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Protein

Ribosome maturation factor RimM

Gene

rimM

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

Functioni

An accessory protein needed during the final step in assembly of the 30S ribosomal subunit, probably for assembly of the head region (also called the 3' domain). It may act while Era is associated and after RimM in 30S subunit assembly. Interacts with S19. Essential for efficient processing of 16S rRNA; a deletion mutant accumulates 17S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes.3 Publications

GO - Molecular functioni

GO - Biological processi

  • maturation of SSU-rRNA Source: EcoliWiki
  • ribosomal small subunit assembly Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Chaperone

Keywords - Biological processi

Ribosome biogenesis

Enzyme and pathway databases

BioCyciEcoCyc:EG11153-MONOMER.
ECOL316407:JW5413-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosome maturation factor RimM
Alternative name(s):
21K
Gene namesi
Name:rimM
Synonyms:yfjA
Ordered Locus Names:b2608, JW5413
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11153. rimM.

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • ribosome Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Disruption causes incomplete processing of 17S rRNA, accumulation of 30S and 50S subunits and decreased translational efficiency. Deletion is partially suppressed by mutations in rpsM, the gene for ribosomal protein S13, by a mutation in rpsS, the gene for S19 and also by overexpression of RbfA. Suppressors due to in-frame fusions with rpsP, the upstream gene for ribosomal protein S16 have been isolated. Suppression is probably due to increased expression of RimM; the fusion proteins are found in translationally active 70S ribosomes.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi106 – 1072YY → AA: 3-fold decreased growth rate; loss of association with 30S ribosomal subunit; loss of interaction with S19. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 182182Ribosome maturation factor RimMPRO_0000163286Add
BLAST

Proteomic databases

EPDiP0A7X6.
PaxDbiP0A7X6.
PRIDEiP0A7X6.

2D gel databases

SWISS-2DPAGEP0A7X6.

Expressioni

Inductioni

Translation of the mRNA is repressed by a stem-loop in the first 150 nucleotides of the transcript. Part of the rpsP-rimM-trmD-rplS operon.

Interactioni

Subunit structurei

Binds ribosomal protein S19.

Protein-protein interaction databases

BioGridi4263071. 13 interactions.
IntActiP0A7X6. 7 interactions.
STRINGi511145.b2608.

Structurei

3D structure databases

ProteinModelPortaliP0A7X6.
SMRiP0A7X6. Positions 15-182.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini103 – 18280PRC barrelAdd
BLAST

Domaini

The PRC barrel domain binds ribosomal protein S19.

Sequence similaritiesi

Belongs to the RimM family.Curated
Contains 1 PRC barrel domain.Curated

Phylogenomic databases

eggNOGiENOG4108ZR6. Bacteria.
COG0806. LUCA.
HOGENOMiHOG000220989.
InParanoidiP0A7X6.
KOiK02860.
OMAiQPWFIQR.
OrthoDBiEOG6SBT2K.
PhylomeDBiP0A7X6.

Family and domain databases

Gene3Di2.40.30.60. 1 hit.
HAMAPiMF_00014. Ribosome_mat_RimM.
InterProiIPR011961. 16S_RimM.
IPR027275. PRC-brl_dom.
IPR011033. PRC_barrel-like.
IPR002676. RimM.
IPR009000. Transl_B-barrel.
[Graphical view]
PfamiPF05239. PRC. 1 hit.
PF01782. RimM. 1 hit.
[Graphical view]
SUPFAMiSSF50346. SSF50346. 1 hit.
SSF50447. SSF50447. 1 hit.
TIGRFAMsiTIGR02273. 16S_RimM. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A7X6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKQLTAQAP VDPIVLGKMG SSYGIRGWLR VFSSTEDAES IFDYQPWFIQ
60 70 80 90 100
KAGQWQQVQL ESWKHHNQDM IIKLKGVDDR DAANLLTNCE IVVDSSQLPQ
110 120 130 140 150
LEEGDYYWKD LMGCQVVTTE GYDLGKVVDM METGSNDVLV IKANLKDAFG
160 170 180
IKERLVPFLD GQVIKKVDLT TRSIEVDWDP GF
Length:182
Mass (Da):20,605
Last modified:June 7, 2005 - v1
Checksum:iD8512AB9E4FD3D75
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01818 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAC75657.2.
AP009048 Genomic DNA. Translation: BAA16493.2.
PIRiC65039.
RefSeqiNP_417099.4. NC_000913.3.
WP_000043335.1. NZ_CP014272.1.

Genome annotation databases

EnsemblBacteriaiAAC75657; AAC75657; b2608.
BAA16493; BAA16493; BAA16493.
GeneIDi947101.
KEGGiecj:JW5413.
eco:b2608.
PATRICi32120615. VBIEscCol129921_2706.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01818 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAC75657.2.
AP009048 Genomic DNA. Translation: BAA16493.2.
PIRiC65039.
RefSeqiNP_417099.4. NC_000913.3.
WP_000043335.1. NZ_CP014272.1.

3D structure databases

ProteinModelPortaliP0A7X6.
SMRiP0A7X6. Positions 15-182.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263071. 13 interactions.
IntActiP0A7X6. 7 interactions.
STRINGi511145.b2608.

2D gel databases

SWISS-2DPAGEP0A7X6.

Proteomic databases

EPDiP0A7X6.
PaxDbiP0A7X6.
PRIDEiP0A7X6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75657; AAC75657; b2608.
BAA16493; BAA16493; BAA16493.
GeneIDi947101.
KEGGiecj:JW5413.
eco:b2608.
PATRICi32120615. VBIEscCol129921_2706.

Organism-specific databases

EchoBASEiEB1142.
EcoGeneiEG11153. rimM.

Phylogenomic databases

eggNOGiENOG4108ZR6. Bacteria.
COG0806. LUCA.
HOGENOMiHOG000220989.
InParanoidiP0A7X6.
KOiK02860.
OMAiQPWFIQR.
OrthoDBiEOG6SBT2K.
PhylomeDBiP0A7X6.

Enzyme and pathway databases

BioCyciEcoCyc:EG11153-MONOMER.
ECOL316407:JW5413-MONOMER.

Miscellaneous databases

PROiP0A7X6.

Family and domain databases

Gene3Di2.40.30.60. 1 hit.
HAMAPiMF_00014. Ribosome_mat_RimM.
InterProiIPR011961. 16S_RimM.
IPR027275. PRC-brl_dom.
IPR011033. PRC_barrel-like.
IPR002676. RimM.
IPR009000. Transl_B-barrel.
[Graphical view]
PfamiPF05239. PRC. 1 hit.
PF01782. RimM. 1 hit.
[Graphical view]
SUPFAMiSSF50346. SSF50346. 1 hit.
SSF50447. SSF50447. 1 hit.
TIGRFAMsiTIGR02273. 16S_RimM. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of an Escherichia coli operon containing genes for the tRNA(m1G)methyltransferase, the ribosomal proteins S16 and L19 and a 21-K polypeptide."
    Bystroem A.S., Hjalmarsson K.J., Wikstroem P.M., Bjoerk G.R.
    EMBO J. 2:899-905(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], OPERON STRUCTURE.
    Strain: K12.
  2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
    Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
    , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
    DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "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.
  5. "Importance of mRNA folding and start codon accessibility in the expression of genes in a ribosomal protein operon of Escherichia coli."
    Wikstroem P.M., Lind L.K., Berg D.E., Bjoerk G.R.
    J. Mol. Biol. 224:949-966(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: CONTROL OF TRANSLATION, OPERON STRUCTURE.
  6. "A novel ribosome-associated protein is important for efficient translation in Escherichia coli."
    Bylund G.O., Persson B.C., Lundberg L.A., Wikstroem P.M.
    J. Bacteriol. 179:4567-4574(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, PARTIAL SUPPRESSION BY S13 MUTATIONS.
    Strain: MW100.
  7. "RimM and RbfA are essential for efficient processing of 16S rRNA in Escherichia coli."
    Bylund G.O., Wipemo L.C., Lundberg L.A., Wikstroem P.M.
    J. Bacteriol. 180:73-82(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, PARTIAL SUPPRESSION BY RBFA OVEREXPRESSION.
    Strain: MW100.
  8. "Hybrid protein between ribosomal protein S16 and RimM of Escherichia coli retains the ribosome maturation function of both proteins."
    Loevgren J.M., Wikstroem P.M.
    J. Bacteriol. 183:5352-5357(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF 106-TYR-TYR-107, SUBCELLULAR LOCATION, FUSION WITH RIBOSOMAL PROTEIN S16.
    Strain: MW100.
  9. "The PRC-barrel domain of the ribosome maturation protein RimM mediates binding to ribosomal protein S19 in the 30S ribosomal subunits."
    Loevgren J.M., Bylund G.O., Srivastava M.K., Lundberg L.A.C., Persson O.P., Wingsle G., Wikstroem P.M.
    RNA 10:1798-1812(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RIBOSOMAL PROTEIN S19.
    Strain: MW100.
  10. "The effect of ribosome assembly cofactors on in vitro 30S subunit reconstitution."
    Bunner A.E., Nord S., Wikstrom P.M., Williamson J.R.
    J. Mol. Biol. 398:1-7(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN 30S SUBUNIT PROTEIN ASSEMBLY.

Entry informationi

Entry nameiRIMM_ECOLI
AccessioniPrimary (citable) accession number: P0A7X6
Secondary accession number(s): P21504, Q8X9D2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: May 11, 2016
This is version 85 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. 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.