FDNI_ECOLI
ID FDNI_ECOLI Reviewed; 217 AA.
AC P0AEK7; P24185; P77513;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit;
DE AltName: Full=Anaerobic formate dehydrogenase cytochrome b556 subunit;
DE AltName: Full=Formate dehydrogenase-N subunit gamma;
DE Short=FDH-N subunit gamma;
GN Name=fdnI; OrderedLocusNames=b1476, JW1472;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1834669; DOI=10.1016/s0021-9258(18)54583-x;
RA Berg B.L., Li J., Heider J., Stewart V.;
RT "Nitrate-inducible formate dehydrogenase in Escherichia coli K-12. I.
RT Nucleotide sequence of the fdnGHI operon and evidence that opal (UGA)
RT encodes selenocysteine.";
RL J. Biol. Chem. 266:22380-22385(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP INDUCTION.
RC STRAIN=K12;
RX PubMed=2168848; DOI=10.1093/genetics/125.4.691;
RA Berg B.L., Stewart V.;
RT "Structural genes for nitrate-inducible formate dehydrogenase in
RT Escherichia coli K-12.";
RL Genetics 125:691-702(1990).
RN [6]
RP TOPOLOGY [LARGE SCALE ANALYSIS].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=15919996; DOI=10.1126/science.1109730;
RA Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G.;
RT "Global topology analysis of the Escherichia coli inner membrane
RT proteome.";
RL Science 308:1321-1323(2005).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH ALPHA AND BETA
RP SUBUNITS; HEMES AND QUINONE, FUNCTION, COFACTOR, ELECTRON TRANSFER CHAIN,
RP SUBCELLULAR LOCATION, SUBUNIT, AND METAL BINDING AT HIS-18; HIS-57; HIS-155
RP AND HIS-169.
RX PubMed=11884747; DOI=10.1126/science.1068186;
RA Jormakka M., Tornroth S., Byrne B., Iwata S.;
RT "Molecular basis of proton motive force generation: structure of formate
RT dehydrogenase-N.";
RL Science 295:1863-1868(2002).
CC -!- FUNCTION: Formate dehydrogenase allows E.coli to use formate as major
CC electron donor during anaerobic respiration, when nitrate is used as
CC electron acceptor. Subunit gamma is the cytochrome b556 component of
CC the formate dehydrogenase-N, and also contains a menaquinone reduction
CC site that receives electrons from the beta subunit (FdnH), through its
CC hemes. Formate dehydrogenase-N is part of a system that generates
CC proton motive force, together with the dissimilatory nitrate reductase
CC (Nar). {ECO:0000269|PubMed:11884747}.
CC -!- COFACTOR:
CC Name=heme; Xref=ChEBI:CHEBI:30413;
CC Evidence={ECO:0000269|PubMed:11884747};
CC Note=Binds 2 heme groups per subunit. Heme 1 is located at the
CC cytoplasmic interface, heme 2 is located at the periplasmic interface.
CC Electrons are transferred from the periplasmic to the cytoplasmic heme.
CC {ECO:0000269|PubMed:11884747};
CC -!- SUBUNIT: Trimer of heterotrimers, consisting of subunits alpha, beta
CC and gamma. {ECO:0000269|PubMed:11884747}.
CC -!- SUBCELLULAR LOCATION: Cell inner membrane
CC {ECO:0000269|PubMed:11884747}; Multi-pass membrane protein
CC {ECO:0000269|PubMed:11884747}.
CC -!- INDUCTION: By nitrate under anaerobic conditions.
CC {ECO:0000269|PubMed:2168848}.
CC -!- SIMILARITY: Belongs to the formate dehydrogenase gamma subunit family.
CC {ECO:0000305}.
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DR EMBL; M75029; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U00096; AAD13440.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15125.1; -; Genomic_DNA.
DR PIR; G64900; JS0630.
DR RefSeq; NP_415993.1; NC_000913.3.
DR RefSeq; WP_000045648.1; NZ_STEB01000053.1.
DR PDB; 1KQF; X-ray; 1.60 A; C=1-217.
DR PDB; 1KQG; X-ray; 2.80 A; C=1-217.
DR PDBsum; 1KQF; -.
DR PDBsum; 1KQG; -.
DR AlphaFoldDB; P0AEK7; -.
DR SMR; P0AEK7; -.
DR BioGRID; 4262903; 10.
DR ComplexPortal; CPX-1975; Formate dehydrogenase N complex.
DR IntAct; P0AEK7; 1.
DR STRING; 511145.b1476; -.
DR DrugBank; DB07918; 2-heptyl-4-hydroxyquinoline N-oxide.
DR TCDB; 5.A.3.2.1; the prokaryotic molybdopterin-containing oxidoreductase (pmo) family.
DR jPOST; P0AEK7; -.
DR PaxDb; P0AEK7; -.
DR PRIDE; P0AEK7; -.
DR EnsemblBacteria; AAD13440; AAD13440; b1476.
DR EnsemblBacteria; BAA15125; BAA15125; BAA15125.
DR GeneID; 66674672; -.
DR GeneID; 946038; -.
DR KEGG; ecj:JW1472; -.
DR KEGG; eco:b1476; -.
DR PATRIC; fig|1411691.4.peg.791; -.
DR EchoBASE; EB1211; -.
DR eggNOG; COG2864; Bacteria.
DR HOGENOM; CLU_091368_1_1_6; -.
DR InParanoid; P0AEK7; -.
DR OMA; TIMSMIF; -.
DR PhylomeDB; P0AEK7; -.
DR BioCyc; EcoCyc:FDNI-MON; -.
DR BioCyc; MetaCyc:FDNI-MON; -.
DR BRENDA; 1.17.5.3; 2026.
DR EvolutionaryTrace; P0AEK7; -.
DR PRO; PR:P0AEK7; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0009326; C:formate dehydrogenase complex; IDA:EcoCyc.
DR GO; GO:0016021; C:integral component of membrane; IBA:GO_Central.
DR GO; GO:0005887; C:integral component of plasma membrane; IDA:EcoCyc.
DR GO; GO:0016020; C:membrane; IDA:ComplexPortal.
DR GO; GO:0005886; C:plasma membrane; IDA:EcoCyc.
DR GO; GO:0009055; F:electron transfer activity; IDA:EcoCyc.
DR GO; GO:0008863; F:formate dehydrogenase (NAD+) activity; IEA:InterPro.
DR GO; GO:0036397; F:formate dehydrogenase (quinone) activity; IDA:EcoCyc.
DR GO; GO:0020037; F:heme binding; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019645; P:anaerobic electron transport chain; IC:ComplexPortal.
DR GO; GO:0009061; P:anaerobic respiration; IEP:EcoCyc.
DR GO; GO:0015944; P:formate oxidation; IDA:EcoCyc.
DR GO; GO:0006788; P:heme oxidation; IC:ComplexPortal.
DR InterPro; IPR011577; Cyt_b561_bac/Ni-Hgenase.
DR InterPro; IPR016174; Di-haem_cyt_TM.
DR InterPro; IPR006471; Formate_DH_gsu.
DR Pfam; PF01292; Ni_hydr_CYTB; 1.
DR SUPFAM; SSF81342; SSF81342; 1.
DR TIGRFAMs; TIGR01583; formate-DH-gamm; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell inner membrane; Cell membrane; Electron transport; Heme;
KW Iron; Membrane; Metal-binding; Reference proteome; Transmembrane;
KW Transmembrane helix; Transport.
FT CHAIN 1..217
FT /note="Formate dehydrogenase, nitrate-inducible, cytochrome
FT b556(Fdn) subunit"
FT /id="PRO_0000087210"
FT TOPO_DOM 1..11
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:15919996"
FT TRANSMEM 12..36
FT /note="Helical"
FT TOPO_DOM 37..52
FT /note="Periplasmic"
FT /evidence="ECO:0000269|PubMed:15919996"
FT TRANSMEM 53..74
FT /note="Helical"
FT TOPO_DOM 75..110
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:15919996"
FT TRANSMEM 111..134
FT /note="Helical"
FT TOPO_DOM 135..150
FT /note="Periplasmic"
FT /evidence="ECO:0000269|PubMed:15919996"
FT TRANSMEM 151..175
FT /note="Helical"
FT TOPO_DOM 176..217
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:15919996"
FT BINDING 18
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /ligand_label="1"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT BINDING 57
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /ligand_label="2"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT BINDING 155
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /ligand_label="2"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT BINDING 169
FT /ligand="a menaquinone"
FT /ligand_id="ChEBI:CHEBI:16374"
FT BINDING 169
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /ligand_label="1"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT CONFLICT 160..217
FT /note="IILIHAILIHMYMAFWVKGSIKGMIEGKVSRRWAKKHHPRWYREIEKAEAKK
FT ESEEGI -> YHPDPRHPDPYVYGILGERID (in Ref. 1)"
FT /evidence="ECO:0000305"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 12..36
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 41..45
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 50..75
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 76..78
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 83..85
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 86..90
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 92..96
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 100..103
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 111..133
FT /evidence="ECO:0007829|PDB:1KQF"
FT TURN 136..139
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 140..142
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 145..175
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 179..184
FT /evidence="ECO:0007829|PDB:1KQF"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 190..196
FT /evidence="ECO:0007829|PDB:1KQF"
FT HELIX 198..215
FT /evidence="ECO:0007829|PDB:1KQF"
SQ SEQUENCE 217 AA; 25368 MW; B10073F14343515E CRC64;
MSKSKMIVRT KFIDRACHWT VVICFFLVAL SGISFFFPTL QWLTQTFGTP QMGRILHPFF
GIAIFVALMF MFVRFVHHNI PDKKDIPWLL NIVEVLKGNE HKVADVGKYN AGQKMMFWSI
MSMIFVLLVT GVIIWRPYFA QYFPMQVVRY SLLIHAAAGI ILIHAILIHM YMAFWVKGSI
KGMIEGKVSR RWAKKHHPRW YREIEKAEAK KESEEGI
