc mpstruc Database Homepage
Chains | Resource Link | Group | Subgroup | Protein |
---|---|---|---|---|
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 |
---|---|---|---|
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). | EC: 1.2.1.2 (PDB Primary Data) |