RegulonDB RegulonDB 11.0: Gene Form
   

rnr gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rnr rlmB nsrR TSS_5052 TSS_5052 TSS_5051 TSS_5051 TSS_5050 (cluster) TSS_5050 (cluster) TSS_5049 TSS_5049 TSS_5048 TSS_5048 TSS_5047 (cluster) TSS_5047 (cluster) TSS_5046 TSS_5046

Gene      
Name: rnr    Texpresso search in the literature
Synonym(s): ECK4175, EG11259, b4179, vacB, yjeC
Genome position(nucleotides): 4406654 --> 4409095
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
55.28
External database links:  
ASAP:
ABE-0013678
ECHOBASE:
EB1239
ECOLIHUB:
rnr
OU-MICROARRAY:
b4179
STRING:
511145.b4179
COLOMBOS: rnr


Product      
Name: RNase R
Synonym(s): Rnr, VacB, YjeC
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 92.109
Isoelectric point: 8.873
Motif(s):
 
Type Positions Sequence Comment
2 -> 813 SQDPFQEREAEKYANPIPSREFILEHLTKREKPASRDELAVELHIEGEEQLEGLRRRLRAMERDGQLVFTRRQCYALPERLDLVKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTEAGVGFVVPDDSRLSFDILIPPDQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPSTPLDREARNRGTSVYFPSQVIPMLPEVLSNGLCSLNPQVDRLCMVCEMTVSSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLTLHRAIKYLLAKEQGHQGNTTETGGYHYSMEEMLQLGQHCSMAERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLMGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLISSERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKTKPKAAKKDARKAKKPSAKTQKIAAATKAKRAAKKKVAE UniProt: Ribonuclease R.
23 -> 83 FILEHLTKREKPASRDELAVELHIEGEEQLEGLRRRLRAMERDGQLVFTRRQCYALPERLD
87 -> 144 GTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRV
164 -> 238 FVVPDDSRLSFDILIPPDQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWP
260 -> 587 RVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPSTPLDREARNRGTSVYFPSQVIPMLPEVLSNGLCSLNPQVDRLCMVCEMTVSSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLTLHRAIKYLLA

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.1 - RNA
  2 - information transfer --> 2.2 - RNA related --> 2.2.4 - RNA degradation
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0004518 - nuclease activity
GO:0004527 - exonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0000175 - 3'-5'-exoribonuclease activity
GO:0003723 - RNA binding
GO:0004540 - ribonuclease activity
GO:0016896 - exoribonuclease activity, producing 5'-phosphomonoesters
GO:0008859 - exoribonuclease II activity
GO:0034458 - 3'-5' RNA helicase activity
GO:0008997 - ribonuclease R activity
biological_process GO:0016070 - RNA metabolic process
GO:0006950 - response to stress
GO:0006402 - mRNA catabolic process
GO:0009409 - response to cold
GO:0034470 - ncRNA processing
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0090501 - RNA phosphodiester bond hydrolysis
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic
Note(s): Note(s): ...[more].
Reference(s): [1] Barbas A., et al., 2008
[2] Jain C. 2012
[3] Karzai AW., et al., 2001
[4] Nikolaev N., et al., 1976
[5] Phadtare S. 2011
[6] Phadtare S. 2012
[7] Polissi A., et al., 2003
[8] Prossliner T., et al., 2021
[9] Sundermeier T., et al., 2008
[10] Tamura M., et al., 2012
[11] Wellner K., et al., 2018
External database links:  
ALPHAFOLD:
P21499
DIP:
DIP-10733N
ECOCYC:
EG11259-MONOMER
ECOLIWIKI:
b4179
INTERPRO:
IPR012340
INTERPRO:
IPR011805
INTERPRO:
IPR011129
INTERPRO:
IPR004476
INTERPRO:
IPR003029
INTERPRO:
IPR001900
INTERPRO:
IPR013223
INTERPRO:
IPR013668
INTERPRO:
IPR022966
INTERPRO:
IPR022967
INTERPRO:
IPR040476
MODBASE:
P21499
PFAM:
PF17876
PFAM:
PF08206
PFAM:
PF00575
PFAM:
PF00773
PFAM:
PF08461
PRIDE:
P21499
PRODB:
PRO_000023799
PROSITE:
PS50126
PROSITE:
PS01175
REFSEQ:
NP_418600
SMART:
SM00357
SMART:
SM00316
SMART:
SM00955
SMR:
P21499
UNIPROT:
P21499


Operon      
Name: nsrR-rnr-rlmB-yjfIJ         
Operon arrangement:
Transcription unit        Promoter
nsrR-rnr-rlmB-yjfI
yjfIJ


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_5046 4406415 forward nd [RS-EPT-CBR] [12]
  promoter TSS_5047 (cluster) 4406597 forward nd [RS-EPT-CBR] [12]
  promoter TSS_5048 4406668 forward nd [RS-EPT-CBR] [12]
  promoter TSS_5049 4406974 forward nd [RS-EPT-CBR] [12]
  promoter TSS_5050 (cluster) 4407052 forward nd [RS-EPT-CBR] [12]
  promoter TSS_5051 4407074 forward nd [RS-EPT-CBR] [12]
  promoter TSS_5052 4409223 forward nd [RS-EPT-CBR] [12]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Barbas A., Matos RG., Amblar M., Lopez-Vinas E., Gomez-Puertas P., Arraiano CM., 2008, New insights into the mechanism of RNA degradation by ribonuclease II: identification of the residue responsible for setting the RNase II end product., J Biol Chem 283(19):13070-6

 [2] Jain C., 2012, Novel role for RNase PH in the degradation of structured RNA., J Bacteriol 194(15):3883-90

 [3] Karzai AW., Sauer RT., 2001, Protein factors associated with the SsrA.SmpB tagging and ribosome rescue complex., Proc Natl Acad Sci U S A 98(6):3040-4

 [4] Nikolaev N., Folsom V., Schlessinger D., 1976, Escherichia coli mutants deficient in exoribonucleases., Biochem Biophys Res Commun 70(3):920-4

 [5] Phadtare S., 2011, Unwinding activity of cold shock proteins and RNA metabolism., RNA Biol 8(3):394-7

 [6] Phadtare S., 2012, Escherichia coli cold-shock gene profiles in response to over-expression/deletion of CsdA, RNase R and PNPase and relevance to low-temperature RNA metabolism., Genes Cells 17(10):850-74

 [7] Polissi A., De Laurentis W., Zangrossi S., Briani F., Longhi V., Pesole G., Deho G., 2003, Changes in Escherichia coli transcriptome during acclimatization at low temperature., Res Microbiol 154(8):573-80

 [8] Prossliner T., Gerdes K., Sorensen MA., Winther KS., 2021, Hibernation factors directly block ribonucleases from entering the ribosome in response to starvation., Nucleic Acids Res 49(4):2226-2239

 [9] Sundermeier T., Ge Z., Richards J., Dulebohn D., Karzai AW., 2008, Studying tmRNA-mediated surveillance and nonstop mRNA decay., Methods Enzymol 447:329-58

 [10] Tamura M., Kers JA., Cohen SN., 2012, Second-site suppression of RNase E essentiality by mutation of the deaD RNA helicase in Escherichia coli., J Bacteriol 194(8):1919-26

 [11] Wellner K., Czech A., Ignatova Z., Betat H., Morl M., 2018, Examining tRNA 3'-ends in Escherichia coli: teamwork between CCA-adding enzyme, RNase T, and RNase R., RNA 24(3):361-370

 [12] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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