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Protein

Ribonuclease R

Gene

rnr

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

Functioni

3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs (rRNAs, tRNAs and SsrA/tmRNA). In stationary phase, involved in the post-transcriptional regulation of ompA mRNA stability. Shortens RNA processively to di- and trinucleotides. In vitro, exhibits helicase activity, which is independent of its RNase activity. Required for the expression of virulence genes in enteroinvasive strains of E.coli.4 Publications

Catalytic activityi

Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates.1 Publication

Cofactori

Mg2+1 Publication

Enzyme regulationi

Stimulated by the presence of a monovalent cation. Highly unstable in exponential growth phase. This instability is due to the binding of SsrA/tmRNA and its associated protein SmpB to the C-terminal region of RNase R. In contrast, RNase R becomes stabilized upon entry into stationary phase. The difference in stability between exponential and stationary phase is due to the acetylation of a single lysine residue.3 Publications

Kineticsi

    1. Vmax=26900 nmol/min/mg enzyme with Poly(A) as substrate1 Publication
    2. Vmax=4840 nmol/min/mg enzyme with 23S rRNA as substrate1 Publication
    3. Vmax=2750 nmol/min/mg enzyme with 16S rRNA as substrate1 Publication
    4. Vmax=290 nmol/min/mg enzyme with 5S rRNA as substrate1 Publication
    5. Vmax=350 nmol/min/mg enzyme with tRNA as substrate1 Publication

    pH dependencei

    Optimum pH is 7.5-9.5.1 Publication

    Temperature dependencei

    Optimum temperature is 50 degrees Celsius.1 Publication

    GO - Molecular functioni

    • 3'-5'-exoribonuclease activity Source: EcoCyc
    • 3'-5' RNA helicase activity Source: EcoCyc
    • exoribonuclease activity, producing 5'-phosphomonoesters Source: EcoliWiki
    • exoribonuclease II activity Source: UniProtKB-HAMAP
    • ribonuclease activity Source: EcoliWiki
    • ribonuclease R activity Source: EcoCyc
    • RNA binding Source: UniProtKB-HAMAP

    GO - Biological processi

    • mRNA catabolic process Source: EcoCyc
    • ncRNA processing Source: EcoCyc
    • pathogenesis Source: UniProtKB-KW
    • response to cold Source: EcoCyc
    • RNA phosphodiester bond hydrolysis Source: GOC
    • RNA phosphodiester bond hydrolysis, exonucleolytic Source: GOC
    • rRNA processing Source: GO_Central
    Complete GO annotation...

    Keywords - Molecular functioni

    Exonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    Stress response, Virulence

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11259-MONOMER.
    ECOL316407:JW5741-MONOMER.
    MetaCyc:EG11259-MONOMER.
    RETL1328306-WGS:GSTH-1661-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonuclease R (EC:3.1.13.1)
    Short name:
    RNase R
    Alternative name(s):
    Protein VacB
    Gene namesi
    Name:rnr
    Synonyms:vacB, yjeC
    Ordered Locus Names:b4179, JW5741
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11259. rnr.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    • exosome (RNase complex) Source: GO_Central
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi272 – 2721D → N: Loss of RNase activity, but exhibits helicase activity. 1 Publication
    Mutagenesisi280 – 2801D → N: Loss of RNase activity, but exhibits helicase activity. 1 Publication
    Mutagenesisi544 – 5441K → A: Lack of acetylation. Maintains protein's instability in exponential phase. Becomes unstable in stationary phase. 1 Publication
    Mutagenesisi544 – 5441K → R: Lack of acetylation. Stabilizes exponential phase RNase R. 1 Publication
    Mutagenesisi764 – 7641E → A: Becomes unstable in stationary phase; when associated with A-766. 1 Publication
    Mutagenesisi766 – 7661D → A: Becomes unstable in stationary phase; when associated with A-764. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 813812Ribonuclease RPRO_0000166402Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei544 – 5441N6-acetyllysine; by Pka2 Publications

    Post-translational modificationi

    Acetylated at Lys-544 by Pka during exponential growth phase. Acetylation alters RNase R structure and enhances binding of SsrA/tmRNA and SmpB, leading to instability and degradation of RNase R. Not acetylated and stable in stationary phase cells.3 Publications

    Keywords - PTMi

    Acetylation

    Proteomic databases

    EPDiP21499.
    PaxDbiP21499.
    PRIDEiP21499.

    Expressioni

    Inductioni

    Induced seven- to eightfold by cold shock. Induction is mainly a result of the stabilization of the rnr transcripts. Also induced at stationary phase.3 Publications

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    BioGridi4261892. 10 interactions.
    DIPiDIP-10733N.
    IntActiP21499. 60 interactions.
    STRINGi511145.b4179.

    Structurei

    3D structure databases

    ProteinModelPortaliP21499.
    SMRiP21499. Positions 86-720.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini644 – 72582S1 motifAdd
    BLAST

    Sequence similaritiesi

    Contains 1 S1 motif domain.Curated

    Phylogenomic databases

    eggNOGiENOG4105C40. Bacteria.
    COG0557. LUCA.
    HOGENOMiHOG000071120.
    InParanoidiP21499.
    KOiK12573.
    OMAiYRVHEGP.
    OrthoDBiEOG6Q5NRD.
    PhylomeDBiP21499.

    Family and domain databases

    Gene3Di2.40.50.140. 1 hit.
    HAMAPiMF_01895. RNase_R.
    InterProiIPR011129. Cold_shock_prot.
    IPR012340. NA-bd_OB-fold.
    IPR013223. RNase_B_OB_dom.
    IPR022966. RNase_II/R_CS.
    IPR004476. RNase_II/RNase_R.
    IPR011805. RNase_R.
    IPR013668. RNase_R_HTH_12.
    IPR022967. S1_dom.
    IPR003029. S1_domain.
    [Graphical view]
    PfamiPF08461. HTH_12. 1 hit.
    PF08206. OB_RNB. 2 hits.
    PF00575. S1. 1 hit.
    [Graphical view]
    SMARTiSM00357. CSP. 1 hit.
    SM00316. S1. 1 hit.
    [Graphical view]
    SUPFAMiSSF50249. SSF50249. 4 hits.
    TIGRFAMsiTIGR00358. 3_prime_RNase. 1 hit.
    TIGR02063. RNase_R. 1 hit.
    PROSITEiPS01175. RIBONUCLEASE_II. 1 hit.
    PS50126. S1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P21499-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSQDPFQERE AEKYANPIPS REFILEHLTK REKPASRDEL AVELHIEGEE
    60 70 80 90 100
    QLEGLRRRLR AMERDGQLVF TRRQCYALPE RLDLVKGTVI GHRDGYGFLR
    110 120 130 140 150
    VEGRKDDLYL SSEQMKTCIH GDQVLAQPLG ADRKGRREAR IVRVLVPKTS
    160 170 180 190 200
    QIVGRYFTEA GVGFVVPDDS RLSFDILIPP DQIMGARMGF VVVVELTQRP
    210 220 230 240 250
    TRRTKAVGKI VEVLGDNMGT GMAVDIALRT HEIPYIWPQA VEQQVAGLKE
    260 270 280 290 300
    EVPEEAKAGR VDLRDLPLVT IDGEDARDFD DAVYCEKKRG GGWRLWVAIA
    310 320 330 340 350
    DVSYYVRPST PLDREARNRG TSVYFPSQVI PMLPEVLSNG LCSLNPQVDR
    360 370 380 390 400
    LCMVCEMTVS SKGRLTGYKF YEAVMSSHAR LTYTKVWHIL QGDQDLREQY
    410 420 430 440 450
    APLVKHLEEL HNLYKVLDKA REERGGISFE SEEAKFIFNA ERRIERIEQT
    460 470 480 490 500
    QRNDAHKLIE ECMILANISA ARFVEKAKEP ALFRIHDKPS TEAITSFRSV
    510 520 530 540 550
    LAELGLELPG GNKPEPRDYA ELLESVADRP DAEMLQTMLL RSMKQAIYDP
    560 570 580 590 600
    ENRGHFGLAL QSYAHFTSPI RRYPDLTLHR AIKYLLAKEQ GHQGNTTETG
    610 620 630 640 650
    GYHYSMEEML QLGQHCSMAE RRADEATRDV ADWLKCDFML DQVGNVFKGV
    660 670 680 690 700
    ISSVTGFGFF VRLDDLFIDG LVHVSSLDND YYRFDQVGQR LMGESSGQTY
    710 720 730 740 750
    RLGDRVEVRV EAVNMDERKI DFSLISSERA PRNVGKTARE KAKKGDAGKK
    760 770 780 790 800
    GGKRRQVGKK VNFEPDSAFR GEKKTKPKAA KKDARKAKKP SAKTQKIAAA
    810
    TKAKRAAKKK VAE
    Length:813
    Mass (Da):92,109
    Last modified:February 1, 1995 - v2
    Checksum:i7516DF0A40D35594
    GO

    Sequence cautioni

    The sequence AAA97075.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U14003 Genomic DNA. Translation: AAA97075.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC77136.2.
    AP009048 Genomic DNA. Translation: BAE78180.1.
    J04199 Genomic DNA. No translation available.
    PIRiS56404.
    RefSeqiNP_418600.4. NC_000913.3.
    WP_000076332.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77136; AAC77136; b4179.
    BAE78180; BAE78180; BAE78180.
    GeneIDi948692.
    KEGGiecj:JW5741.
    eco:b4179.
    PATRICi32123931. VBIEscCol129921_4310.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U14003 Genomic DNA. Translation: AAA97075.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC77136.2.
    AP009048 Genomic DNA. Translation: BAE78180.1.
    J04199 Genomic DNA. No translation available.
    PIRiS56404.
    RefSeqiNP_418600.4. NC_000913.3.
    WP_000076332.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP21499.
    SMRiP21499. Positions 86-720.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4261892. 10 interactions.
    DIPiDIP-10733N.
    IntActiP21499. 60 interactions.
    STRINGi511145.b4179.

    Proteomic databases

    EPDiP21499.
    PaxDbiP21499.
    PRIDEiP21499.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77136; AAC77136; b4179.
    BAE78180; BAE78180; BAE78180.
    GeneIDi948692.
    KEGGiecj:JW5741.
    eco:b4179.
    PATRICi32123931. VBIEscCol129921_4310.

    Organism-specific databases

    EchoBASEiEB1239.
    EcoGeneiEG11259. rnr.

    Phylogenomic databases

    eggNOGiENOG4105C40. Bacteria.
    COG0557. LUCA.
    HOGENOMiHOG000071120.
    InParanoidiP21499.
    KOiK12573.
    OMAiYRVHEGP.
    OrthoDBiEOG6Q5NRD.
    PhylomeDBiP21499.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11259-MONOMER.
    ECOL316407:JW5741-MONOMER.
    MetaCyc:EG11259-MONOMER.
    RETL1328306-WGS:GSTH-1661-MONOMER.

    Miscellaneous databases

    PROiP21499.

    Family and domain databases

    Gene3Di2.40.50.140. 1 hit.
    HAMAPiMF_01895. RNase_R.
    InterProiIPR011129. Cold_shock_prot.
    IPR012340. NA-bd_OB-fold.
    IPR013223. RNase_B_OB_dom.
    IPR022966. RNase_II/R_CS.
    IPR004476. RNase_II/RNase_R.
    IPR011805. RNase_R.
    IPR013668. RNase_R_HTH_12.
    IPR022967. S1_dom.
    IPR003029. S1_domain.
    [Graphical view]
    PfamiPF08461. HTH_12. 1 hit.
    PF08206. OB_RNB. 2 hits.
    PF00575. S1. 1 hit.
    [Graphical view]
    SMARTiSM00357. CSP. 1 hit.
    SM00316. S1. 1 hit.
    [Graphical view]
    SUPFAMiSSF50249. SSF50249. 4 hits.
    TIGRFAMsiTIGR00358. 3_prime_RNase. 1 hit.
    TIGR02063. RNase_R. 1 hit.
    PROSITEiPS01175. RIBONUCLEASE_II. 1 hit.
    PS50126. S1. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
      Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
      Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "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.
    4. "Nucleotide sequence and analysis of the purA gene encoding adenylosuccinate synthetase of Escherichia coli K12."
      Wolfe S.A., Smith J.M.
      J. Biol. Chem. 263:19147-19153(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-86.
      Strain: K12.
    5. "Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II."
      Cheng Z.F., Deutscher M.P.
      J. Biol. Chem. 277:21624-21629(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-8, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    6. "vacB, a novel chromosomal gene required for expression of virulence genes on the large plasmid of Shigella flexneri."
      Tobe T., Sasakawa C., Okada N., Honma Y., Yoshikawa M.
      J. Bacteriol. 174:6359-6367(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION.
    7. "The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R."
      Cheng Z.-F., Zuo Y., Li Z., Rudd K.E., Deutscher M.P.
      J. Biol. Chem. 273:14077-14080(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    8. "Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA."
      Cairrao F., Cruz A., Mori H., Arraiano C.M.
      Mol. Microbiol. 50:1349-1360(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN MATURATION OF SSRA/TMRNA, INDUCTION.
      Strain: K12 / MG1693.
    9. "Changes in Escherichia coli transcriptome during acclimatization at low temperature."
      Polissi A., De Laurentis W., Zangrossi S., Briani F., Longhi V., Pesole G., Deho G.
      Res. Microbiol. 154:573-580(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION BY COLD SHOCK.
      Strain: K12 / MG1655 / ATCC 47076.
    10. "RNase R affects gene expression in stationary phase: regulation of ompA."
      Andrade J.M., Cairrao F., Arraiano C.M.
      Mol. Microbiol. 60:219-228(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN REGULATION OF OMPA, INDUCTION.
      Strain: K12 / MG1693.
    11. "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
      Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
      Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-544, IDENTIFICATION BY MASS SPECTROMETRY.
      Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
    12. "Escherichia coli RNase R has dual activities, helicase and RNase."
      Awano N., Rajagopal V., Arbing M., Patel S., Hunt J., Inouye M., Phadtare S.
      J. Bacteriol. 192:1344-1352(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS HELICASE, MUTAGENESIS OF ASP-272 AND ASP-280.
      Strain: K12 / ATCC 35607 / JM83.
    13. "A novel mechanism for ribonuclease regulation: transfer-messenger RNA (tmRNA) and its associated protein SmpB regulate the stability of RNase R."
      Liang W., Deutscher M.P.
      J. Biol. Chem. 285:29054-29058(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: ENZYME REGULATION.
      Strain: K12 / MG1655 / ATCC 47076.
    14. "Acetylation regulates the stability of a bacterial protein: growth stage-dependent modification of RNase R."
      Liang W., Malhotra A., Deutscher M.P.
      Mol. Cell 44:160-166(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: ENZYME REGULATION, ACETYLATION AT LYS-544, MUTAGENESIS OF LYS-544; GLU-764 AND ASP-766.
      Strain: K12 / MG1655 / ATCC 47076.
    15. "Post-translational modification of RNase R is regulated by stress-dependent reduction in the acetylating enzyme Pka (YfiQ)."
      Liang W., Deutscher M.P.
      RNA 18:37-41(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION.
      Strain: K12 / MG1655 / ATCC 47076.

    Entry informationi

    Entry nameiRNR_ECOLI
    AccessioniPrimary (citable) accession number: P21499
    Secondary accession number(s): P76800, Q2M6C6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1991
    Last sequence update: February 1, 1995
    Last modified: June 8, 2016
    This is version 137 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, 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.