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Protein

Ribonuclease 3

Gene

rnc

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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. Complements the pre-crRNA processing defect in an rnc deletion in S.pyogenes strain 370, although this E.coli strain does not have the corresponding CRISPR locus (strain TOP10) (PubMed:23535272).11 Publications

Catalytic activityi

Endonucleolytic cleavage to 5'-phosphomonoester.1 Publication

Cofactori

Mg2+3 PublicationsNote: Divalent metal 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.3 Publications

Enzyme regulationi

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.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi41MagnesiumCurated1
Active sitei45Sequence analysis1
Metal bindingi114MagnesiumBy similarity1
Active sitei117Curated1
Metal bindingi117MagnesiumCurated1

GO - Molecular functioni

GO - Biological processi

  • mRNA processing Source: UniProtKB-HAMAP
  • RNA processing Source: EcoCyc
  • rRNA catabolic process Source: InterPro
  • rRNA processing Source: UniProtKB-HAMAP
  • tRNA processing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing, rRNA processing, tRNA processing

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding, RNA-binding, rRNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10857-MONOMER.
ECOL316407:JW2551-MONOMER.
MetaCyc:EG10857-MONOMER.
BRENDAi3.1.26.3. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease 3 (EC:3.1.26.3)
Alternative name(s):
Ribonuclease III
Short name:
RNase III
Gene namesi
Name:rnc
Ordered Locus Names:b2567, JW2551
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10857. rnc.

Subcellular locationi

  • Cytoplasm 1 Publication

  • Note: Loosely associated with ribosomes.

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

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. In strain HT115, loss of immunity against a plasmid with homology to CRISPR spacer sequences (PubMed:23535272).6 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi38E → A: Reduced affinity for Mg(2+), no catalytic defect at 10 mM Mg(2+). 1 Publication1
Mutagenesisi40L → G, D or R: Loss of activity. 1 Publication1
Mutagenesisi40L → M or W: No effect. 1 Publication1
Mutagenesisi41E → A: Reduced affinity for Mg(2+), catalytic defect. 85-fold reduced affinity for Mg(2+); when associated with A-114. 1 Publication1
Mutagenesisi44G → S in rnc-105; slower growth, loss of RNase activity. 2 Publications1
Mutagenesisi45D → A, E or N: 30000-fold reduction in catalytic efficiency, binds RNA normally. Partially rescued by Mn(2+). 1 Publication1
Mutagenesisi65E → A: Reduced affinity for Mg(2+), no catalytic defect at 10 mM Mg(2+). 1 Publication1
Mutagenesisi100E → A: Reduced affinity for Mg(2+) and RNA. 1 Publication1
Mutagenesisi114D → 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. 1 Publication1
Mutagenesisi117E → D: Nearly complete loss of RNase activity, still binds RNA. Partially rescued by Mn(2+). 2 Publications1
Mutagenesisi117E → K in rnc70; slower growth, loss of RNase activity. Dominant over wild-type. Binds ds-RNA. 2 Publications1
Mutagenesisi117E → Q: Loss of RNase activity, still binds RNA. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001803951 – 226Ribonuclease 3Add BLAST226

Proteomic databases

PaxDbiP0A7Y0.
PRIDEiP0A7Y0.

Expressioni

Inductioni

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.2 Publications

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi4260597. 13 interactors.
DIPiDIP-48223N.
IntActiP0A7Y0. 6 interactors.
MINTiMINT-1227120.
STRINGi511145.b2567.

Structurei

3D structure databases

ProteinModelPortaliP0A7Y0.
SMRiP0A7Y0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini6 – 128RNase IIIAdd BLAST123
Domaini155 – 225DRBMAdd BLAST71

Sequence similaritiesi

Contains 1 RNase III domain.Curated

Phylogenomic databases

eggNOGiENOG4108ZBM. Bacteria.
COG0571. LUCA.
HOGENOMiHOG000246809.
InParanoidiP0A7Y0.
KOiK03685.
OMAiLTHKSCK.
PhylomeDBiP0A7Y0.

Family and domain databases

CDDicd00593. RIBOc. 1 hit.
Gene3Di1.10.1520.10. 1 hit.
3.30.160.20. 1 hit.
HAMAPiMF_00104. RNase_III. 1 hit.
InterProiIPR014720. dsRBD_dom.
IPR011907. RNase_III.
IPR000999. RNase_III_dom.
[Graphical view]
PfamiPF00035. dsrm. 1 hit.
PF14622. Ribonucleas_3_3. 1 hit.
[Graphical view]
SMARTiSM00358. DSRM. 1 hit.
SM00535. RIBOc. 1 hit.
[Graphical view]
SUPFAMiSSF69065. SSF69065. 1 hit.
TIGRFAMsiTIGR02191. RNaseIII. 1 hit.
PROSITEiPS50137. DS_RBD. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A7Y0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNPIVINRLQ RKLGYTFNHQ ELLQQALTHR SASSKHNERL EFLGDSILSY
60 70 80 90 100
VIANALYHRF PRVDEGDMSR MRATLVRGNT LAELAREFEL GECLRLGPGE
110 120 130 140 150
LKSGGFRRES ILADTVEALI GGVFLDSDIQ TVEKLILNWY QTRLDEISPG
160 170 180 190 200
DKQKDPKTRL QEYLQGRHLP LPTYLVVQVR GEAHDQEFTI HCQVSGLSEP
210 220
VVGTGSSRRK AEQAAAEQAL KKLELE
Length:226
Mass (Da):25,550
Last modified:January 1, 1988 - v1
Checksum:iD9E2858F2E0AA3A5
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti168 – 195HLPLP…HCQVS → PSAAADLSGSPGTWSKRTIR NLLSTARSV in CAA26504 (PubMed:3895158).CuratedAdd BLAST28

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiF65034. NREC3.
RefSeqiNP_417062.1. NC_000913.3.
WP_001068343.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75620; AAC75620; b2567.
BAE76743; BAE76743; BAE76743.
GeneIDi947033.
KEGGiecj:JW2551.
eco:b2567.
PATRICi32120533. VBIEscCol129921_2669.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiF65034. NREC3.
RefSeqiNP_417062.1. NC_000913.3.
WP_001068343.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP0A7Y0.
SMRiP0A7Y0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260597. 13 interactors.
DIPiDIP-48223N.
IntActiP0A7Y0. 6 interactors.
MINTiMINT-1227120.
STRINGi511145.b2567.

Proteomic databases

PaxDbiP0A7Y0.
PRIDEiP0A7Y0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75620; AAC75620; b2567.
BAE76743; BAE76743; BAE76743.
GeneIDi947033.
KEGGiecj:JW2551.
eco:b2567.
PATRICi32120533. VBIEscCol129921_2669.

Organism-specific databases

EchoBASEiEB0850.
EcoGeneiEG10857. rnc.

Phylogenomic databases

eggNOGiENOG4108ZBM. Bacteria.
COG0571. LUCA.
HOGENOMiHOG000246809.
InParanoidiP0A7Y0.
KOiK03685.
OMAiLTHKSCK.
PhylomeDBiP0A7Y0.

Enzyme and pathway databases

BioCyciEcoCyc:EG10857-MONOMER.
ECOL316407:JW2551-MONOMER.
MetaCyc:EG10857-MONOMER.
BRENDAi3.1.26.3. 2026.

Miscellaneous databases

PROiP0A7Y0.

Family and domain databases

CDDicd00593. RIBOc. 1 hit.
Gene3Di1.10.1520.10. 1 hit.
3.30.160.20. 1 hit.
HAMAPiMF_00104. RNase_III. 1 hit.
InterProiIPR014720. dsRBD_dom.
IPR011907. RNase_III.
IPR000999. RNase_III_dom.
[Graphical view]
PfamiPF00035. dsrm. 1 hit.
PF14622. Ribonucleas_3_3. 1 hit.
[Graphical view]
SMARTiSM00358. DSRM. 1 hit.
SM00535. RIBOc. 1 hit.
[Graphical view]
SUPFAMiSSF69065. SSF69065. 1 hit.
TIGRFAMsiTIGR02191. RNaseIII. 1 hit.
PROSITEiPS50137. DS_RBD. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRNC_ECOLI
AccessioniPrimary (citable) accession number: P0A7Y0
Secondary accession number(s): P05797, P06141, Q2MAG3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 1, 1988
Last modified: November 2, 2016
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

The original rnc-105 mutation is described as G44->D but the nucleotide sequence given indicates G44->S (PubMed:3903434). A later paper calls the same mutation G45->K (PubMed:9632264), which alters the residue and mutation.2 Publications

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.