RNR_ECOLI
ID RNR_ECOLI Reviewed; 813 AA.
AC P21499; P76800; Q2M6C6;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 2.
DT 03-AUG-2022, entry version 174.
DE RecName: Full=Ribonuclease R;
DE Short=RNase R;
DE EC=3.1.13.1;
DE AltName: Full=Protein VacB;
GN Name=rnr; Synonyms=vacB, yjeC; OrderedLocusNames=b4179, JW5741;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
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 [2]
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-86.
RC STRAIN=K12;
RX PubMed=3058695; DOI=10.1016/s0021-9258(18)37402-7;
RA Wolfe S.A., Smith J.M.;
RT "Nucleotide sequence and analysis of the purA gene encoding
RT adenylosuccinate synthetase of Escherichia coli K12.";
RL J. Biol. Chem. 263:19147-19153(1988).
RN [5]
RP PROTEIN SEQUENCE OF 2-8, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY
RP REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=11948193; DOI=10.1074/jbc.m202942200;
RA Cheng Z.F., Deutscher M.P.;
RT "Purification and characterization of the Escherichia coli exoribonuclease
RT RNase R. Comparison with RNase II.";
RL J. Biol. Chem. 277:21624-21629(2002).
RN [6]
RP IDENTIFICATION.
RX PubMed=1400189; DOI=10.1128/jb.174.20.6359-6367.1992;
RA Tobe T., Sasakawa C., Okada N., Honma Y., Yoshikawa M.;
RT "vacB, a novel chromosomal gene required for expression of virulence genes
RT on the large plasmid of Shigella flexneri.";
RL J. Bacteriol. 174:6359-6367(1992).
RN [7]
RP CHARACTERIZATION.
RX PubMed=9603904; DOI=10.1074/jbc.273.23.14077;
RA Cheng Z.-F., Zuo Y., Li Z., Rudd K.E., Deutscher M.P.;
RT "The vacB gene required for virulence in Shigella flexneri and Escherichia
RT coli encodes the exoribonuclease RNase R.";
RL J. Biol. Chem. 273:14077-14080(1998).
RN [8]
RP FUNCTION IN MATURATION OF SSRA/TMRNA, AND INDUCTION.
RC STRAIN=K12 / MG1693;
RX PubMed=14622421; DOI=10.1046/j.1365-2958.2003.03766.x;
RA Cairrao F., Cruz A., Mori H., Arraiano C.M.;
RT "Cold shock induction of RNase R and its role in the maturation of the
RT quality control mediator SsrA/tmRNA.";
RL Mol. Microbiol. 50:1349-1360(2003).
RN [9]
RP INDUCTION BY COLD SHOCK.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=14527658; DOI=10.1016/s0923-2508(03)00167-0;
RA Polissi A., De Laurentis W., Zangrossi S., Briani F., Longhi V., Pesole G.,
RA Deho G.;
RT "Changes in Escherichia coli transcriptome during acclimatization at low
RT temperature.";
RL Res. Microbiol. 154:573-580(2003).
RN [10]
RP FUNCTION IN REGULATION OF OMPA, AND INDUCTION.
RC STRAIN=K12 / MG1693;
RX PubMed=16556233; DOI=10.1111/j.1365-2958.2006.05092.x;
RA Andrade J.M., Cairrao F., Arraiano C.M.;
RT "RNase R affects gene expression in stationary phase: regulation of ompA.";
RL Mol. Microbiol. 60:219-228(2006).
RN [11]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-544, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
RX PubMed=18723842; DOI=10.1074/mcp.m800187-mcp200;
RA Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
RA Grishin N.V., Zhao Y.;
RT "Lysine acetylation is a highly abundant and evolutionarily conserved
RT modification in Escherichia coli.";
RL Mol. Cell. Proteomics 8:215-225(2009).
RN [12]
RP FUNCTION AS HELICASE, AND MUTAGENESIS OF ASP-272 AND ASP-280.
RC STRAIN=K12 / ATCC 35607 / JM83;
RX PubMed=20023028; DOI=10.1128/jb.01368-09;
RA Awano N., Rajagopal V., Arbing M., Patel S., Hunt J., Inouye M.,
RA Phadtare S.;
RT "Escherichia coli RNase R has dual activities, helicase and RNase.";
RL J. Bacteriol. 192:1344-1352(2010).
RN [13]
RP ACTIVITY REGULATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=20688916; DOI=10.1074/jbc.c110.168641;
RA Liang W., Deutscher M.P.;
RT "A novel mechanism for ribonuclease regulation: transfer-messenger RNA
RT (tmRNA) and its associated protein SmpB regulate the stability of RNase
RT R.";
RL J. Biol. Chem. 285:29054-29058(2010).
RN [14]
RP ACTIVITY REGULATION, ACETYLATION AT LYS-544, AND MUTAGENESIS OF LYS-544;
RP GLU-764 AND ASP-766.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=21981926; DOI=10.1016/j.molcel.2011.06.037;
RA Liang W., Malhotra A., Deutscher M.P.;
RT "Acetylation regulates the stability of a bacterial protein: growth stage-
RT dependent modification of RNase R.";
RL Mol. Cell 44:160-166(2011).
RN [15]
RP FUNCTION IN RIBOSOME DEGRADATION DURING STARVATION.
RC STRAIN=K12 / MG1655(Seq)*;
RX PubMed=21135037; DOI=10.1261/rna.2448911;
RA Basturea G.N., Zundel M.A., Deutscher M.P.;
RT "Degradation of ribosomal RNA during starvation: comparison to quality
RT control during steady-state growth and a role for RNase PH.";
RL RNA 17:338-345(2011).
RN [16]
RP ACETYLATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=22124017; DOI=10.1261/rna.030213.111;
RA Liang W., Deutscher M.P.;
RT "Post-translational modification of RNase R is regulated by stress-
RT dependent reduction in the acetylating enzyme Pka (YfiQ).";
RL RNA 18:37-41(2012).
CC -!- FUNCTION: 3'-5' exoribonuclease that releases 5'-nucleoside
CC monophosphates and is involved in maturation of structured RNAs (rRNAs,
CC tRNAs and SsrA/tmRNA). In stationary phase, involved in the post-
CC transcriptional regulation of ompA mRNA stability. Shortens RNA
CC processively to di- and trinucleotides. In vitro, exhibits helicase
CC activity, which is independent of its RNase activity. RNases 2 and R
CC (rnb and this entry) contribute to rRNA degradation during starvation,
CC while RNase R and PNPase (this entry and pnp) are the major
CC contributors to quality control of rRNA during steady state growth
CC (PubMed:21135037). Required for the expression of virulence genes in
CC enteroinvasive strains of E.coli. {ECO:0000269|PubMed:11948193,
CC ECO:0000269|PubMed:14622421, ECO:0000269|PubMed:16556233,
CC ECO:0000269|PubMed:20023028, ECO:0000269|PubMed:21135037}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage in the 3'- to 5'-direction to yield
CC nucleoside 5'-phosphates.; EC=3.1.13.1;
CC Evidence={ECO:0000269|PubMed:11948193};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11948193};
CC -!- ACTIVITY REGULATION: Stimulated by the presence of a monovalent cation
CC (PubMed:11948193). Highly unstable in exponential growth phase. This
CC instability is due to the binding of SsrA/tmRNA and its associated
CC protein SmpB to the C-terminal region of RNase R (PubMed:20688916). In
CC contrast, RNase R becomes stabilized upon entry into stationary phase.
CC The difference in stability between exponential and stationary phase is
CC due to the acetylation of a single lysine residue (PubMed:21981926).
CC {ECO:0000269|PubMed:11948193, ECO:0000269|PubMed:20688916,
CC ECO:0000269|PubMed:21981926}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Vmax=26900 nmol/min/mg enzyme with Poly(A) as substrate
CC {ECO:0000269|PubMed:11948193};
CC Vmax=4840 nmol/min/mg enzyme with 23S rRNA as substrate
CC {ECO:0000269|PubMed:11948193};
CC Vmax=2750 nmol/min/mg enzyme with 16S rRNA as substrate
CC {ECO:0000269|PubMed:11948193};
CC Vmax=290 nmol/min/mg enzyme with 5S rRNA as substrate
CC {ECO:0000269|PubMed:11948193};
CC Vmax=350 nmol/min/mg enzyme with tRNA as substrate
CC {ECO:0000269|PubMed:11948193};
CC pH dependence:
CC Optimum pH is 7.5-9.5. {ECO:0000269|PubMed:11948193};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius.
CC {ECO:0000269|PubMed:11948193};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:11948193}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- INDUCTION: Induced seven- to eightfold by cold shock. Induction is
CC mainly a result of the stabilization of the rnr transcripts. Also
CC induced at stationary phase. {ECO:0000269|PubMed:14527658,
CC ECO:0000269|PubMed:14622421, ECO:0000269|PubMed:16556233}.
CC -!- PTM: Acetylated at Lys-544 by PatZ during exponential growth phase.
CC Acetylation alters RNase R structure and enhances binding of SsrA/tmRNA
CC and SmpB, leading to instability and degradation of RNase R. Not
CC acetylated and stable in stationary phase cells.
CC {ECO:0000269|PubMed:18723842, ECO:0000269|PubMed:21981926,
CC ECO:0000269|PubMed:22124017}.
CC -!- SIMILARITY: Belongs to the RNR ribonuclease family. RNase R subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA97075.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; U14003; AAA97075.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC77136.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE78180.1; -; Genomic_DNA.
DR EMBL; J04199; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; S56404; S56404.
DR RefSeq; NP_418600.4; NC_000913.3.
DR RefSeq; WP_000076332.1; NZ_LN832404.1.
DR AlphaFoldDB; P21499; -.
DR SMR; P21499; -.
DR BioGRID; 4261892; 65.
DR DIP; DIP-10733N; -.
DR IntAct; P21499; 61.
DR STRING; 511145.b4179; -.
DR iPTMnet; P21499; -.
DR jPOST; P21499; -.
DR PaxDb; P21499; -.
DR PRIDE; P21499; -.
DR EnsemblBacteria; AAC77136; AAC77136; b4179.
DR EnsemblBacteria; BAE78180; BAE78180; BAE78180.
DR GeneID; 948692; -.
DR KEGG; ecj:JW5741; -.
DR KEGG; eco:b4179; -.
DR PATRIC; fig|1411691.4.peg.2522; -.
DR EchoBASE; EB1239; -.
DR eggNOG; COG0557; Bacteria.
DR HOGENOM; CLU_002333_7_0_6; -.
DR InParanoid; P21499; -.
DR OMA; DWYEYRS; -.
DR PhylomeDB; P21499; -.
DR BioCyc; EcoCyc:EG11259-MON; -.
DR BioCyc; MetaCyc:EG11259-MON; -.
DR BRENDA; 3.1.13.1; 2026.
DR PRO; PR:P21499; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0034458; F:3'-5' RNA helicase activity; IDA:EcoCyc.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IDA:EcoCyc.
DR GO; GO:0016896; F:exoribonuclease activity, producing 5'-phosphomonoesters; IDA:EcoliWiki.
DR GO; GO:0008859; F:exoribonuclease II activity; IEA:UniProtKB-UniRule.
DR GO; GO:0004540; F:ribonuclease activity; IMP:EcoliWiki.
DR GO; GO:0008997; F:ribonuclease R activity; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006402; P:mRNA catabolic process; IMP:EcoCyc.
DR GO; GO:0034470; P:ncRNA processing; IMP:EcoCyc.
DR GO; GO:0009409; P:response to cold; IEP:EcoCyc.
DR Gene3D; 2.40.50.140; -; 3.
DR HAMAP; MF_01895; RNase_R; 1.
DR InterPro; IPR011129; CSD.
DR InterPro; IPR040476; CSD2.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR013223; RNase_B_OB_dom.
DR InterPro; IPR001900; RNase_II/R.
DR InterPro; IPR022966; RNase_II/R_CS.
DR InterPro; IPR004476; RNase_II/RNase_R.
DR InterPro; IPR011805; RNase_R.
DR InterPro; IPR013668; RNase_R_HTH_12.
DR InterPro; IPR022967; S1_dom.
DR InterPro; IPR003029; S1_domain.
DR Pfam; PF17876; CSD2; 1.
DR Pfam; PF08461; HTH_12; 1.
DR Pfam; PF08206; OB_RNB; 1.
DR Pfam; PF00773; RNB; 1.
DR Pfam; PF00575; S1; 1.
DR SMART; SM00357; CSP; 1.
DR SMART; SM00955; RNB; 1.
DR SMART; SM00316; S1; 1.
DR SUPFAM; SSF50249; SSF50249; 4.
DR TIGRFAMs; TIGR00358; 3_prime_RNase; 1.
DR TIGRFAMs; TIGR02063; RNase_R; 1.
DR PROSITE; PS01175; RIBONUCLEASE_II; 1.
DR PROSITE; PS50126; S1; 1.
PE 1: Evidence at protein level;
KW Acetylation; Cytoplasm; Direct protein sequencing; Exonuclease; Hydrolase;
KW Nuclease; Reference proteome; RNA-binding; Stress response; Virulence.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:11948193"
FT CHAIN 2..813
FT /note="Ribonuclease R"
FT /id="PRO_0000166402"
FT DOMAIN 644..725
FT /note="S1 motif"
FT REGION 731..813
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 733..747
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 757..778
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 544
FT /note="N6-acetyllysine; by PatZ"
FT /evidence="ECO:0000269|PubMed:18723842,
FT ECO:0000269|PubMed:21981926"
FT MUTAGEN 272
FT /note="D->N: Loss of RNase activity, but exhibits helicase
FT activity."
FT /evidence="ECO:0000269|PubMed:20023028"
FT MUTAGEN 280
FT /note="D->N: Loss of RNase activity, but exhibits helicase
FT activity."
FT /evidence="ECO:0000269|PubMed:20023028"
FT MUTAGEN 544
FT /note="K->A: Lack of acetylation. Maintains protein's
FT instability in exponential phase. Becomes unstable in
FT stationary phase."
FT /evidence="ECO:0000269|PubMed:21981926"
FT MUTAGEN 544
FT /note="K->R: Lack of acetylation. Stabilizes exponential
FT phase RNase R."
FT /evidence="ECO:0000269|PubMed:21981926"
FT MUTAGEN 764
FT /note="E->A: Becomes unstable in stationary phase; when
FT associated with A-766."
FT /evidence="ECO:0000269|PubMed:21981926"
FT MUTAGEN 766
FT /note="D->A: Becomes unstable in stationary phase; when
FT associated with A-764."
FT /evidence="ECO:0000269|PubMed:21981926"
SQ SEQUENCE 813 AA; 92109 MW; 7516DF0A40D35594 CRC64;
MSQDPFQERE AEKYANPIPS REFILEHLTK REKPASRDEL AVELHIEGEE QLEGLRRRLR
AMERDGQLVF TRRQCYALPE RLDLVKGTVI GHRDGYGFLR VEGRKDDLYL SSEQMKTCIH
GDQVLAQPLG ADRKGRREAR IVRVLVPKTS QIVGRYFTEA GVGFVVPDDS RLSFDILIPP
DQIMGARMGF VVVVELTQRP TRRTKAVGKI VEVLGDNMGT GMAVDIALRT HEIPYIWPQA
VEQQVAGLKE EVPEEAKAGR VDLRDLPLVT IDGEDARDFD DAVYCEKKRG GGWRLWVAIA
DVSYYVRPST PLDREARNRG TSVYFPSQVI PMLPEVLSNG LCSLNPQVDR LCMVCEMTVS
SKGRLTGYKF YEAVMSSHAR LTYTKVWHIL QGDQDLREQY APLVKHLEEL HNLYKVLDKA
REERGGISFE SEEAKFIFNA ERRIERIEQT QRNDAHKLIE ECMILANISA ARFVEKAKEP
ALFRIHDKPS TEAITSFRSV LAELGLELPG GNKPEPRDYA ELLESVADRP DAEMLQTMLL
RSMKQAIYDP ENRGHFGLAL QSYAHFTSPI RRYPDLTLHR AIKYLLAKEQ GHQGNTTETG
GYHYSMEEML QLGQHCSMAE RRADEATRDV ADWLKCDFML DQVGNVFKGV ISSVTGFGFF
VRLDDLFIDG LVHVSSLDND YYRFDQVGQR LMGESSGQTY RLGDRVEVRV EAVNMDERKI
DFSLISSERA PRNVGKTARE KAKKGDAGKK GGKRRQVGKK VNFEPDSAFR GEKKTKPKAA
KKDARKAKKP SAKTQKIAAA TKAKRAAKKK VAE
