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 15-MAR-2017, entry version 103.
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;
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.,
RA Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K.,
RA Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N.,
RA Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J.,
RA Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome
RT corresponding to 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.,
RA Mau B., 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
RT MG1655 and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP INDUCTION.
RC STRAIN=K12;
RX PubMed=2168848;
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
RP CHAIN, SUBCELLULAR LOCATION, SUBUNIT, AND METAL BINDING AT HIS-18;
RP HIS-57; HIS-155 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
RT formate dehydrogenase-N.";
RL Science 295:1863-1868(2002).
CC -!- FUNCTION: Formate dehydrogenase allows E.coli to use formate as
CC major electron donor during anaerobic respiration, when nitrate is
CC used as electron acceptor. Subunit gamma is the cytochrome b556
CC component of the formate dehydrogenase-N, and also contains a
CC menaquinone reduction site that receives electrons from the beta
CC subunit (FdnH), through its hemes. Formate dehydrogenase-N is part
CC of a system that generates proton motive force, together with the
CC dissimilatory nitrate reductase (Nar).
CC {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
CC interface. Electrons are transferred from the periplasmic to the
CC cytoplasmic heme. {ECO:0000269|PubMed:11884747};
CC -!- SUBUNIT: Trimer of heterotrimers, consisting of subunits alpha,
CC beta 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
CC family. {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_LN832404.1.
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 ProteinModelPortal; P0AEK7; -.
DR SMR; P0AEK7; -.
DR BioGrid; 4262903; 6.
DR IntAct; P0AEK7; 1.
DR STRING; 511145.b1476; -.
DR DrugBank; DB07918; 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE.
DR TCDB; 5.A.3.2.1; the prokaryotic molybdopterin-containing oxidoreductase (pmo) family.
DR PaxDb; P0AEK7; -.
DR PRIDE; P0AEK7; -.
DR EnsemblBacteria; AAD13440; AAD13440; b1476.
DR EnsemblBacteria; BAA15125; BAA15125; BAA15125.
DR GeneID; 946038; -.
DR KEGG; ecj:JW1472; -.
DR KEGG; eco:b1476; -.
DR PATRIC; 32118244; VBIEscCol129921_1542.
DR EchoBASE; EB1211; -.
DR EcoGene; EG11229; fdnI.
DR eggNOG; ENOG4108MG3; Bacteria.
DR eggNOG; COG2864; LUCA.
DR HOGENOM; HOG000163500; -.
DR InParanoid; P0AEK7; -.
DR KO; K08350; -.
DR OMA; KQDIPWL; -.
DR PhylomeDB; P0AEK7; -.
DR BioCyc; EcoCyc:FDNI-MONOMER; -.
DR BioCyc; MetaCyc:FDNI-MONOMER; -.
DR BRENDA; 1.1.5.6; 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:0005887; C:integral component of plasma membrane; IDA:EcoCyc.
DR GO; GO:0005886; C:plasma membrane; IDA:EcoCyc.
DR GO; GO:0009055; F:electron carrier 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:0009061; P:anaerobic respiration; IEP:EcoCyc.
DR GO; GO:0015944; P:formate oxidation; IDA:EcoCyc.
DR GO; GO:0022904; P:respiratory electron transport chain; IEA:InterPro.
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; Complete proteome;
KW Electron transport; Heme; Iron; Membrane; Metal-binding;
KW Reference proteome; Transmembrane; Transmembrane helix; Transport.
FT CHAIN 1 217 Formate dehydrogenase, nitrate-inducible,
FT cytochrome b556(Fdn) subunit.
FT /FTId=PRO_0000087210.
FT TOPO_DOM 1 11 Cytoplasmic.
FT {ECO:0000269|PubMed:15919996}.
FT TRANSMEM 12 36 Helical.
FT TOPO_DOM 37 52 Periplasmic.
FT {ECO:0000269|PubMed:15919996}.
FT TRANSMEM 53 74 Helical.
FT TOPO_DOM 75 110 Cytoplasmic.
FT {ECO:0000269|PubMed:15919996}.
FT TRANSMEM 111 134 Helical.
FT TOPO_DOM 135 150 Periplasmic.
FT {ECO:0000269|PubMed:15919996}.
FT TRANSMEM 151 175 Helical.
FT TOPO_DOM 176 217 Cytoplasmic.
FT {ECO:0000269|PubMed:15919996}.
FT METAL 18 18 Iron (heme B 1 axial ligand); via tele
FT nitrogen.
FT METAL 57 57 Iron (heme B 2 axial ligand); via tele
FT nitrogen.
FT METAL 155 155 Iron (heme B 2 axial ligand); via tele
FT nitrogen.
FT METAL 169 169 Iron (heme B 1 axial ligand); via tele
FT nitrogen.
FT BINDING 169 169 Menaquinone; via pros nitrogen.
FT CONFLICT 160 217 IILIHAILIHMYMAFWVKGSIKGMIEGKVSRRWAKKHHPRW
FT YREIEKAEAKKESEEGI -> YHPDPRHPDPYVYGILGERI
FT D (in Ref. 1). {ECO:0000305}.
FT STRAND 4 8 {ECO:0000244|PDB:1KQF}.
FT HELIX 12 36 {ECO:0000244|PDB:1KQF}.
FT HELIX 41 45 {ECO:0000244|PDB:1KQF}.
FT HELIX 50 75 {ECO:0000244|PDB:1KQF}.
FT HELIX 76 78 {ECO:0000244|PDB:1KQF}.
FT HELIX 83 85 {ECO:0000244|PDB:1KQF}.
FT HELIX 86 90 {ECO:0000244|PDB:1KQF}.
FT HELIX 92 96 {ECO:0000244|PDB:1KQF}.
FT HELIX 100 103 {ECO:0000244|PDB:1KQF}.
FT HELIX 111 133 {ECO:0000244|PDB:1KQF}.
FT TURN 136 139 {ECO:0000244|PDB:1KQF}.
FT HELIX 140 142 {ECO:0000244|PDB:1KQF}.
FT HELIX 145 175 {ECO:0000244|PDB:1KQF}.
FT HELIX 179 184 {ECO:0000244|PDB:1KQF}.
FT STRAND 187 189 {ECO:0000244|PDB:1KQF}.
FT HELIX 190 196 {ECO:0000244|PDB:1KQF}.
FT HELIX 198 215 {ECO:0000244|PDB:1KQF}.
CC --------------------------------------------------------------------------
CC The following FT lines are automated annotations from the MyHits database.
CC --------------------------------------------------------------------------
FT MYHIT 13 186 ipfam:Ni_hydr_CYTB [T]
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
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