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P0A7Y0 (RNC_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 80. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribonuclease 3

EC=3.1.26.3
Alternative name(s):
Ribonuclease III
Short name=RNase III
Gene names
Name:rnc
Ordered Locus Names:b2567, JW2551
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length226 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. Involved in the processing of rRNA precursors, viral transcripts, some mRNAs and at least 1 tRNA (metY, a minor form of tRNA-init-Met). Cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs; cleavage can occur in assembled 30S, 50S and even 70S subunits and is influenced by the presence of ribosomal proteins. The E.coli enzyme does not cleave R.capsulatus rRNA precursor, although R.capsulatus will complement an E.coli disruption, showing substrate recognition is different. Removes the intervening sequences from Salmonella typhimurium rRNA precursor. Ref.1 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.16 Ref.17 Ref.18

Catalytic activity

Endonucleolytic cleavage to 5'-phosphomonoester. Ref.11

Cofactor

Divalent cations, preferably Mg2+. While only 1 Mg2+ is detected by crystallography, other evidence indicates there may be more than 1 metal necessary for catalysis. Binding of the second metal my be promoted by substrate binding. Ref.13 Ref.22 Ref.26

Enzyme regulation

Non-competitively inhibited by 2-hydroxy-4H-isoquinoline-1,3-dione. Activity is down-regulated during cold shock by direct interaction with YmdB. Also down-regulated during entry into stationary phase by an YmdB-independent mechanism. Ref.26 Ref.27

Subunit structure

Homodimer. Ref.13

Subcellular location

Cytoplasm. Note: Loosely associated with ribosomes. Ref.9

Induction

Expression increases as the growth rate increases. Encoded in the rnc-era-recO operon. Processes the 5' end of its own transcript leading to mRNA instability. Ref.17 Ref.20 Ref.26 Ref.27

Disruption phenotype

Slower than wild-type growth. Transient accumulation of the 30S rRNA precursor occurs; 90% of 16S rRNA is correctly processed while an extended version of 23S rRNA accumulates in the ribosome. Half-life of a number of RNase III processed transcripts increases. In the absence of era and rnc there is a defect in chromosome partitioning. Ref.6 Ref.10 Ref.15 Ref.19 Ref.20

Sequence similarities

Contains 1 DRBM (double-stranded RNA-binding) domain.

Contains 1 RNase III domain.

Caution

The original rnc-105 mutation is described as G44->D but the nucleotide sequence given indicates G44->S (Ref.1). A later paper calls the same mutation G45->K (Ref.19), which alters the residue and mutation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 226226Ribonuclease 3 HAMAP-Rule MF_00104
PRO_0000180395

Regions

Domain6 – 128123RNase III
Domain155 – 22571DRBM

Sites

Active site451 Potential
Active site1171 Probable
Metal binding411Magnesium Probable
Metal binding1141Magnesium By similarity
Metal binding1171Magnesium Probable

Experimental info

Mutagenesis381E → A: Reduced affinity for Mg(2+), no catalytic defect at 10 mM Mg(2+). Ref.25
Mutagenesis401L → G, D or R: Loss of activity. Ref.23
Mutagenesis401L → M or W: No effect. Ref.23
Mutagenesis411E → A: Reduced affinity for Mg(2+), catalytic defect. 85-fold reduced affinity for Mg(2+); when associated with A-114. Ref.25
Mutagenesis441G → S in rnc-105; slower growth, loss of RNase activity. Ref.1 Ref.19
Mutagenesis451D → A, E or N: 30000-fold reduction in catalytic efficiency, binds RNA normally. Partially rescued by Mn(2+). Ref.25
Mutagenesis651E → A: Reduced affinity for Mg(2+), no catalytic defect at 10 mM Mg(2+). Ref.25
Mutagenesis1001E → A: Reduced affinity for Mg(2+) and RNA. Ref.25
Mutagenesis1141D → A: Reduced affinity for Mg(2+), no catalytic defect at 10 mM Mg(2+). 85-fold reduced affinity for Mg(2+); when associated with A-41. Ref.25
Mutagenesis1171E → D: Nearly complete loss of RNase activity, still binds RNA. Partially rescued by Mn(2+). Ref.19 Ref.22
Mutagenesis1171E → K in rnc70; slower growth, loss of RNase activity. Dominant over wild-type. Binds ds-RNA. Ref.19 Ref.22
Mutagenesis1171E → Q: Loss of RNase activity, still binds RNA. Ref.19 Ref.22
Sequence conflict168 – 19528HLPLP…HCQVS → PSAAADLSGSPGTWSKRTIR NLLSTARSV in CAA26504. Ref.2

Sequences

Sequence LengthMass (Da)Tools
P0A7Y0 [UniParc].

Last modified January 1, 1988. Version 1.
Checksum: D9E2858F2E0AA3A5

FASTA22625,550
        10         20         30         40         50         60 
MNPIVINRLQ RKLGYTFNHQ ELLQQALTHR SASSKHNERL EFLGDSILSY VIANALYHRF 

        70         80         90        100        110        120 
PRVDEGDMSR MRATLVRGNT LAELAREFEL GECLRLGPGE LKSGGFRRES ILADTVEALI 

       130        140        150        160        170        180 
GGVFLDSDIQ TVEKLILNWY QTRLDEISPG DKQKDPKTRL QEYLQGRHLP LPTYLVVQVR 

       190        200        210        220 
GEAHDQEFTI HCQVSGLSEP VVGTGSSRRK AEQAAAEQAL KKLELE 

« Hide

References

« Hide 'large scale' references
[1]"DNA sequencing of the Escherichia coli ribonuclease III gene and its mutations."
Nashimoto H., Uchida H.
Mol. Gen. Genet. 201:25-29(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION AS AN ENDORIBONUCLEASE, MUTAGENESIS OF GLY-44.
Strain: K12.
[2]"The DNA sequence of the gene (rnc) encoding ribonuclease III of Escherichia coli."
March P.E., Ahnn J., Inouye M.
Nucleic Acids Res. 13:4677-4685(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12 / CS520.
[3]Nashimoto H., Saito N.
Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[4]"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 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[5]"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.
[6]"Genetic analysis of the rnc operon of Escherichia coli."
Takiff H.E., Chen S.M., Court D.L.
J. Bacteriol. 171:2581-2590(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-45, DISRUPTION PHENOTYPE, OPERON STRUCTURE.
Strain: K12 / W3110.
[7]"Expression and characterization of RNase III and Era proteins. Products of the rnc operon of Escherichia coli."
Chen S.M., Takiff H.E., Barber A.M., Dubois G.C., Bardwell J.C., Court D.L.
J. Biol. Chem. 265:2888-2895(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-30, MRNA PROCESSING, ATP-BINDING.
Strain: K12 / W3110.
[8]"A GTP-binding protein of Escherichia coli has homology to yeast RAS proteins."
Ahnn J., March P.E., Takiff H.E., Inouye M.
Proc. Natl. Acad. Sci. U.S.A. 83:8849-8853(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 211-226.
[9]"Purification and properties of ribonuclease III from Escherichia coli."
Robertson H.D., Webster R.E., Zinder N.D.
J. Biol. Chem. 243:82-91(1968) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS A DS-RNA SPECIFIC ENDORIBONUCLEASE, SUBCELLULAR LOCATION, ASSOCIATION WITH RIBOSOMES.
Strain: K12 / K38 / S26.
[10]"T7 early RNAs and Escherichia coli ribosomal RNAs are cut from large precursor RNAs in vivo by ribonuclease 3."
Dunn J.J., Studier F.W.
Proc. Natl. Acad. Sci. U.S.A. 70:3296-3300(1973) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN ENTEROBACTERIA PHAGE T7 RNA PROCESSING, FUNCTION IN PROCESSING OF RRNA, DISRUPTION PHENOTYPE.
Strain: K12 / A19.
[11]"Ribonuclease 3 does not degrade deoxyribonucleic acid-ribonucleic acid hybrids."
Crouch R.J.
J. Biol. Chem. 249:1314-1316(1974) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS A DS-RNA SPECIFIC ENDORIBONUCLEASE, CATALYTIC ACTIVITY.
Strain: K12 / D10.
[12]"30 S pre-ribosomal RNA of Escherichia coli and products of cleavage by ribonuclease III: length and molecular weight."
Nikolaev N., Schlessinger D., Wellauer P.K.
J. Mol. Biol. 86:741-747(1974) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN PROCESSING OF RRNA.
[13]"RNase III cleavage of single-stranded RNA. Effect of ionic strength on the fideltiy of cleavage."
Dunn J.J.
J. Biol. Chem. 251:3807-3814(1976) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN PROCESSING OF RRNA, COFACTOR, SUBUNIT.
[14]"The synthesis of some proteins is affected in RNA processing mutants of Escherichia coli."
Gitelman D.R., Apirion D.
Biochem. Biophys. Res. Commun. 96:1063-1070(1980) [PubMed] [Europe PMC] [Abstract]
Cited for: ROLE IN PROTEIN SYNTHESIS.
[15]"RNase III cleavage is obligate for maturation but not for function of Escherichia coli pre-23S rRNA."
King T.C., Sirdeshmukh R., Schlessinger D.
Proc. Natl. Acad. Sci. U.S.A. 81:185-188(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
[16]"Cleavage by RNase III in the transcripts of the met Y-nus-A-infB operon of Escherichia coli releases the tRNA and initiates the decay of the downstream mRNA."
Regnier P., Grunberg-Manago M.
J. Mol. Biol. 210:293-302(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN PROCESSING OF TRNA.
[17]"RNase III cleavages in non-coding leaders of Escherichia coli transcripts control mRNA stability and genetic expression."
Regnier P., Grunberg-Manago M.
Biochimie 72:825-834(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN PROCESSING OF MRNA, INDUCTION.
[18]"The excision of intervening sequences from Salmonella 23S ribosomal RNA."
Burgin A.B., Parodos K., Lane D.J., Pace N.R.
Cell 60:405-414(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: ROLE IN EXCISION OF INTERVENING SEQUENCES.
Strain: N2076.
[19]"Genetic uncoupling of the dsRNA-binding and RNA cleavage activities of the Escherichia coli endoribonuclease RNase III--the effect of dsRNA binding on gene expression."
Dasgupta S., Fernandez L., Kameyama L., Inada T., Nakamura Y., Pappas A., Court D.L.
Mol. Microbiol. 28:629-640(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF GLY-44 AND GLU-117, DISRUPTION PHENOTYPE.
Strain: K12 / W3110.
[20]"Cell cycle arrest in Era GTPase mutants: a potential growth rate-regulated checkpoint in Escherichia coli."
Britton R.A., Powell B.S., Dasgupta S., Sun Q., Margolin W., Lupski J.R., Court D.L.
Mol. Microbiol. 27:739-750(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION, DISRUPTION PHENOTYPE.
Strain: K12 / W3110.
[21]"Different cleavage specificities of RNases III from Rhodobacter capsulatus and Escherichia coli."
Conrad C., Rauhut R., Klug G.
Nucleic Acids Res. 26:4446-4453(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBSTRATE SPECIFICITY.
[22]"Mechanism of action of Escherichia coli ribonuclease III. Stringent chemical requirement for the glutamic acid 117 side chain and Mn2+ rescue of the Glu117Asp mutant."
Sun W., Nicholson A.W.
Biochemistry 40:5102-5110(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: COFACTOR, MUTAGENESIS OF GLU-117, CATALYTIC MODEL.
[23]"Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage."
Blaszczyk J., Tropea J.E., Bubunenko M., Routzahn K.M., Waugh D.S., Court D.L., Ji X.
Structure 9:1225-1236(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF LEU-40.
[24]"Functional interaction between RNase III and the Escherichia coli ribosome."
Allas U., Liiv A., Remme J.
BMC Mol. Biol. 4:8-8(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: ASSOCIATION WITH RIBOSOMES.
[25]"Mutational analysis of the nuclease domain of Escherichia coli ribonuclease III. Identification of conserved acidic residues that are important for catalytic function in vitro."
Sun W., Li G., Nicholson A.W.
Biochemistry 43:13054-13062(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF GLU-38; GLU-41; ASP-45; GLU-65; GLU-100 AND ASP-114.
[26]"Catalytic mechanism of Escherichia coli ribonuclease III: kinetic and inhibitor evidence for the involvement of two magnesium ions in RNA phosphodiester hydrolysis."
Sun W., Pertzev A., Nicholson A.W.
Nucleic Acids Res. 33:807-815(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME REGULATION, COFACTOR, CATALYTIC MODEL.
[27]"YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity."
Kim K.S., Manasherob R., Cohen S.N.
Genes Dev. 22:3497-3508(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME REGULATION.
[28]"Structure of the dsRNA binding domain of E. coli RNase III."
Kharrat A., Macias M.J., Gibson T.J., Nilges M., Pastore A.
EMBO J. 14:3572-3584(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 153-226, RNA-BINDING.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X02946 Genomic DNA. Translation: CAA26692.1.
X02673 Genomic DNA. Translation: CAA26504.1.
D64044 Genomic DNA. Translation: BAA10914.1.
U36841 Genomic DNA. Translation: AAA79829.1.
U00096 Genomic DNA. Translation: AAC75620.1.
AP009048 Genomic DNA. Translation: BAE76743.1.
M26415 Genomic DNA. Translation: AAA21843.1.
M14658 Unassigned DNA. Translation: AAA03241.1.
PIRNREC3. F65034.
RefSeqNP_417062.1. NC_000913.3.
YP_490795.1. NC_007779.1.

3D structure databases

ProteinModelPortalP0A7Y0.
SMRP0A7Y0. Positions 5-224.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-48223N.
IntActP0A7Y0. 6 interactions.
MINTMINT-1227120.
STRING511145.b2567.

PTM databases

PhosSiteP010446.

Proteomic databases

PaxDbP0A7Y0.
PRIDEP0A7Y0.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75620; AAC75620; b2567.
BAE76743; BAE76743; BAE76743.
GeneID12931603.
947033.
KEGGecj:Y75_p2520.
eco:b2567.
PATRIC32120533. VBIEscCol129921_2669.

Organism-specific databases

EchoBASEEB0850.
EcoGeneEG10857. rnc.

Phylogenomic databases

eggNOGCOG0571.
HOGENOMHOG000246809.
KOK03685.
OMAAQKDPKT.
OrthoDBEOG6T1WVS.
PhylomeDBP0A7Y0.

Enzyme and pathway databases

BioCycEcoCyc:EG10857-MONOMER.
ECOL316407:JW2551-MONOMER.
MetaCyc:EG10857-MONOMER.
BRENDA3.1.26.3. 2026.

Gene expression databases

GenevestigatorP0A7Y0.

Family and domain databases

Gene3D1.10.1520.10. 1 hit.
3.30.160.20. 1 hit.
HAMAPMF_00104. RNase_III.
InterProIPR014720. dsRNA-bd_dom.
IPR011907. RNase_III.
IPR000999. RNase_III_dom.
[Graphical view]
PANTHERPTHR11207. PTHR11207. 1 hit.
PfamPF00035. dsrm. 1 hit.
PF14622. Ribonucleas_3_3. 1 hit.
[Graphical view]
SMARTSM00358. DSRM. 1 hit.
SM00535. RIBOc. 1 hit.
[Graphical view]
SUPFAMSSF69065. SSF69065. 1 hit.
TIGRFAMsTIGR02191. RNaseIII. 1 hit.
PROSITEPS50137. DS_RBD. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROP0A7Y0.

Entry information

Entry nameRNC_ECOLI
AccessionPrimary (citable) accession number: P0A7Y0
Secondary accession number(s): P05797, P06141, Q2MAG3
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 1, 1988
Last modified: May 14, 2014
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Escherichia coli

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