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Protein

Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit

Gene

fdnI

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Formate dehydrogenase allows E.coli to use formate as major electron donor during anaerobic respiration, when nitrate is used as electron acceptor. Subunit gamma is the cytochrome b556 component of the formate dehydrogenase-N, and also contains a menaquinone reduction site that receives electrons from the beta subunit (FdnH), through its hemes. Formate dehydrogenase-N is part of a system that generates proton motive force, together with the dissimilatory nitrate reductase (Nar).1 Publication

Cofactori

heme1 PublicationNote: Binds 2 heme groups per subunit. Heme 1 is located at the cytoplasmic interface, heme 2 is located at the periplasmic interface. Electrons are transferred from the periplasmic to the cytoplasmic heme.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi18 – 181Iron (heme B 1 axial ligand); via tele nitrogen
Metal bindingi57 – 571Iron (heme B 2 axial ligand); via tele nitrogen
Metal bindingi155 – 1551Iron (heme B 2 axial ligand); via tele nitrogen
Metal bindingi169 – 1691Iron (heme B 1 axial ligand); via tele nitrogen
Binding sitei169 – 1691Menaquinone; via pros nitrogen

GO - Molecular functioni

  • electron carrier activity Source: EcoCyc
  • formate dehydrogenase (NAD+) activity Source: InterPro
  • formate dehydrogenase (quinone) activity Source: EcoCyc
  • heme binding Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • anaerobic respiration Source: EcoCyc
  • formate oxidation Source: EcoCyc
  • respiratory electron transport chain Source: InterPro
Complete GO annotation...

Keywords - Biological processi

Electron transport, Transport

Keywords - Ligandi

Heme, Iron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:FDNI-MONOMER.
ECOL316407:JW1472-MONOMER.
MetaCyc:FDNI-MONOMER.
BRENDAi1.1.5.6. 2026.

Protein family/group databases

TCDBi5.A.3.2.1. the prokaryotic molybdopterin-containing oxidoreductase (pmo) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit
Alternative name(s):
Anaerobic formate dehydrogenase cytochrome b556 subunit
Formate dehydrogenase-N subunit gamma
Short name:
FDH-N subunit gamma
Gene namesi
Name:fdnI
Ordered Locus Names:b1476, JW1472
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11229. fdnI.

Subcellular locationi

  • Cell inner membrane 1 Publication; Multi-pass membrane protein 1 Publication

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 1111Cytoplasmic1 PublicationAdd
BLAST
Transmembranei12 – 3625HelicalAdd
BLAST
Topological domaini37 – 5216Periplasmic1 PublicationAdd
BLAST
Transmembranei53 – 7422HelicalAdd
BLAST
Topological domaini75 – 11036Cytoplasmic1 PublicationAdd
BLAST
Transmembranei111 – 13424HelicalAdd
BLAST
Topological domaini135 – 15016Periplasmic1 PublicationAdd
BLAST
Transmembranei151 – 17525HelicalAdd
BLAST
Topological domaini176 – 21742Cytoplasmic1 PublicationAdd
BLAST

GO - Cellular componenti

  • formate dehydrogenase complex Source: EcoCyc
  • integral component of plasma membrane Source: EcoCyc
  • plasma membrane Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 217217Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunitPRO_0000087210Add
BLAST

Proteomic databases

PaxDbiP0AEK7.

Expressioni

Inductioni

By nitrate under anaerobic conditions.1 Publication

Interactioni

Subunit structurei

Trimer of heterotrimers, consisting of subunits alpha, beta and gamma.1 Publication

Protein-protein interaction databases

BioGridi4262903. 6 interactions.
IntActiP0AEK7. 1 interaction.
STRINGi511145.b1476.

Structurei

Secondary structure

1
217
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 85Combined sources
Helixi12 – 3625Combined sources
Helixi41 – 455Combined sources
Helixi50 – 7526Combined sources
Helixi76 – 783Combined sources
Helixi83 – 853Combined sources
Helixi86 – 905Combined sources
Helixi92 – 965Combined sources
Helixi100 – 1034Combined sources
Helixi111 – 13323Combined sources
Turni136 – 1394Combined sources
Helixi140 – 1423Combined sources
Helixi145 – 17531Combined sources
Helixi179 – 1846Combined sources
Beta strandi187 – 1893Combined sources
Helixi190 – 1967Combined sources
Helixi198 – 21518Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1KQFX-ray1.60C1-217[»]
1KQGX-ray2.80C1-217[»]
ProteinModelPortaliP0AEK7.
SMRiP0AEK7. Positions 2-217.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AEK7.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4108MG3. Bacteria.
COG2864. LUCA.
HOGENOMiHOG000163500.
InParanoidiP0AEK7.
KOiK08350.
OMAiKQDIPWL.
OrthoDBiEOG6B8XH2.
PhylomeDBiP0AEK7.

Family and domain databases

InterProiIPR011577. Cyt_b561_bac/Ni-Hgenase.
IPR016174. Di-haem_cyt_TM.
IPR006471. Formate_DH_gsu.
[Graphical view]
PfamiPF01292. Ni_hydr_CYTB. 1 hit.
[Graphical view]
SUPFAMiSSF81342. SSF81342. 1 hit.
TIGRFAMsiTIGR01583. formate-DH-gamm. 1 hit.

Sequencei

Sequence statusi: Complete.

P0AEK7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKSKMIVRT KFIDRACHWT VVICFFLVAL SGISFFFPTL QWLTQTFGTP
60 70 80 90 100
QMGRILHPFF GIAIFVALMF MFVRFVHHNI PDKKDIPWLL NIVEVLKGNE
110 120 130 140 150
HKVADVGKYN AGQKMMFWSI MSMIFVLLVT GVIIWRPYFA QYFPMQVVRY
160 170 180 190 200
SLLIHAAAGI ILIHAILIHM YMAFWVKGSI KGMIEGKVSR RWAKKHHPRW
210
YREIEKAEAK KESEEGI
Length:217
Mass (Da):25,368
Last modified:December 20, 2005 - v1
Checksum:iB10073F14343515E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti160 – 21758IILIH…SEEGI → YHPDPRHPDPYVYGILGERI D (PubMed:1834669).CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M75029 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAD13440.1.
AP009048 Genomic DNA. Translation: BAA15125.1.
PIRiG64900. JS0630.
RefSeqiNP_415993.1. NC_000913.3.
WP_000045648.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAD13440; AAD13440; b1476.
BAA15125; BAA15125; BAA15125.
GeneIDi946038.
KEGGiecj:JW1472.
eco:b1476.
PATRICi32118244. VBIEscCol129921_1542.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M75029 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAD13440.1.
AP009048 Genomic DNA. Translation: BAA15125.1.
PIRiG64900. JS0630.
RefSeqiNP_415993.1. NC_000913.3.
WP_000045648.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1KQFX-ray1.60C1-217[»]
1KQGX-ray2.80C1-217[»]
ProteinModelPortaliP0AEK7.
SMRiP0AEK7. Positions 2-217.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262903. 6 interactions.
IntActiP0AEK7. 1 interaction.
STRINGi511145.b1476.

Protein family/group databases

TCDBi5.A.3.2.1. the prokaryotic molybdopterin-containing oxidoreductase (pmo) family.

Proteomic databases

PaxDbiP0AEK7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD13440; AAD13440; b1476.
BAA15125; BAA15125; BAA15125.
GeneIDi946038.
KEGGiecj:JW1472.
eco:b1476.
PATRICi32118244. VBIEscCol129921_1542.

Organism-specific databases

EchoBASEiEB1211.
EcoGeneiEG11229. fdnI.

Phylogenomic databases

eggNOGiENOG4108MG3. Bacteria.
COG2864. LUCA.
HOGENOMiHOG000163500.
InParanoidiP0AEK7.
KOiK08350.
OMAiKQDIPWL.
OrthoDBiEOG6B8XH2.
PhylomeDBiP0AEK7.

Enzyme and pathway databases

BioCyciEcoCyc:FDNI-MONOMER.
ECOL316407:JW1472-MONOMER.
MetaCyc:FDNI-MONOMER.
BRENDAi1.1.5.6. 2026.

Miscellaneous databases

EvolutionaryTraceiP0AEK7.
PROiP0AEK7.

Family and domain databases

InterProiIPR011577. Cyt_b561_bac/Ni-Hgenase.
IPR016174. Di-haem_cyt_TM.
IPR006471. Formate_DH_gsu.
[Graphical view]
PfamiPF01292. Ni_hydr_CYTB. 1 hit.
[Graphical view]
SUPFAMiSSF81342. SSF81342. 1 hit.
TIGRFAMsiTIGR01583. formate-DH-gamm. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nitrate-inducible formate dehydrogenase in Escherichia coli K-12. I. Nucleotide sequence of the fdnGHI operon and evidence that opal (UGA) encodes selenocysteine."
    Berg B.L., Li J., Heider J., Stewart V.
    J. Biol. Chem. 266:22380-22385(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12."
    Berg B.L., Stewart V.
    Genetics 125:691-702(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
    Strain: K12.
  6. "Global topology analysis of the Escherichia coli inner membrane proteome."
    Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G.
    Science 308:1321-1323(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: TOPOLOGY [LARGE SCALE ANALYSIS].
    Strain: K12 / MG1655 / ATCC 47076.
  7. "Molecular basis of proton motive force generation: structure of formate dehydrogenase-N."
    Jormakka M., Tornroth S., Byrne B., Iwata S.
    Science 295:1863-1868(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH ALPHA AND BETA SUBUNITS; HEMES AND QUINONE, FUNCTION, COFACTOR, ELECTRON TRANSFER CHAIN, SUBCELLULAR LOCATION, SUBUNIT, METAL BINDING AT HIS-18; HIS-57; HIS-155 AND HIS-169.

Entry informationi

Entry nameiFDNI_ECOLI
AccessioniPrimary (citable) accession number: P0AEK7
Secondary accession number(s): P24185, P77513
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: May 11, 2016
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.