UniProtKB - P0A7Y0 (RNC_ECOLI)
Protein
Ribonuclease 3
Gene
rnc
Organism
Escherichia coli (strain K12)
Status
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
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
Catalytic activityi
- Endonucleolytic cleavage to 5'-phosphomonoester.1 Publication EC:3.1.26.3
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
Activity 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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 41 | MagnesiumCurated | 1 | |
Active sitei | 45 | Sequence analysis | 1 | |
Metal bindingi | 114 | MagnesiumBy similarity | 1 | |
Active sitei | 117 | Curated | 1 | |
Metal bindingi | 117 | MagnesiumCurated | 1 |
GO - Molecular functioni
- ATP binding Source: UniProtKB-KW
- double-stranded RNA binding Source: GO_Central
- enzyme binding Source: EcoCyc
- magnesium ion binding Source: EcoCyc
- ribonuclease III activity Source: EcoCyc
- rRNA binding Source: UniProtKB-KW
GO - Biological processi
- mRNA processing Source: EcoCyc
- RNA processing Source: EcoCyc
- rRNA catabolic process Source: InterPro
- rRNA processing Source: EcoCyc
- tRNA processing Source: UniProtKB-KW
Keywordsi
Molecular function | Endonuclease, Hydrolase, Nuclease, RNA-binding, rRNA-binding |
Biological process | mRNA processing, rRNA processing, tRNA processing |
Ligand | ATP-binding, Magnesium, Metal-binding, Nucleotide-binding |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10857-MONOMER ECOL316407:JW2551-MONOMER MetaCyc:EG10857-MONOMER |
BRENDAi | 3.1.26.3 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 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Subcellular locationi
- Cytoplasm 1 Publication Note: Loosely associated with ribosomes.
GO - Cellular componenti
- cytosol Source: EcoCyc
Keywords - Cellular componenti
CytoplasmPathology & 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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 38 | E → A: Reduced affinity for Mg(2+), no catalytic defect at 10 mM Mg(2+). 1 Publication | 1 | |
Mutagenesisi | 40 | L → G, D or R: Loss of activity. 1 Publication | 1 | |
Mutagenesisi | 40 | L → M or W: No effect. 1 Publication | 1 | |
Mutagenesisi | 41 | E → A: Reduced affinity for Mg(2+), catalytic defect. 85-fold reduced affinity for Mg(2+); when associated with A-114. 1 Publication | 1 | |
Mutagenesisi | 44 | G → S in rnc-105; slower growth, loss of RNase activity. 2 Publications | 1 | |
Mutagenesisi | 45 | D → A, E or N: 30000-fold reduction in catalytic efficiency, binds RNA normally. Partially rescued by Mn(2+). 1 Publication | 1 | |
Mutagenesisi | 65 | E → A: Reduced affinity for Mg(2+), no catalytic defect at 10 mM Mg(2+). 1 Publication | 1 | |
Mutagenesisi | 100 | E → A: Reduced affinity for Mg(2+) and RNA. 1 Publication | 1 | |
Mutagenesisi | 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. 1 Publication | 1 | |
Mutagenesisi | 117 | E → D: Nearly complete loss of RNase activity, still binds RNA. Partially rescued by Mn(2+). 2 Publications | 1 | |
Mutagenesisi | 117 | E → K in rnc70; slower growth, loss of RNase activity. Dominant over wild-type. Binds ds-RNA. 2 Publications | 1 | |
Mutagenesisi | 117 | E → Q: Loss of RNase activity, still binds RNA. 2 Publications | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000180395 | 1 – 226 | Ribonuclease 3Add BLAST | 226 |
Proteomic databases
jPOSTi | P0A7Y0 |
PaxDbi | P0A7Y0 |
PRIDEi | P0A7Y0 |
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 PublicationBinary interactionsi
With | Entry | #Exp. | IntAct | Notes |
---|---|---|---|---|
P30850 | 2 | EBI-557336,EBI-557325 |
GO - Molecular functioni
- enzyme binding Source: EcoCyc
Protein-protein interaction databases
BioGridi | 4260597, 62 interactors 851372, 1 interactor |
DIPi | DIP-48223N |
IntActi | P0A7Y0, 6 interactors |
STRINGi | 511145.b2567 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 6 – 128 | RNase IIIAdd BLAST | 123 | |
Domaini | 155 – 225 | DRBMAdd BLAST | 71 |
Sequence similaritiesi
Belongs to the ribonuclease III family.Curated
Phylogenomic databases
eggNOGi | ENOG4108ZBM Bacteria COG0571 LUCA |
HOGENOMi | HOG000246809 |
InParanoidi | P0A7Y0 |
KOi | K03685 |
PhylomeDBi | P0A7Y0 |
Family and domain databases
CDDi | cd00048 DSRM, 1 hit cd00593 RIBOc, 1 hit |
Gene3Di | 1.10.1520.10, 1 hit |
HAMAPi | MF_00104 RNase_III, 1 hit |
InterProi | View protein in InterPro IPR014720 dsRBD_dom IPR011907 RNase_III IPR000999 RNase_III_dom IPR036389 RNase_III_sf |
Pfami | View protein in Pfam PF00035 dsrm, 1 hit PF14622 Ribonucleas_3_3, 1 hit |
SMARTi | View protein in SMART SM00358 DSRM, 1 hit SM00535 RIBOc, 1 hit |
SUPFAMi | SSF69065 SSF69065, 1 hit |
TIGRFAMsi | TIGR02191 RNaseIII, 1 hit |
PROSITEi | View protein in PROSITE PS50137 DS_RBD, 1 hit PS00517 RNASE_3_1, 1 hit PS50142 RNASE_3_2, 1 hit |
i Sequence
Sequence statusi: Complete.
P0A7Y0-1 [UniParc]FASTAAdd to basket
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
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 168 – 195 | HLPLP…HCQVS → PSAAADLSGSPGTWSKRTIR NLLSTARSV in CAA26504 (PubMed:3895158).CuratedAdd BLAST | 28 |
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 |
PIRi | F65034 NREC3 |
RefSeqi | NP_417062.1, NC_000913.3 WP_001068343.1, NZ_STEB01000011.1 |
Genome annotation databases
EnsemblBacteriai | AAC75620; AAC75620; b2567 BAE76743; BAE76743; BAE76743 |
GeneIDi | 947033 |
KEGGi | ecj:JW2551 eco:b2567 |
PATRICi | fig|1411691.4.peg.4167 |
Similar proteinsi
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 |
PIRi | F65034 NREC3 |
RefSeqi | NP_417062.1, NC_000913.3 WP_001068343.1, NZ_STEB01000011.1 |
3D structure databases
SMRi | P0A7Y0 |
ModBasei | Search... |
Protein-protein interaction databases
BioGridi | 4260597, 62 interactors 851372, 1 interactor |
DIPi | DIP-48223N |
IntActi | P0A7Y0, 6 interactors |
STRINGi | 511145.b2567 |
Proteomic databases
jPOSTi | P0A7Y0 |
PaxDbi | P0A7Y0 |
PRIDEi | P0A7Y0 |
Genome annotation databases
EnsemblBacteriai | AAC75620; AAC75620; b2567 BAE76743; BAE76743; BAE76743 |
GeneIDi | 947033 |
KEGGi | ecj:JW2551 eco:b2567 |
PATRICi | fig|1411691.4.peg.4167 |
Organism-specific databases
EchoBASEi | EB0850 |
Phylogenomic databases
eggNOGi | ENOG4108ZBM Bacteria COG0571 LUCA |
HOGENOMi | HOG000246809 |
InParanoidi | P0A7Y0 |
KOi | K03685 |
PhylomeDBi | P0A7Y0 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10857-MONOMER ECOL316407:JW2551-MONOMER MetaCyc:EG10857-MONOMER |
BRENDAi | 3.1.26.3 2026 |
Miscellaneous databases
PROi | PR:P0A7Y0 |
Family and domain databases
CDDi | cd00048 DSRM, 1 hit cd00593 RIBOc, 1 hit |
Gene3Di | 1.10.1520.10, 1 hit |
HAMAPi | MF_00104 RNase_III, 1 hit |
InterProi | View protein in InterPro IPR014720 dsRBD_dom IPR011907 RNase_III IPR000999 RNase_III_dom IPR036389 RNase_III_sf |
Pfami | View protein in Pfam PF00035 dsrm, 1 hit PF14622 Ribonucleas_3_3, 1 hit |
SMARTi | View protein in SMART SM00358 DSRM, 1 hit SM00535 RIBOc, 1 hit |
SUPFAMi | SSF69065 SSF69065, 1 hit |
TIGRFAMsi | TIGR02191 RNaseIII, 1 hit |
PROSITEi | View protein in PROSITE PS50137 DS_RBD, 1 hit PS00517 RNASE_3_1, 1 hit PS50142 RNASE_3_2, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | RNC_ECOLI | |
Accessioni | P0A7Y0Primary (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 13, 2019 | |
This is version 122 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Complete proteome, Direct protein sequencing, Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families - Escherichia coli
Escherichia coli (strain K12): entries and cross-references to EcoGene