HPF_ECOLI
ID HPF_ECOLI Reviewed; 95 AA.
AC P0AFX0; P31221; Q2M909;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Ribosome hibernation promoting factor {ECO:0000303|PubMed:16324148};
DE Short=HPF {ECO:0000303|PubMed:16324148};
DE AltName: Full=Hibernation factor HPF {ECO:0000303|PubMed:22605777};
GN Name=hpf {ECO:0000303|PubMed:16324148}; Synonyms=yhbH;
GN OrderedLocusNames=b3203, JW3170;
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=8444818; DOI=10.1128/jb.175.5.1550-1551.1993;
RA Imaishi H., Gomada M., Inouye S., Nakazawa A.;
RT "Physical map location of the rpoN gene of Escherichia coli.";
RL J. Bacteriol. 175:1550-1551(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=8025669; DOI=10.1099/13500872-140-5-1035;
RA Jones D.H.A., Franklin C.F.H., Thomas C.M.;
RT "Molecular analysis of the operon which encodes the RNA polymerase sigma
RT factor sigma 54 of Escherichia coli.";
RL Microbiology 140:1035-1043(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=7876255; DOI=10.1074/jbc.270.9.4822;
RA Powell B.S., Court D.L., Inada T., Nakamura Y., Michotey V., Cui X.,
RA Reizer A., Saier M.H. Jr., Reizer J.;
RT "Novel proteins of the phosphotransferase system encoded within the rpoN
RT operon of Escherichia coli. Enzyme IIANtr affects growth on organic
RT nitrogen and the conditional lethality of an erats mutant.";
RL J. Biol. Chem. 270:4822-4839(1995).
RN [4]
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 [5]
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 [6]
RP PROTEIN SEQUENCE OF 1-12, FUNCTION, INTERACTION WITH 100S RIBOSOMES, AND
RP INDUCTION.
RC STRAIN=K12 / MC4100 / AD202;
RX PubMed=11168583; DOI=10.1046/j.1365-2443.2000.00389.x;
RA Maki Y., Yoshida H., Wada A.;
RT "Two proteins, YfiA and YhbH, associated with resting ribosomes in
RT stationary phase Escherichia coli.";
RL Genes Cells 5:965-974(2000).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=B / BL21;
RX PubMed=10493123;
RX DOI=10.1002/(sici)1522-2683(19990801)20:11<2181::aid-elps2181>3.0.co;2-q;
RA Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B.;
RT "Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite
RT chromatography.";
RL Electrophoresis 20:2181-2195(1999).
RN [8]
RP INDUCTION.
RX PubMed=11514505; DOI=10.1128/jb.183.18.5239-5247.2001;
RA DeLisa M.P., Wu C.-F., Wang L., Valdes J.J., Bentley W.E.;
RT "DNA microarray-based identification of genes controlled by autoinducer 2-
RT stimulated quorum sensing in Escherichia coli.";
RL J. Bacteriol. 183:5239-5247(2001).
RN [9]
RP FUNCTION, GENE NAME, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16324148; DOI=10.1111/j.1365-2443.2005.00903.x;
RA Ueta M., Yoshida H., Wada C., Baba T., Mori H., Wada A.;
RT "Ribosome binding proteins YhbH and YfiA have opposite functions during
RT 100S formation in the stationary phase of Escherichia coli.";
RL Genes Cells 10:1103-1112(2005).
RN [10]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=17277072; DOI=10.1128/jb.01713-06;
RA Bubunenko M., Baker T., Court D.L.;
RT "Essentiality of ribosomal and transcription antitermination proteins
RT analyzed by systematic gene replacement in Escherichia coli.";
RL J. Bacteriol. 189:2844-2853(2007).
RN [11]
RP FUNCTION.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=18174192; DOI=10.1093/jb/mvm243;
RA Ueta M., Ohniwa R.L., Yoshida H., Maki Y., Wada C., Wada A.;
RT "Role of HPF (hibernation promoting factor) in translational activity in
RT Escherichia coli.";
RL J. Biochem. 143:425-433(2008).
RN [12]
RP FUNCTION.
RX PubMed=19170772; DOI=10.1111/j.1365-2443.2008.01272.x;
RA Yoshida H., Ueta M., Maki Y., Sakai A., Wada A.;
RT "Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare
RT 100S ribosome formation on entering the stationary growth phase.";
RL Genes Cells 14:271-280(2009).
RN [13]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=26324267; DOI=10.1128/aac.01532-15;
RA McKay S.L., Portnoy D.A.;
RT "Ribosome hibernation facilitates tolerance of stationary-phase bacteria to
RT aminoglycosides.";
RL Antimicrob. Agents Chemother. 59:6992-6999(2015).
RN [14]
RP STRUCTURE BY NMR.
RX PubMed=19747895; DOI=10.1016/j.bbrc.2009.09.022;
RA Sato A., Watanabe T., Maki Y., Ueta M., Yoshida H., Ito Y., Wada A.,
RA Mishima M.;
RT "Solution structure of the E. coli ribosome hibernation promoting factor
RT HPF: Implications for the relationship between structure and function.";
RL Biochem. Biophys. Res. Commun. 389:580-585(2009).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (3.10 ANGSTROMS) BOUND TO THE T.THERMOPHILUS 70S
RP RIBOSOME, FUNCTION, AND SUBUNIT.
RX PubMed=22605777; DOI=10.1126/science.1218538;
RA Polikanov Y.S., Blaha G.M., Steitz T.A.;
RT "How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.";
RL Science 336:915-918(2012).
CC -!- FUNCTION: During stationary phase, promotes and stabilizes dimerization
CC of 70S ribosomes by the ribosome modulation factor (RMF), leading to
CC the formation of inactive 100S ribosomes (PubMed:18174192). Converts
CC immature 90S particles formed by RMF into 100S ribosomes
CC (PubMed:16324148). Crystallization with T.thermophilus 70S ribosomes
CC shows it binds in the channel between the head and body of the 30S
CC subunit, where mRNA, tRNAs, initiation factors IF1 and IF3 and
CC elongation factor G would bind; however RMF is still able to bind
CC (PubMed:22605777). In this crystal binding of HPF induces movement of
CC the 30S head domain away from the rest of the ribosome, presumably so
CC they would more easily form dimers (PubMed:22605777). May also function
CC as a potential translational inhibitor (PubMed:18174192).
CC {ECO:0000269|PubMed:11168583, ECO:0000269|PubMed:16324148,
CC ECO:0000269|PubMed:18174192, ECO:0000269|PubMed:19170772,
CC ECO:0000269|PubMed:22605777}.
CC -!- SUBUNIT: Associates exclusively with 100S ribosomes, which are dimers
CC of 70S ribosomes. {ECO:0000269|PubMed:11168583,
CC ECO:0000269|PubMed:22605777}.
CC -!- INTERACTION:
CC P0AFX0; P0A988: dnaN; NbExp=2; IntAct=EBI-561113, EBI-542385;
CC -!- INDUCTION: Induced during stationary growth phase (at protein level)
CC (PubMed:11168583). Induced by the signal autoinducer AI-2
CC (PubMed:11514505). {ECO:0000269|PubMed:11168583,
CC ECO:0000269|PubMed:11514505}.
CC -!- DISRUPTION PHENOTYPE: Non-essential gene, no formation of inactive 100S
CC ribosomes. Double hpf-yfiA deletion mutants form 90S ribosomes
CC (PubMed:16324148). A quadruple yfiA-hpf-rmf-sra knockout strain is
CC significantly outcompeted by wild-type after 4 days growth
CC (PubMed:17277072). No change in sensitivity to aminoglycoside
CC antiobiotic gentamicin in stationary phase cultures (PubMed:26324267).
CC {ECO:0000269|PubMed:16324148, ECO:0000269|PubMed:17277072,
CC ECO:0000269|PubMed:26324267}.
CC -!- SIMILARITY: Belongs to the HPF/YfiA ribosome-associated protein family.
CC Short HPF subfamily. {ECO:0000305}.
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DR EMBL; D12938; BAA02316.1; -; Genomic_DNA.
DR EMBL; Z27094; CAA81618.1; -; Genomic_DNA.
DR EMBL; U12684; AAB60164.1; -; Genomic_DNA.
DR EMBL; U18997; AAA58005.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76235.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77247.1; -; Genomic_DNA.
DR PIR; I76719; I76719.
DR RefSeq; NP_417670.1; NC_000913.3.
DR RefSeq; WP_001176599.1; NZ_STEB01000012.1.
DR PDB; 2RQL; NMR; -; A=1-95.
DR PDB; 4V8H; X-ray; 3.10 A; AX/CX=1-95.
DR PDB; 6H4N; EM; 3.00 A; x=1-95.
DR PDB; 6H58; EM; 7.90 A; x/xx=1-95.
DR PDB; 6Y69; EM; 2.86 A; x=1-95.
DR PDBsum; 2RQL; -.
DR PDBsum; 4V8H; -.
DR PDBsum; 6H4N; -.
DR PDBsum; 6H58; -.
DR PDBsum; 6Y69; -.
DR AlphaFoldDB; P0AFX0; -.
DR BMRB; P0AFX0; -.
DR SMR; P0AFX0; -.
DR BioGRID; 4259283; 29.
DR DIP; DIP-48273N; -.
DR IntAct; P0AFX0; 55.
DR STRING; 511145.b3203; -.
DR jPOST; P0AFX0; -.
DR PaxDb; P0AFX0; -.
DR PRIDE; P0AFX0; -.
DR EnsemblBacteria; AAC76235; AAC76235; b3203.
DR EnsemblBacteria; BAE77247; BAE77247; BAE77247.
DR GeneID; 66672895; -.
DR GeneID; 947718; -.
DR KEGG; ecj:JW3170; -.
DR KEGG; eco:b3203; -.
DR PATRIC; fig|1411691.4.peg.3528; -.
DR EchoBASE; EB1632; -.
DR eggNOG; COG1544; Bacteria.
DR HOGENOM; CLU_071472_3_1_6; -.
DR InParanoid; P0AFX0; -.
DR OMA; NLTGHHI; -.
DR PhylomeDB; P0AFX0; -.
DR BioCyc; EcoCyc:EG11681-MON; -.
DR EvolutionaryTrace; P0AFX0; -.
DR PRO; PR:P0AFX0; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0022627; C:cytosolic small ribosomal subunit; IBA:GO_Central.
DR GO; GO:0043024; F:ribosomal small subunit binding; IDA:EcoCyc.
DR GO; GO:0043022; F:ribosome binding; IDA:EcoCyc.
DR GO; GO:0017148; P:negative regulation of translation; IDA:EcoCyc.
DR GO; GO:0045900; P:negative regulation of translational elongation; IBA:GO_Central.
DR GO; GO:0044238; P:primary metabolic process; IEA:InterPro.
DR CDD; cd00552; RaiA; 1.
DR Gene3D; 3.30.160.100; -; 1.
DR InterPro; IPR036567; RHF-like.
DR InterPro; IPR003489; RHF/RaiA.
DR Pfam; PF02482; Ribosomal_S30AE; 1.
DR SUPFAM; SSF69754; SSF69754; 1.
DR TIGRFAMs; TIGR00741; yfiA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Reference proteome;
KW Translation regulation.
FT CHAIN 1..95
FT /note="Ribosome hibernation promoting factor"
FT /id="PRO_0000097417"
FT STRAND 2..10
FT /evidence="ECO:0007829|PDB:2RQL"
FT HELIX 14..28
FT /evidence="ECO:0007829|PDB:2RQL"
FT STRAND 35..43
FT /evidence="ECO:0007829|PDB:2RQL"
FT STRAND 48..56
FT /evidence="ECO:0007829|PDB:2RQL"
FT STRAND 59..69
FT /evidence="ECO:0007829|PDB:2RQL"
FT HELIX 70..92
FT /evidence="ECO:0007829|PDB:2RQL"
SQ SEQUENCE 95 AA; 10750 MW; 5B8F737E6E3A91AE CRC64;
MQLNITGNNV EITEALREFV TAKFAKLEQY FDRINQVYVV LKVEKVTHTS DATLHVNGGE
IHASAEGQDM YAAIDGLIDK LARQLTKHKD KLKQH
