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Ribonuclease R

 
Known also as: Protein vacB

Known abbreviations: RNase R, rnr, vacB, yjeC, b4179, JW5741

 

FUNCTION:
 
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. 
 
CATALYTIC ACTIVITY:
 
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates. 
 
COFACTOR:
 
Magnesium. 
 
ENZYME REGULATION:
 
Stimulated by the presence of a monovalent cation. 
 
SUBUNIT STRUCTURE:
 
Monomer. 
 
CELLULAR LOCALIZATION:
 
Cytoplasm (Potential)
 
INDUCTION:
 
Induced seven- to eightfold by cold shock. Induction is mainly a result of the stabilization of the rnr transcripts. Also induced at stationary phase. 
 
BIOPHYSICOCHEMICAL PROPERTIES:
 
Kinetic parameters:
Vmax=26900 nmol/min/mg enzyme with Poly(A) as substrate 
Vmax=4840 nmol/min/mg enzyme with 23S rRNA as substrate
Vmax=2750 nmol/min/mg enzyme with 16S rRNA as substrate
Vmax=290 nmol/min/mg enzyme with 5S rRNA as substrate
Vmax=350 nmol/min/mg enzyme with tRNA as substrate
pH dependence:
Optimum pH is 7.5-9.5.
 
TEMPERATURE DEPENDENCE:
 
Optimum temperature is 50 degrees Celsius.



Activities in which Ribonuclease R is involved: Pathways in which Ribonuclease R is involved:

NCBI GI number(s): 90111698
49175990
Species: Escherichia coli

Links to other databases:

Database ID Link
Uniprot P21499 P21499
BRENDA - -
KEGG eco:b4179 eco:b4179
PFAM: PF08461
PF08206
PF00773
PF00575
PF08461
PF08206
PF00773
PF00575
InterPro: IPR011129
IPR012340
IPR016027
IPR003029
IPR022967
IPR013223
IPR001900
IPR022966
IPR004476
IPR011805
IPR013668
IPR011129
IPR012340
IPR016027
IPR003029
IPR022967
IPR013223
IPR001900
IPR022966
IPR004476
IPR011805
IPR013668
CATH: - -
SCOP: - -


Protein sequence:
MSQDPFQEREAEKYANPIPSREFILEHLTKREKPASRDELAVELHIEGEE
QLEGLRRRLRAMERDGQLVFTRRQCYALPERLDLVKGTVIGHRDGYGFLR
VEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTS
QIVGRYFTEAGVGFVVPDDSRLSFDILIPPDQIMGARMGFVVVVELTQRP
TRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQAVEQQVAGLKE
EVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIA
DVSYYVRPSTPLDREARNRGTSVYFPSQVIPMLPEVLSNGLCSLNPQVDR
LCMVCEMTVSSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQY
APLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQT
QRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRSV
LAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDP
ENRGHFGLALQSYAHFTSPIRRYPDLTLHRAIKYLLAKEQGHQGNTTETG
GYHYSMEEMLQLGQHCSMAERRADEATRDVADWLKCDFMLDQVGNVFKGV
ISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLMGESSGQTY
RLGDRVEVRVEAVNMDERKIDFSLISSERAPRNVGKTAREKAKKGDAGKK
GGKRRQVGKKVNFEPDSAFRGEKKTKPKAAKKDARKAKKPSAKTQKIAAA
TKAKRAAKKKVAE

Ribonuclease R (Escherichia coli) is product of expression of rnr gene.

References:

Title Authors Journal Publication date (Issue) PubMed ID
The complete genome sequence of Escherichia coli K-12. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y Science 1997-09-05 (277) 9278503
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 BL, Mori H, Horiuchi T Mol Syst Biol 2006-01-01 (2) 16738553
Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II. Cheng ZF, Deutscher MP J Biol Chem 2002-06-14 (277) 11948193
Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes. Burland V, Plunkett G 3rd, Sofia HJ, Daniels DL, Blattner FR Nucleic Acids Res 1995-06-25 (23) 7610040
Nucleotide sequence and analysis of the purA gene encoding adenylosuccinate synthetase of Escherichia coli K12. Wolfe SA, Smith JM J Biol Chem 1988-12-15 (263) 3058695
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 1992-10-01 (174) 1400189
The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. Cheng ZF, Zuo Y, Li Z, Rudd KE, Deutscher MP J Biol Chem 1998-06-05 (273) 9603904
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 CM Mol Microbiol 2003-11-01 (50) 14622421
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 2003-10-01 (154) 14527658
RNase R affects gene expression in stationary phase: regulation of ompA. Andrade JM, Cairrao F, Arraiano CM Mol Microbiol 2006-04-01 (60) 16556233
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 CF, Grishin NV, Zhao Y Mol Cell Proteomics 2009-01-01 (8) 18723842
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 2010-03-01 (192) 20023028



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Last modification of this entry: Sept. 25, 2012.

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