Ribonuclease 3 - Escherichia coli (strain K12)

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P0A7Y0 (RNC_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 72. 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 3
EC=3.1.26.3

Alternative name(s):
Ribonuclease III
Short name=RNase III

Gene names

Name:	rnc
Ordered Locus Names:	b2567, JW2551

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	226 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	mRNA processing rRNA processing tRNA processing
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding RNA-binding rRNA-binding
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	RNA processing Inferred from direct assay PubMed 1091644. Source: EcoCyc mRNA processing Inferred from electronic annotation. Source: HAMAP rRNA catabolic process Inferred from electronic annotation. Source: InterPro rRNA processing Inferred from electronic annotation. Source: HAMAP tRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW double-stranded RNA binding Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW rRNA binding Inferred from electronic annotation. Source: UniProtKB-KW ribonuclease III activity Inferred from direct assay PubMed 1091644. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 226

226

Ribonuclease 3 HAMAP-Rule MF_00104

PRO_0000180395

Regions

Domain

6 – 128

123

RNase III

Domain

155 – 225

DRBM

Sites

Active site

Potential

Active site

117

Probable

Metal binding

Magnesium Probable

Metal binding

114

Magnesium By similarity

Metal binding

117

Magnesium Probable

Experimental info

Mutagenesis

E → A: Reduced affinity for Mg(2+), no catalytic defect at 10 mM Mg(2+). Ref.25

Mutagenesis

L → G, D or R: Loss of activity. Ref.23

Mutagenesis

L → M or W: No effect. Ref.23

Mutagenesis

E → A: Reduced affinity for Mg(2+), catalytic defect. 85-fold reduced affinity for Mg(2+); when associated with A-114. Ref.25

Mutagenesis

G → S in rnc-105; slower growth, loss of RNase activity. Ref.1 Ref.19

Mutagenesis

D → A, E or N: 30000-fold reduction in catalytic efficiency, binds RNA normally. Partially rescued by Mn(2+). Ref.25

Mutagenesis

E → A: Reduced affinity for Mg(2+), no catalytic defect at 10 mM Mg(2+). Ref.25

Mutagenesis

100

E → A: Reduced affinity for Mg(2+) and RNA. Ref.25

Mutagenesis

114

D → 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

Mutagenesis

117

E → D: Nearly complete loss of RNase activity, still binds RNA. Partially rescued by Mn(2+). Ref.19 Ref.22

Mutagenesis

117

E → K in rnc70; slower growth, loss of RNase activity. Dominant over wild-type. Binds ds-RNA. Ref.19 Ref.22

Mutagenesis

117

E → Q: Loss of RNase activity, still binds RNA. Ref.19 Ref.22

Sequence conflict

168 – 195

HLPLP…HCQVS → PSAAADLSGSPGTWSKRTIR NLLSTARSV in CAA26504. Ref.2

Sequences

Sequence

Length

Mass (Da)

Tools

P0A7Y0 [UniParc].

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

FASTA

226

25,550

        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' referencesShow '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 277:1453-1474(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.
PIR	NREC3. F65034.
RefSeq	NP_417062.1. NC_000913.2. YP_490795.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0A7Y0.
SMR	P0A7Y0. Positions 5-224.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-48223N.
IntAct	P0A7Y0. 5 interactions.
MINT	MINT-1227120.
STRING	511145.b2567.
PTM databases
PhosSite	P010446.
Proteomic databases
PaxDb	P0A7Y0.
PRIDE	P0A7Y0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC75620; AAC75620; b2567. BAE76743; BAE76743; BAE76743.
GeneID	12931603. 947033.
KEGG	ecj:Y75_p2520. eco:b2567.
PATRIC	32120533. VBIEscCol129921_2669.
Organism-specific databases
EchoBASE	EB0850.
EcoGene	EG10857. rnc.
Phylogenomic databases
eggNOG	COG0571.
HOGENOM	HOG000246809.
KO	K03685.
OMA	LTHKSCK.
ProtClustDB	PRK00102.
Enzyme and pathway databases
BioCyc	EcoCyc:EG10857-MONOMER. ECOL316407:JW2551-MONOMER. MetaCyc:EG10857-MONOMER.
BRENDA	3.1.26.3. 2026.
Gene expression databases
Genevestigator	P0A7Y0.
Family and domain databases
Gene3D	1.10.1520.10. 1 hit. 3.30.160.20. 1 hit.
HAMAP	MF_00104. RNase_III.
InterPro	IPR001159. Ds-RNA-bd. IPR014720. dsRNA-bd-like_dom. IPR011907. RNase_III. IPR000999. RNase_III_dom. [Graphical view]
PANTHER	PTHR11207. PTHR11207. 1 hit.
Pfam	PF00035. dsrm. 1 hit. PF00636. Ribonuclease_3. 1 hit. [Graphical view]
SMART	SM00358. DSRM. 1 hit. SM00535. RIBOc. 1 hit. [Graphical view]
SUPFAM	SSF69065. RNase_III. 1 hit.
TIGRFAMs	TIGR02191. RNaseIII. 1 hit.
PROSITE	PS50137. DS_RBD. 1 hit. PS00517. RNASE_3_1. 1 hit. PS50142. RNASE_3_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RNC_ECOLI

Accession

Primary (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 1, 2013
This is version 72 of the entry and version 1 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

Sites

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM 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