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Protein

Ribosome modulation factor

Gene

rmf

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

During stationary phase, converts 70S ribosomes to an immature dimeric form (90S ribosomes) which are converted to inactive 100S ribosomes (a process called ribosomal hibernation) by the hibernation promoting factor HPF (PubMed:7677746, PubMed:18174192). Inactivates ribosomes by covering the peptidyl transferase (PTase) center of the 23S rRNA and the entrance of peptide exit tunnel (PubMed:12473202, PubMed:15066119). However crystallization with T.thermophilus 70S ribosomes shows it binds near the 3'-end of the 16S rRNA near the anti-Shine-Dalgarno sequence, where it would sterically hinder translation inititation (PubMed:22605777). In this crystal binding of RMF induces movement of the 30S head domain away from the rest of the ribosome, presumably so they would more easily form dimers (PubMed:22605777). Also involved in protection against heat stress, but this role is not dependent on the maintenance of ribosome dimers (PubMed:15278243).UniRule annotation8 Publications

GO - Molecular functioni

  • ribosomal small subunit binding Source: EcoCyc
  • ribosome binding Source: EcoCyc
  • rRNA binding Source: UniProtKB-KW

GO - Biological processi

  • negative regulation of translation in response to stress Source: EcoCyc
Complete GO annotation...

Keywords - Biological processi

Stress response, Translation regulation

Keywords - Ligandi

RNA-binding, rRNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG50004-MONOMER.
ECOL316407:JW0936-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosome modulation factor1 PublicationUniRule annotation
Short name:
RMFUniRule annotation
Alternative name(s):
Hibernation factor RMF1 Publication
Protein E
Gene namesi
Name:rmf1 PublicationUniRule annotation
Ordered Locus Names:b0953, JW0936
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG50004. rmf.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Non-essential gene, 100S ribosome dimers are not formed, decreased cell viability during stationary phase (PubMed:8440252). A quadruple raiA-hpf-rmf-sra knockout strain is significantly outcompeted by wild-type after 4 days growth (PubMed:17277072). Very high sensitivity to aminoglycoside antiobiotic gentamicin in stationary phase cultures (PubMed:26324267).3 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5555Ribosome modulation factorPRO_0000097363Add
BLAST

Proteomic databases

EPDiP0AFW2.
PaxDbiP0AFW2.
PRIDEiP0AFW2.

Expressioni

Inductioni

Induced during stationary growth phase (PubMed:8440252). Requires ppGpp for translation (PubMed:11532026).UniRule annotation2 Publications

Interactioni

Subunit structurei

Associates exclusively with 100S ribosomes (PubMed:2181444, PubMed:12473202, PubMed:15066119). Contacts 16S rRNA, might contact ribosomal protein S18 (PubMed:22605777).4 Publications

Protein-protein interaction databases

BioGridi4260019. 268 interactions.
DIPiDIP-48260N.
IntActiP0AFW2. 3 interactions.
STRINGi511145.b0953.

Structurei

Secondary structure

1
55
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 2015Combined sources
Beta strandi21 – 244Combined sources
Beta strandi32 – 343Combined sources
Helixi35 – 4915Combined sources
Turni50 – 523Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4V8GX-ray3.00AV/CV1-55[»]
ProteinModelPortaliP0AFW2.
SMRiP0AFW2. Positions 1-51.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosome modulation factor family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105WFT. Bacteria.
COG3130. LUCA.
HOGENOMiHOG000277840.
InParanoidiP0AFW2.
KOiK03812.
OMAiQRSHWLG.
OrthoDBiEOG6V4GJD.

Family and domain databases

Gene3Di1.10.10.620. 1 hit.
HAMAPiMF_00919. RMF.
InterProiIPR007040. Ribosome_modulation_factor.
IPR023200. Ribosome_modulation_factor_dom.
[Graphical view]
PfamiPF04957. RMF. 1 hit.
[Graphical view]
ProDomiPD051650. Ribosome_modulation_factor. 1 hit.
[Graphical view] [Entries sharing at least one domain]

Sequencei

Sequence statusi: Complete.

P0AFW2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKRQKRDRLE RAHQRGYQAG IAGRSKEMCP YQTLNQRSQW LGGWREAMAD

RVVMA
Length:55
Mass (Da):6,507
Last modified:December 20, 2005 - v1
Checksum:iD264AF285BBF24AB
GO

Sequence cautioni

The sequence J03186 differs from that shown. Reason: Frameshift at positions 4, 11 and 30. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti3 – 31R → I AA sequence (PubMed:2181444).Curated
Sequence conflicti25 – 251S → V AA sequence (PubMed:2181444).Curated
Sequence conflicti33 – 331T → S in CAA49706 (PubMed:8440252).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X70111 Genomic DNA. Translation: CAA49706.1.
J03186 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAC74039.1.
AP009048 Genomic DNA. Translation: BAA35711.1.
PIRiH64835.
RefSeqiNP_415473.1. NC_000913.3.
WP_000828648.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74039; AAC74039; b0953.
BAA35711; BAA35711; BAA35711.
GeneIDi945567.
KEGGiecj:JW0936.
eco:b0953.
PATRICi32117125. VBIEscCol129921_0987.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X70111 Genomic DNA. Translation: CAA49706.1.
J03186 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAC74039.1.
AP009048 Genomic DNA. Translation: BAA35711.1.
PIRiH64835.
RefSeqiNP_415473.1. NC_000913.3.
WP_000828648.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4V8GX-ray3.00AV/CV1-55[»]
ProteinModelPortaliP0AFW2.
SMRiP0AFW2. Positions 1-51.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260019. 268 interactions.
DIPiDIP-48260N.
IntActiP0AFW2. 3 interactions.
STRINGi511145.b0953.

Proteomic databases

EPDiP0AFW2.
PaxDbiP0AFW2.
PRIDEiP0AFW2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74039; AAC74039; b0953.
BAA35711; BAA35711; BAA35711.
GeneIDi945567.
KEGGiecj:JW0936.
eco:b0953.
PATRICi32117125. VBIEscCol129921_0987.

Organism-specific databases

EchoBASEiEB4298.
EcoGeneiEG50004. rmf.

Phylogenomic databases

eggNOGiENOG4105WFT. Bacteria.
COG3130. LUCA.
HOGENOMiHOG000277840.
InParanoidiP0AFW2.
KOiK03812.
OMAiQRSHWLG.
OrthoDBiEOG6V4GJD.

Enzyme and pathway databases

BioCyciEcoCyc:EG50004-MONOMER.
ECOL316407:JW0936-MONOMER.

Miscellaneous databases

PROiP0AFW2.

Family and domain databases

Gene3Di1.10.10.620. 1 hit.
HAMAPiMF_00919. RMF.
InterProiIPR007040. Ribosome_modulation_factor.
IPR023200. Ribosome_modulation_factor_dom.
[Graphical view]
PfamiPF04957. RMF. 1 hit.
[Graphical view]
ProDomiPD051650. Ribosome_modulation_factor. 1 hit.
[Graphical view] [Entries sharing at least one domain]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Regulation of the Escherichia coli rmf gene encoding the ribosome modulation factor: growth phase- and growth rate-dependent control."
    Yamagishi M., Matsushima H., Wada A., Sakagami M., Fujita N., Ishihama A.
    EMBO J. 12:625-630(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INDUCTION, DISRUPTION PHENOTYPE.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. "Derived amino acid sequence and identification of active site residues of Escherichia coli beta-hydroxydecanoyl thioester dehydrase."
    Cronan J.E. Jr., Li W.-B., Coleman R., Narasimhan M., de Mendoza D., Schwab J.M.
    J. Biol. Chem. 263:4641-4646(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Structure and probable genetic location of a 'ribosome modulation factor' associated with 100S ribosomes in stationary-phase Escherichia coli cells."
    Wada A., Yamazaki Y., Fujita N., Ishihama A.
    Proc. Natl. Acad. Sci. U.S.A. 87:2657-2661(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-30, INTERACTION WITH 100S RIBOSOMES.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  7. "Ribosome modulation factor: stationary growth phase-specific inhibitor of ribosome functions from Escherichia coli."
    Wada A., Igarashi K., Yoshimura S., Aimoto S., Ishihama A.
    Biochem. Biophys. Res. Commun. 214:410-417(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
    Strain: K12 / W3350 / ATCC 27020.
  8. "Expression of ribosome modulation factor (RMF) in Escherichia coli requires ppGpp."
    Izutsu K., Wada A., Wada C.
    Genes Cells 6:665-676(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
    Strain: K12.
  9. "The ribosome modulation factor (RMF) binding site on the 100S ribosome of Escherichia coli."
    Yoshida H., Maki Y., Kato H., Fujisawa H., Izutsu K., Wada C., Wada A.
    J. Biochem. 132:983-989(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RIBOSOME.
    Strain: K12.
  10. "Ribosome modulation factor protects Escherichia coli during heat stress, but this may not be dependent on ribosome dimerisation."
    Niven G.W.
    Arch. Microbiol. 182:60-66(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PROTECTION DURING HEAT STRESS.
  11. "RMF inactivates ribosomes by covering the peptidyl transferase centre and entrance of peptide exit tunnel."
    Yoshida H., Yamamoto H., Uchiumi T., Wada A.
    Genes Cells 9:271-278(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RIBOSOME.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  12. "Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli."
    Bubunenko M., Baker T., Court D.L.
    J. Bacteriol. 189:2844-2853(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  13. "Role of HPF (hibernation promoting factor) in translational activity in Escherichia coli."
    Ueta M., Ohniwa R.L., Yoshida H., Maki Y., Wada C., Wada A.
    J. Biochem. 143:425-433(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  14. "Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare 100S ribosome formation on entering the stationary growth phase."
    Yoshida H., Ueta M., Maki Y., Sakai A., Wada A.
    Genes Cells 14:271-280(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  15. "Ribosome hibernation facilitates tolerance of stationary-phase bacteria to aminoglycosides."
    McKay S.L., Portnoy D.A.
    Antimicrob. Agents Chemother. 59:6992-6999(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
    Strain: K12 / BW25113.
  16. "How hibernation factors RMF, HPF, and YfiA turn off protein synthesis."
    Polikanov Y.S., Blaha G.M., Steitz T.A.
    Science 336:915-918(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) BOUND TO THE T.THERMOPHILUS 70S RIBOSOME, FUNCTION, SUBUNIT, RRNA-BINDING.

Entry informationi

Entry nameiRMF_ECOLI
AccessioniPrimary (citable) accession number: P0AFW2
Secondary accession number(s): P22986, P77441
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: July 6, 2016
This is version 83 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

When cells are transferred to rich nutritious culture medium, RMF is quickly released from 100S ribosomes, which dissociate into 70S ribosomes (PubMed:12473202). It indicates that this interconversion is a major system regulating translation activity during the transition of growth phases.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.