Ribonuclease R - Escherichia coli (strain K12)

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P21499 (RNR_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 112. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Ribonuclease R
Short name=RNase R
EC=3.1.13.1

Alternative name(s):
Protein VacB

Gene names

Name:	rnr
Synonyms:	vacB, yjeC
Ordered Locus Names:	b4179, JW5741

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	813 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

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. Ref.5 Ref.8 Ref.10 Ref.12
Catalytic activity	Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates. Ref.5
Cofactor	Magnesium. Ref.5
Enzyme regulation	Stimulated by the presence of a monovalent cation. Ref.5
Subunit structure	Monomer. Ref.5
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01895.
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. Ref.5 Ref.8 Ref.9 Ref.10
Sequence similarities	Belongs to the RNR ribonuclease family. RNase R subfamily. Contains 1 S1 motif domain.
Biophysicochemical properties	Kinetic parameters: V_max=26900 nmol/min/mg enzyme with Poly(A) as substrate Ref.5 V_max=4840 nmol/min/mg enzyme with 23S rRNA as substrate V_max=2750 nmol/min/mg enzyme with 16S rRNA as substrate V_max=290 nmol/min/mg enzyme with 5S rRNA as substrate V_max=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.
Sequence caution	The sequence AAA97075.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Stress response Virulence
Cellular component	Cytoplasm
Ligand	RNA-binding
Molecular function	Exonuclease Hydrolase Nuclease
PTM	Acetylation
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	mRNA catabolic process Inferred from mutant phenotype PubMed 15664199. Source: EcoCyc ncRNA processing Inferred from mutant phenotype Ref.8. Source: EcoCyc pathogenesis Inferred from electronic annotation. Source: UniProtKB-KW response to cold Inferred from expression pattern Ref.8. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	3'-5' RNA helicase activity Inferred from direct assay Ref.12. Source: EcoCyc 3'-5'-exoribonuclease activity Inferred from direct assay Ref.5 PubMed 336626. Source: EcoCyc RNA binding Inferred from electronic annotation. Source: HAMAP exoribonuclease II activity Inferred from electronic annotation. Source: HAMAP ribonuclease R activity Inferred from direct assay Ref.5. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.5

Chain

2 – 813

812

Ribonuclease R HAMAP-Rule MF_01895

PRO_0000166402

Regions

Domain

644 – 725

S1 motif

Amino acid modifications

Modified residue

544

N6-acetyllysine Ref.11

Experimental info

Mutagenesis

272

D → N: Loss of RNase activity, but exhibits helicase activity. Ref.12

Mutagenesis

280

D → N: Loss of RNase activity, but exhibits helicase activity. Ref.12

Sequences

Sequence

Length

Mass (Da)

Tools

P21499 [UniParc].

Last modified February 1, 1995. Version 2.
Checksum: 7516DF0A40D35594
Show »

FASTA

813

92,109

        10         20         30         40         50         60 
MSQDPFQERE AEKYANPIPS REFILEHLTK REKPASRDEL AVELHIEGEE QLEGLRRRLR 

        70         80         90        100        110        120 
AMERDGQLVF TRRQCYALPE RLDLVKGTVI GHRDGYGFLR VEGRKDDLYL SSEQMKTCIH 

       130        140        150        160        170        180 
GDQVLAQPLG ADRKGRREAR IVRVLVPKTS QIVGRYFTEA GVGFVVPDDS RLSFDILIPP 

       190        200        210        220        230        240 
DQIMGARMGF VVVVELTQRP TRRTKAVGKI VEVLGDNMGT GMAVDIALRT HEIPYIWPQA 

       250        260        270        280        290        300 
VEQQVAGLKE EVPEEAKAGR VDLRDLPLVT IDGEDARDFD DAVYCEKKRG GGWRLWVAIA 

       310        320        330        340        350        360 
DVSYYVRPST PLDREARNRG TSVYFPSQVI PMLPEVLSNG LCSLNPQVDR LCMVCEMTVS 

       370        380        390        400        410        420 
SKGRLTGYKF YEAVMSSHAR LTYTKVWHIL QGDQDLREQY APLVKHLEEL HNLYKVLDKA 

       430        440        450        460        470        480 
REERGGISFE SEEAKFIFNA ERRIERIEQT QRNDAHKLIE ECMILANISA ARFVEKAKEP 

       490        500        510        520        530        540 
ALFRIHDKPS TEAITSFRSV LAELGLELPG GNKPEPRDYA ELLESVADRP DAEMLQTMLL 

       550        560        570        580        590        600 
RSMKQAIYDP ENRGHFGLAL QSYAHFTSPI RRYPDLTLHR AIKYLLAKEQ GHQGNTTETG 

       610        620        630        640        650        660 
GYHYSMEEML QLGQHCSMAE RRADEATRDV ADWLKCDFML DQVGNVFKGV ISSVTGFGFF 

       670        680        690        700        710        720 
VRLDDLFIDG LVHVSSLDND YYRFDQVGQR LMGESSGQTY RLGDRVEVRV EAVNMDERKI 

       730        740        750        760        770        780 
DFSLISSERA PRNVGKTARE KAKKGDAGKK GGKRRQVGKK VNFEPDSAFR GEKKTKPKAA 

       790        800        810 
KKDARKAKKP SAKTQKIAAA TKAKRAAKKK VAE

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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, 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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
PIR	S56404.
RefSeq	NP_418600.4. NC_000913.2. YP_492321.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P21499.
SMR	P21499. Positions 86-744.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-10733N.
IntAct	P21499. 59 interactions.
STRING	511145.b4179.
Proteomic databases
PaxDb	P21499.
PRIDE	P21499.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC77136; AAC77136; b4179. BAE78180; BAE78180; BAE78180.
GeneID	12932898. 948692.
KEGG	ecj:Y75_p4065. eco:b4179.
PATRIC	32123931. VBIEscCol129921_4310.
Organism-specific databases
EchoBASE	EB1239.
EcoGene	EG11259. rnr.
Phylogenomic databases
eggNOG	COG0557.
HOGENOM	HOG000071120.
KO	K12573.
OMA	FGFLIPD.
ProtClustDB	PRK11642.
Enzyme and pathway databases
BioCyc	EcoCyc:EG11259-MONOMER. ECOL316407:JW5741-MONOMER. MetaCyc:EG11259-MONOMER.
Gene expression databases
Genevestigator	P21499.
Family and domain databases
Gene3D	2.40.50.140. 1 hit.
HAMAP	MF_01895. RNase_R.
InterPro	IPR011129. Cold_shock_prot. IPR012340. NA-bd_OB-fold. IPR003029. Rbsml_prot_S1_RNA-bd_dom. IPR022967. RNA-binding_domain_S1. IPR013223. RNase_B_OB_dom. IPR001900. RNase_II/R. IPR022966. RNase_II/R_CS. IPR004476. RNase_II/RNase_R. IPR011805. RNase_R. IPR013668. RNase_R_HTH_12. [Graphical view]
Pfam	PF08461. HTH_12. 1 hit. PF08206. OB_RNB. 2 hits. PF00773. RNB. 1 hit. PF00575. S1. 1 hit. [Graphical view]
SMART	SM00357. CSP. 1 hit. SM00955. RNB. 1 hit. SM00316. S1. 1 hit. [Graphical view]
SUPFAM	SSF50249. Nucleic_acid_OB. 2 hits.
TIGRFAMs	TIGR00358. 3_prime_RNase. 1 hit. TIGR02063. RNase_R. 1 hit.
PROSITE	PS01175. RIBONUCLEASE_II. 1 hit. PS50126. S1. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RNR_ECOLI

Accession

Primary (citable) accession number: P21499
Secondary accession number(s): P76800, Q2M6C6

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	February 1, 1995
Last modified:	May 1, 2013
This is version 112 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents