HFQ_ECOLI
ID HFQ_ECOLI Reviewed; 102 AA.
AC P0A6X3; O24728; P25521; Q2M6D3; Q47383;
DT 29-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=RNA-binding protein Hfq {ECO:0000255|HAMAP-Rule:MF_00436};
DE AltName: Full=HF-1;
DE AltName: Full=Host factor-I protein;
DE Short=HF-I;
GN Name=hfq {ECO:0000255|HAMAP-Rule:MF_00436};
GN OrderedLocusNames=b4172, JW4130;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-45, AND SUBUNIT.
RX PubMed=2020545; DOI=10.1093/nar/19.5.1063;
RA Kajitani M., Ishihama A.;
RT "Identification and sequence determination of the host factor gene for
RT bacteriophage Q beta.";
RL Nucleic Acids Res. 19:1063-1066(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-79.
RC STRAIN=K12;
RX PubMed=1999389; DOI=10.1128/jb.173.5.1711-1721.1991;
RA Winkler M.E., Connolly D.M.;
RT "Structure of Escherichia coli K-12 miaA and characterization of the
RT mutator phenotype caused by miaA insertion mutations.";
RL J. Bacteriol. 173:1711-1721(1991).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 89-102.
RC STRAIN=K12;
RX PubMed=8248183; DOI=10.1073/pnas.90.22.10866;
RA Noble J.A., Innis M.A., Koonin E.V., Rudd K.E., Banuett F., Herskowitz I.;
RT "The Escherichia coli hflA locus encodes a putative GTP-binding protein and
RT two membrane proteins, one of which contains a protease-like domain.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:10866-10870(1993).
RN [7]
RP PROTEIN SEQUENCE OF 2-19, AND DNA-BINDING.
RX PubMed=9245691; DOI=10.1006/bbrc.1997.7013;
RA Takada A., Wachi M., Kaidow A., Takamura M., Nagai K.;
RT "DNA binding properties of the hfq gene product of Escherichia coli.";
RL Biochem. Biophys. Res. Commun. 236:576-579(1997).
RN [8]
RP PROTEIN SEQUENCE OF 2-6, AND ROLE IN PHAGE QBETA REPLICATION.
RX PubMed=805130; DOI=10.1016/s0021-9258(19)41440-3;
RA Carmichael G.G., Weber K., Niveleau A., Wahba A.J.;
RT "The host factor required for RNA phage Qbeta RNA replication in vitro.
RT Intracellular location, quantitation, and purification by polyadenylate-
RT cellulose chromatography.";
RL J. Biol. Chem. 250:3607-3612(1975).
RN [9]
RP ROLE IN ELONGATION OF MRNA POLY(A) TAILS.
RX PubMed=10677490; DOI=10.1073/pnas.040549897;
RA Hajnsdorf E., Regnier P.;
RT "Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails
RT by poly(A) polymerase I.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:1501-1505(2000).
RN [10]
RP FUNCTION IN REGULATORY ACTIVITY OF DSRA.
RX PubMed=11222598; DOI=10.1128/jb.183.6.1997-2005.2001;
RA Sledjeski D.D., Whitman C., Zhang A.;
RT "Hfq is necessary for regulation by the untranslated RNA DsrA.";
RL J. Bacteriol. 183:1997-2005(2001).
RN [11]
RP FUNCTION IN REGULATION OF STRESS RESPONSE.
RX PubMed=17158661; DOI=10.1128/jb.01243-06;
RA Guisbert E., Rhodius V.A., Ahuja N., Witkin E., Gross C.A.;
RT "Hfq modulates the sigmaE-mediated envelope stress response and the
RT sigma32-mediated cytoplasmic stress response in Escherichia coli.";
RL J. Bacteriol. 189:1963-1973(2007).
RN [12]
RP INTERACTION WITH TRNAS.
RC STRAIN=K12;
RX PubMed=18230766; DOI=10.1261/rna.531408;
RA Lee T., Feig A.L.;
RT "The RNA binding protein Hfq interacts specifically with tRNAs.";
RL RNA 14:514-523(2008).
RN [13]
RP FUNCTION IN PERSISTER CELL FORMATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=19909729; DOI=10.1016/j.bbrc.2009.11.033;
RA Kim Y., Wood T.K.;
RT "Toxins Hha and CspD and small RNA regulator Hfq are involved in persister
RT cell formation through MqsR in Escherichia coli.";
RL Biochem. Biophys. Res. Commun. 391:209-213(2010).
RN [14]
RP FUNCTION, DISRUPTION PHENOTYPE, AND RNA-BINDING.
RC STRAIN=K12 / BW25113;
RX PubMed=24748661; DOI=10.1093/nar/gku279;
RA Guo Y., Quiroga C., Chen Q., McAnulty M.J., Benedik M.J., Wood T.K.,
RA Wang X.;
RT "RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system
RT in Escherichia coli.";
RL Nucleic Acids Res. 42:6448-6462(2014).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 1-72, AND SUBUNIT.
RX PubMed=12853626; DOI=10.1093/nar/gkg480;
RA Sauter C., Basquin J., Suck D.;
RT "Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein
RT from Escherichia coli.";
RL Nucleic Acids Res. 31:4091-4098(2003).
CC -!- FUNCTION: RNA chaperone that binds small regulatory RNA (sRNAs) and
CC mRNAs to facilitate mRNA translational regulation in response to
CC envelope stress, environmental stress and changes in metabolite
CC concentrations. Involved in the regulation of stress responses mediated
CC by the sigma factors RpoS, sigma-E and sigma-32 (PubMed:17158661).
CC Binds with high specificity to tRNAs (PubMed:18230766). Binds sRNA
CC antitoxin RalA (PubMed:24748661). In vitro, stimulates synthesis of
CC long tails by poly(A) polymerase I (PubMed:10677490). Required for RNA
CC phage Qbeta replication (PubMed:805130). Seems to play a role in
CC persister cell formation; upon overexpression decreases persister cell
CC formation while deletion increases persister formation
CC (PubMed:19909729). {ECO:0000269|PubMed:10677490,
CC ECO:0000269|PubMed:17158661, ECO:0000269|PubMed:18230766,
CC ECO:0000269|PubMed:19909729, ECO:0000269|PubMed:24748661,
CC ECO:0000269|PubMed:805130}.
CC -!- SUBUNIT: Homohexamer (PubMed:12853626). Interacts with H-NS
CC (PubMed:11222598). {ECO:0000255|HAMAP-Rule:MF_00436,
CC ECO:0000269|PubMed:12853626, ECO:0000269|PubMed:2020545}.
CC -!- INTERACTION:
CC P0A6X3; P0AG30: rho; NbExp=5; IntAct=EBI-547637, EBI-545468;
CC -!- DISRUPTION PHENOTYPE: Deletion of hfq seems to lead to a significant
CC translational fidelity problem. Deletion increases persister cell
CC formation (PubMed:19909729). Deletion abolishes the antitoxin activity
CC of sRNA antitoxin RalA, preventing it from neutralizing toxin RalR
CC (PubMed:24748661). {ECO:0000269|PubMed:19909729,
CC ECO:0000269|PubMed:24748661}.
CC -!- SIMILARITY: Belongs to the Hfq family. {ECO:0000255|HAMAP-
CC Rule:MF_00436}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA24175.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; D00743; BAA00644.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97068.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77129.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78173.1; -; Genomic_DNA.
DR EMBL; M63655; AAA24175.1; ALT_FRAME; Genomic_DNA.
DR EMBL; U00005; AAC43397.1; -; Unassigned_DNA.
DR PIR; S26832; S56397.
DR RefSeq; NP_418593.1; NC_000913.3.
DR RefSeq; WP_001051883.1; NZ_STEB01000013.1.
DR PDB; 1HK9; X-ray; 2.15 A; A/B/C/D/E/F=1-72.
DR PDB; 2Y90; X-ray; 2.25 A; A=1-102.
DR PDB; 2YHT; X-ray; 2.90 A; A/B/C/D/E/F/G/H/I/J/K/L=1-72.
DR PDB; 3GIB; X-ray; 2.40 A; A/B/C=2-69.
DR PDB; 3QHS; X-ray; 2.85 A; A/B/C/D/E/F/G/H/I/J/K/L=1-102.
DR PDB; 3QO3; X-ray; 2.15 A; A/B/C/D/E/F=1-65.
DR PDB; 3RER; X-ray; 1.70 A; A/B/C/D/E/F=1-65.
DR PDB; 3RES; X-ray; 2.00 A; A/B/C/D/E/F/G/H/I/J/K/L=1-65.
DR PDB; 3VU3; X-ray; 2.85 A; C/D/E/F/G/H=1-102.
DR PDB; 4JRI; X-ray; 1.83 A; A/B/C/D=2-69.
DR PDB; 4JRK; X-ray; 1.89 A; A/B/C=2-69.
DR PDB; 4JUV; X-ray; 2.19 A; A/B/C/D/E/F=2-69.
DR PDB; 4RCB; X-ray; 1.63 A; A=5-71.
DR PDB; 4RCC; X-ray; 1.98 A; A=5-71.
DR PDB; 4V2S; X-ray; 3.48 A; A/B/C/D/E/F=1-102.
DR PDB; 5UK7; X-ray; 3.00 A; A/B/C/D/E/F/G/H/I/J/K/L=2-69.
DR PDB; 6QLB; X-ray; 2.32 A; E/F/G/H=4-65.
DR PDB; 7OGM; EM; 3.70 A; D/E/F/I/J/K=1-102.
DR PDBsum; 1HK9; -.
DR PDBsum; 2Y90; -.
DR PDBsum; 2YHT; -.
DR PDBsum; 3GIB; -.
DR PDBsum; 3QHS; -.
DR PDBsum; 3QO3; -.
DR PDBsum; 3RER; -.
DR PDBsum; 3RES; -.
DR PDBsum; 3VU3; -.
DR PDBsum; 4JRI; -.
DR PDBsum; 4JRK; -.
DR PDBsum; 4JUV; -.
DR PDBsum; 4RCB; -.
DR PDBsum; 4RCC; -.
DR PDBsum; 4V2S; -.
DR PDBsum; 5UK7; -.
DR PDBsum; 6QLB; -.
DR PDBsum; 7OGM; -.
DR AlphaFoldDB; P0A6X3; -.
DR PCDDB; P0A6X3; -.
DR SMR; P0A6X3; -.
DR BioGRID; 4261250; 265.
DR DIP; DIP-36047N; -.
DR IntAct; P0A6X3; 78.
DR MINT; P0A6X3; -.
DR STRING; 511145.b4172; -.
DR jPOST; P0A6X3; -.
DR PaxDb; P0A6X3; -.
DR PRIDE; P0A6X3; -.
DR EnsemblBacteria; AAC77129; AAC77129; b4172.
DR EnsemblBacteria; BAE78173; BAE78173; BAE78173.
DR GeneID; 67414790; -.
DR GeneID; 948689; -.
DR KEGG; ecj:JW4130; -.
DR KEGG; eco:b4172; -.
DR PATRIC; fig|1411691.4.peg.2529; -.
DR EchoBASE; EB0433; -.
DR eggNOG; COG1923; Bacteria.
DR HOGENOM; CLU_113688_2_1_6; -.
DR InParanoid; P0A6X3; -.
DR OMA; QQMVYKH; -.
DR PhylomeDB; P0A6X3; -.
DR BioCyc; EcoCyc:EG10438-MON; -.
DR EvolutionaryTrace; P0A6X3; -.
DR PRO; PR:P0A6X3; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0003681; F:bent DNA binding; IDA:EcoliWiki.
DR GO; GO:0003723; F:RNA binding; IDA:EcoCyc.
DR GO; GO:0045975; P:positive regulation of translation, ncRNA-mediated; IMP:EcoCyc.
DR GO; GO:0043487; P:regulation of RNA stability; IBA:GO_Central.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:InterPro.
DR GO; GO:0045974; P:regulation of translation, ncRNA-mediated; IBA:GO_Central.
DR GO; GO:0040033; P:sRNA-mediated gene silencing; IEP:EcoliWiki.
DR CDD; cd01716; Hfq; 1.
DR DisProt; DP01050; -.
DR HAMAP; MF_00436; Hfq; 1.
DR InterPro; IPR005001; Hfq.
DR InterPro; IPR010920; LSM_dom_sf.
DR PANTHER; PTHR34772; PTHR34772; 1.
DR Pfam; PF17209; Hfq; 1.
DR SUPFAM; SSF50182; SSF50182; 1.
DR TIGRFAMs; TIGR02383; Hfq; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; DNA-binding; Reference proteome;
KW RNA-binding; Stress response.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:2020545,
FT ECO:0000269|PubMed:805130, ECO:0000269|PubMed:9245691"
FT CHAIN 2..102
FT /note="RNA-binding protein Hfq"
FT /id="PRO_0000095601"
FT REGION 63..102
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 65..102
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 8..17
FT /evidence="ECO:0007829|PDB:4RCB"
FT STRAND 22..26
FT /evidence="ECO:0007829|PDB:4RCB"
FT STRAND 31..39
FT /evidence="ECO:0007829|PDB:4RCB"
FT STRAND 41..55
FT /evidence="ECO:0007829|PDB:4RCB"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:4RCB"
FT STRAND 59..66
FT /evidence="ECO:0007829|PDB:4RCB"
SQ SEQUENCE 102 AA; 11166 MW; E47FA9B07A39304D CRC64;
MAKGQSLQDP FLNALRRERV PVSIYLVNGI KLQGQIESFD QFVILLKNTV SQMVYKHAIS
TVVPSRPVSH HSNNAGGGTS SNYHHGSSAQ NTSAQQDSEE TE
