HYFR_ECOLI
ID HYFR_ECOLI Reviewed; 670 AA.
AC P71229; P76567; P76976; P76977;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=DNA-binding transcriptional activator HyfR;
DE AltName: Full=Hydrogenase-4 transcriptional activator {ECO:0000303|PubMed:12426353};
GN Name=hyfR {ECO:0000303|PubMed:9387241}; OrderedLocusNames=b2491, JW2476;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], POSSIBLE FUNCTION, AND MOTIF.
RC STRAIN=K12;
RX PubMed=9387241; DOI=10.1099/00221287-143-11-3633;
RA Andrews S.C., Berks B.C., McClay J., Ambler A., Quail M.A., Golby P.,
RA Guest J.R.;
RT "A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-
RT translocating formate hydrogenlyase system.";
RL Microbiology 143:3633-3647(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
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 FUNCTION, DNA-BINDING, INDUCTION, OPERON, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=12426353; DOI=10.1128/jb.184.23.6642-6653.2002;
RA Skibinski D.A., Golby P., Chang Y.S., Sargent F., Hoffman R., Harper R.,
RA Guest J.R., Attwood M.M., Berks B.C., Andrews S.C.;
RT "Regulation of the hydrogenase-4 operon of Escherichia coli by the
RT sigma(54)-dependent transcriptional activators FhlA and HyfR.";
RL J. Bacteriol. 184:6642-6653(2002).
RN [6]
RP FUNCTION.
RC STRAIN=K12;
RX PubMed=14702328; DOI=10.1128/jb.186.2.580-587.2004;
RA Self W.T., Hasona A., Shanmugam K.T.;
RT "Expression and regulation of a silent operon, hyf, coding for hydrogenase
RT 4 isoenzyme in Escherichia coli.";
RL J. Bacteriol. 186:580-587(2004).
CC -!- FUNCTION: A transcriptional activator of its own operon; when
CC overexpressed operon expression is strongly enhanced by low pH (under
CC pH 6.0), strongly inhibited by O(2) but only weakly stimulated by
CC fumarate (PubMed:12426353, PubMed:14702328). Expression in situ is very
CC weak (PubMed:12426353, PubMed:14702328). {ECO:0000269|PubMed:12426353,
CC ECO:0000269|PubMed:14702328, ECO:0000305|PubMed:9387241}.
CC -!- INDUCTION: Induced during anaerobic growth in the presence of formate;
CC part of a hyfR-focB transcript, it is not clear where the hyfR promoter
CC is located, nor if the upstream operon (hyfABCDEFGHIJ) includes these
CC last 2 genes. {ECO:0000269|PubMed:12426353}.
CC -!- DOMAIN: A Cys-rich motif in the N-terminus (residues 207-221) may bind
CC a metal cofactor or iron-sulfur cluster and be responsible for sensing
CC redox or other signals. {ECO:0000305|PubMed:9387241}.
CC -!- DISRUPTION PHENOTYPE: No effect on expression of the hyf operon.
CC {ECO:0000269|PubMed:12426353}.
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DR EMBL; M63654; AAB88573.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75544.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA16380.1; -; Genomic_DNA.
DR PIR; B65025; B65025.
DR RefSeq; NP_416986.4; NC_000913.3.
DR RefSeq; WP_001251544.1; NZ_LN832404.1.
DR AlphaFoldDB; P71229; -.
DR SMR; P71229; -.
DR BioGRID; 4261431; 6.
DR BioGRID; 853163; 2.
DR DIP; DIP-9993N; -.
DR IntAct; P71229; 13.
DR STRING; 511145.b2491; -.
DR PaxDb; P71229; -.
DR PRIDE; P71229; -.
DR EnsemblBacteria; AAC75544; AAC75544; b2491.
DR EnsemblBacteria; BAA16380; BAA16380; BAA16380.
DR GeneID; 948886; -.
DR KEGG; ecj:JW2476; -.
DR KEGG; eco:b2491; -.
DR PATRIC; fig|1411691.4.peg.4248; -.
DR EchoBASE; EB3971; -.
DR eggNOG; COG3604; Bacteria.
DR InParanoid; P71229; -.
DR OMA; HCACLPH; -.
DR PhylomeDB; P71229; -.
DR BioCyc; EcoCyc:G7308-MON; -.
DR PRO; PR:P71229; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IDA:EcoliWiki.
DR GO; GO:0006352; P:DNA-templated transcription, initiation; IMP:EcoliWiki.
DR GO; GO:0000160; P:phosphorelay signal transduction system; IEA:UniProtKB-KW.
DR GO; GO:2000142; P:regulation of DNA-templated transcription, initiation; IMP:EcoCyc.
DR Gene3D; 3.30.450.40; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR003018; GAF.
DR InterPro; IPR029016; GAF-like_dom_sf.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR002078; Sigma_54_int.
DR InterPro; IPR025662; Sigma_54_int_dom_ATP-bd_1.
DR InterPro; IPR025943; Sigma_54_int_dom_ATP-bd_2.
DR InterPro; IPR025944; Sigma_54_int_dom_CS.
DR Pfam; PF01590; GAF; 1.
DR Pfam; PF00158; Sigma54_activat; 1.
DR SMART; SM00382; AAA; 1.
DR SMART; SM00065; GAF; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS00675; SIGMA54_INTERACT_1; 1.
DR PROSITE; PS00676; SIGMA54_INTERACT_2; 1.
DR PROSITE; PS00688; SIGMA54_INTERACT_3; 1.
DR PROSITE; PS50045; SIGMA54_INTERACT_4; 1.
PE 1: Evidence at protein level;
KW Activator; ATP-binding; DNA-binding; Nucleotide-binding;
KW Reference proteome; Transcription; Transcription regulation;
KW Two-component regulatory system.
FT CHAIN 1..670
FT /note="DNA-binding transcriptional activator HyfR"
FT /id="PRO_0000081299"
FT DOMAIN 169..311
FT /note="GAF"
FT DOMAIN 347..576
FT /note="Sigma-54 factor interaction"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT DNA_BIND 641..660
FT /note="H-T-H motif"
FT /evidence="ECO:0000250"
FT MOTIF 207..221
FT /note="Cys-rich segment, might bind a metal cluster"
FT /evidence="ECO:0000305|PubMed:9387241"
FT BINDING 375..382
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT BINDING 438..447
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
SQ SEQUENCE 670 AA; 75305 MW; 0EA738D2D6BA96B6 CRC64;
MAMSDEAMFA PPQGITIEAV NGMLAERLAQ KHGKASLLRA FIPLPPPFSP VQLIELHVLK
SNFYYRYHDD GSDVTATTEY QGEMVDYSRH AVLLGSSGMA ELRFIRTHGS RFTSQDCTLF
NWLARIITPV LQSWLNDEEQ QVALRLLEKD RDHHRVLVDI TNAVLSHLDL DDLIADVARE
IHHFFGLASV SMVLGDHRKN EKFSLWCSDL SASHCACLPR CMPGESVLLT QTLQTRQPTL
THRADDLFLW QRDPLLLLLA SNGCESALLI PLTFGNHTPG ALLLAHTSST LFSEENCQLL
QHIADRIAIA VGNADAWRSM TDLQESLQQE NHQLSEQLLS NLGIGDIIYQ SQAMEDLLQQ
VDIVAKSDST VLICGETGTG KEVIARAIHQ LSPRRDKPLV KINCAAIPAS LLESELFGHD
KGAFTGAINT HRGRFEIADG GTLFLDEIGD LPLELQPKLL RVLQEREIER LGGSRTIPVN
VRVIAATNRD LWQMVEDRQF RSDLFYRLNV FPLELPPLRD RPEDIPLLAK HFTQKMARHM
NRAIDAIPTE ALRQLMSWDW PGNVRELENV IERAVLLTRG NSLNLHLNVR QSRLLPTLNE
DSALRSSMAQ LLHPTTPEND EEERQRIVQV LRETNGIVAG PRGAATRLGM KRTTLLSRMQ
RLGISVREVL
