rnc

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

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	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
Inferred from biological aspect of ancestorⁱ
- 21873635
enzyme binding
Source: EcoCyc
Inferred from physical interactionⁱ
- 19141481
magnesium ion binding
Source: EcoCyc
Inferred from direct assayⁱ
- 15699182
ribonuclease III activity
Source: EcoCyc
Inferred from direct assayⁱ
- 1091644
rRNA binding Source: UniProtKB-KW

View the complete GO annotation on QuickGO ...

GO - Biological processⁱ

mRNA processing
Source: EcoCyc
Inferred from mutant phenotypeⁱ
- 3308454
RNA processing
Source: EcoCyc
Inferred from mutant phenotypeⁱ
- 4587248
rRNA catabolic process Source: InterPro
rRNA processing
Source: EcoCyc
Inferred from mutant phenotypeⁱ
- 6364133
tRNA processing Source: UniProtKB-KW

View the complete GO annotation on QuickGO ...

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 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	cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › Escherichia coli
Proteomesⁱ	UP000000318 Componentⁱ: Chromosome UP000000625 Componentⁱ: Chromosome

Organism-specific databases

EcoGeneⁱ	EG10857 rnc

EcoGeneⁱ

EG10857 rnc

Subcellular locationⁱ

Cytoplasm
1 Publication
Manual assertion based on experiment inⁱ
- Ref.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.

Note:

Loosely associated with ribosomes.

GO - Cellular componentⁱ

cytosol
Source: EcoCyc
Inferred from direct assayⁱ

View the complete GO annotation on QuickGO ...

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 key	Position(s)	DescriptionActions	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

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 Publication

Binary interactionsⁱ

With	Entry	#Exp.	IntAct	Notes
rnb	P30850	2	EBI-557336,EBI-557325

With

Entry

#Exp.

IntAct

Notes

rnb

P30850

2

EBI-557336,EBI-557325

GO - Molecular functionⁱ

enzyme binding
Source: EcoCyc
Inferred from physical interactionⁱ
- 19141481

View the complete GO annotation on QuickGO ...

Protein-protein interaction databases

BioGridⁱ	4260597, 62 interactors
Database of interacting proteins More...DIPⁱ	DIP-48223N
IntActⁱ	P0A7Y0, 6 interactors
STRINGⁱ	316385.ECDH10B_2735

Structureⁱ

3D structure databases

ProteinModelPortalⁱ	P0A7Y0
SMRⁱ	P0A7Y0
ModBaseⁱ	Search...
MobiDBⁱ	Search...

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
KEGG Orthology (KO) More...KOⁱ	K03685
PhylomeDBⁱ	P0A7Y0

Family and domain databases

Conserved Domains Database More...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
Pfam protein domain database More...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

Sequenceⁱ

Sequence statusⁱ: Complete.

P0A7Y0-1 [UniParc]FASTA Add 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 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
NCBI Reference Sequences More...RefSeqⁱ	NP_417062.1, NC_000913.3 WP_001068343.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaⁱ	AAC75620; AAC75620; b2567 BAE76743; BAE76743; BAE76743
GeneIDⁱ	947033
KEGGⁱ	ecj:JW2551 eco:b2567
PATRICⁱ	fig\|1411691.4.peg.4167

Protein	Similar proteins		Species	Score	Length	Source
P0A7Y0	Ribonuclease 3		ECO24		226	UniRef100_A7ZQ11
Ribonuclease 3		ECO27		226
Ribonuclease 3		ECO45		226
Ribonuclease 3		ECO55		226
Ribonuclease 3		ECO57		226
+177

Protein	Similar proteins		Species	Score	Length	Source
P0A7Y0	Ribonuclease 3		PANAM		226	UniRef90_D4GKM1
Ribonuclease 3		SALEP		226
Ribonuclease 3		SALG2		226
Ribonuclease 3		SALPA		226
Ribonuclease 3		SALPK		226
+928

Protein	Similar proteins		Species	Score	Length	Source
P0A7Y0	Ribonuclease 3		XYLFA		227	UniRef50_Q9PB98
Ribonuclease 3		XYLFM		227
Ribonuclease 3		XYLF2		227
Ribonuclease 3		XYLFT		227
Ribonuclease 3		BLOPB		229
+1460

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_LN832404.1

3D structure databases

ProteinModelPortalⁱ	P0A7Y0
SMRⁱ	P0A7Y0
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Protein-protein interaction databases

BioGridⁱ	4260597, 62 interactors
DIPⁱ	DIP-48223N
IntActⁱ	P0A7Y0, 6 interactors
STRINGⁱ	316385.ECDH10B_2735

Proteomic databases

PaxDbⁱ	P0A7Y0
PRIDEⁱ	P0A7Y0

Protocols and materials databases

Structural Biology Knowledgebase	Search...

Structural Biology Knowledgebase

Search...

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
EcoGeneⁱ	EG10857 rnc

Phylogenomic databases

eggNOGⁱ	ENOG4108ZBM Bacteria COG0571 LUCA
HOGENOMⁱ	HOG000246809
InParanoidⁱ	P0A7Y0
KOⁱ	K03685
PhylomeDBⁱ	P0A7Y0

Enzyme and pathway databases

BioCycⁱ	EcoCyc:EG10857-MONOMER MetaCyc:EG10857-MONOMER
BRENDAⁱ	3.1.26.3 2026

Miscellaneous databases

Protein Ontology More...PROⁱ	PR:P0A7Y0

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...

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 7, 2018
	This is version 112 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 proteome

Documents

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

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UniProtKB - P0A7Y0 (RNC_ECOLI)

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Ribonuclease 3

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<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Caution

Sites

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GO - Biological processi

Enzyme and pathway databases

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

Organism-specific databases

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Proteomic databases

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

GO - Molecular functioni

Protein-protein interaction databases

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

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Experimental Info

Sequence databases

Genome annotation databases

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Proteomic databases

Protocols and materials databases

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Enzyme and pathway databases

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Functionⁱ

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

GO - Cellular componentⁱ

Keywords - Cellular componentⁱ

Pathology & Biotechⁱ

PTM / Processingⁱ

Expressionⁱ

Interactionⁱ

GO - Molecular functionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ

Keywords - Technical termⁱ