UniProtKB - P21513 (RNE_ECOLI)
Protein
Ribonuclease E
Gene
rne
Organism
Escherichia coli (strain K12)
Status
Functioni
Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs. Can also process other RNA species, such as RNAI, a molecule that controls the replication of ColE1 plasmid, and the cell division inhibitor DicF-RNA. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process. Required to initiate rRNA degradation during both starvation and quality control; acts after RNase PH (rph) exonucleolytically digests the 3'-end of the 16S rRNA (PubMed:27298395). Degradation of 16S rRNA leads to 23S rRNA degradation (PubMed:27298395). Processes the 3 tRNA(Pro) precursors immediately after the 3'-CCA to generate the mature ends (PubMed:27288443).UniRule annotation12 Publications
Prefers 5'-monophosphorylated substrates over 5'-triphosphorylated substrates (PubMed:10762247). 5'-monophosphate-assisted cleavage requires at least 2 and preferably 3 or more unpaired 5'-terminal nucleotides. The optimal spacing between the 5' end and the scissile phosphate appears to be 8 nucleotides. Any sequence of unpaired nucleotides at the 5'-end is tolerated (PubMed:26694614).2 Publications
Miscellaneous
In K12 strains that are derived from W1485 (including MG1655 and W3110) the rph gene has a frameshift that leads to loss of its ribonuclease PH activity. In strain K12 / MG1655(Seq)* the wild-type Rph protein has been restored (PubMed:27298395).1 Publication
Catalytic activityi
- Endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions.UniRule annotation3 Publications EC:3.1.26.12
Cofactori
Protein has several cofactor binding sites:- Zn2+3 PublicationsNote: Binds 2 Zn2+ ions per homotetramer. Zinc ions are bound between subunits and are essential for homotetramerization and catalytic activity, but not for RNA binding. In the absence of zinc, the protein dissociates into inactive dimers.1 Publication
- Mg2+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication
Activity regulationi
The presence of a 5'-monophosphate on substrate RNA accelerates its cleavage by catalytically activating the enzyme (PubMed:15197283). Binding to the membrane stabilizes protein structure and increases affinity for the substrate.2 Publications
Kineticsi
kcat is 0.83 min(-1) for 5'-PO4 substrate and 0.088 min(-1) for 5-OH substrate.1 Publication
- KM=0.60 µM for 5'-phosphorylated fluorogenic substrate1 Publication
- KM=0.57 µM for 5'-OH fluorogenic substrate1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 303 | Magnesium; catalytic1 Publication | 1 | |
Metal bindingi | 346 | Magnesium; catalytic1 Publication | 1 | |
Metal bindingi | 404 | Zinc; shared with dimeric partner2 Publications | 1 | |
Metal bindingi | 407 | Zinc; shared with dimeric partner2 Publications | 1 |
GO - Molecular functioni
- 7S RNA binding Source: CAFA
- DEAD/H-box RNA helicase binding Source: CAFA
- endoribonuclease activity Source: UniProtKB-UniRule
- identical protein binding Source: IntAct
- magnesium ion binding Source: EcoCyc
- ribonuclease activity Source: GO_Central
- ribonuclease E activity Source: EcoCyc
- RNA binding Source: CAFA
- rRNA binding Source: UniProtKB-KW
- tRNA binding Source: UniProtKB-KW
- zinc ion binding Source: UniProtKB-UniRule
GO - Biological processi
- mRNA catabolic process Source: EcoCyc
- protein homotetramerization Source: EcoCyc
- regulation of RNA helicase activity Source: CAFA
- RNA catabolic process Source: EcoCyc
- rRNA 5'-end processing Source: EcoCyc
- rRNA processing Source: GO_Central
- tRNA processing Source: EcoCyc
Keywordsi
Molecular function | Endonuclease, Hydrolase, Nuclease, RNA-binding, rRNA-binding, tRNA-binding |
Biological process | rRNA processing, tRNA processing |
Ligand | Magnesium, Metal-binding, Zinc |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10859-MONOMER MetaCyc:EG10859-MONOMER |
BRENDAi | 3.1.26.12, 2026 |
Names & Taxonomyi
Protein namesi | Recommended name: Ribonuclease EUniRule annotation (EC:3.1.26.12UniRule annotation)Short name: RNase EUniRule annotation |
Gene namesi | Name:rne1 PublicationUniRule annotation Synonyms:ams1 Publication, hmp1 Ordered Locus Names:b1084, JW1071 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Subcellular locationi
Cytoplasm and Cytosol
- Cytoplasm 1 Publication
Plasma membrane
- Cell inner membrane 2 Publications; Peripheral membrane protein 2 Publications; Cytoplasmic side 2 Publications
Note: Associated with the cytoplasmic membrane via the N- and C-terminal regions.2 Publications
Cytosol
- bacterial degradosome Source: EcoCyc
Plasma Membrane
- cytoplasmic side of plasma membrane Source: UniProtKB-UniRule
Other locations
- cytoplasm Source: GO_Central
Keywords - Cellular componenti
Cell inner membrane, Cell membrane, Cytoplasm, MembranePathology & Biotechi
Disruption phenotypei
Essential, it cannot be deleted. In a temperature sensitive mutant at non-permissive temperature, slow processing of the 17S rRNA precursor to 16S rRNA; a double rne-rng mutated strain no longer processes the 17S rRNA precursor.1 Publication
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 57 | F → A: Reduces RNA cleavage by over 98%. 1 Publication | 1 | |
Mutagenesisi | 66 | G → S: Disrupts folding of the S1 motif. 1 Publication | 1 | |
Mutagenesisi | 67 | F → A: Reduces RNA cleavage by over 98%. 1 Publication | 1 | |
Mutagenesisi | 112 | K → A: Reduces RNA cleavage by 98%. 1 Publication | 1 | |
Mutagenesisi | 170 | T → V: Abolishes enzyme activity toward RNA substrates with a 5' monophosphate (PubMed:16237448). Strongly reduces enzyme activity toward cspA mRNA (PubMed:19889093). 2 Publications | 1 | |
Mutagenesisi | 303 | D → N: Reduces RNA cleavage by over 96%. 1 Publication | 1 | |
Mutagenesisi | 305 | N → D or L: Reduces RNA cleavage by over 96%. 1 Publication | 1 | |
Mutagenesisi | 346 | D → N: Reduces RNA cleavage by over 96%. 1 Publication | 1 | |
Mutagenesisi | 373 | R → A or D: Reduces RNA cleavage by 89%. 1 Publication | 1 | |
Mutagenesisi | 404 | C → A: Reduces zinc-binding. Abolishes homotetramerization and enzyme activity. 1 Publication | 1 | |
Mutagenesisi | 407 | C → A: Reduces zinc-binding. Abolishes homotetramerization and enzyme activity. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000097373 | 1 – 1061 | Ribonuclease EAdd BLAST | 1061 |
Proteomic databases
jPOSTi | P21513 |
PaxDbi | P21513 |
PRIDEi | P21513 |
Interactioni
Subunit structurei
Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Within the RNA degradosome, RNase E assembles into a homotetramer formed by a dimer of dimers. Tetramerization is essential for catalytic activity, but not for RNA-binding.
Interacts with RhlB, PNPase (pnp) and enolase (eno).
Interacts with DeaD at reduced temperature.
UniRule annotation11 PublicationsBinary interactionsi
Hide detailsP21513
GO - Molecular functioni
- DEAD/H-box RNA helicase binding Source: CAFA
- identical protein binding Source: IntAct
Protein-protein interaction databases
BioGRIDi | 4261023, 251 interactors 850013, 1 interactor |
ComplexPortali | CPX-403, RNA degradosome |
DIPi | DIP-10727N |
IntActi | P21513, 63 interactors |
MINTi | P21513 |
STRINGi | 511145.b1084 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
BMRBi | P21513 |
SASBDBi | P21513 |
SMRi | P21513 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P21513 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 39 – 119 | S1 motifUniRule annotationAdd BLAST | 81 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 57 – 112 | Interaction with RNAAdd BLAST | 56 | |
Regioni | 169 – 170 | Interaction with RNA 5'-terminal monophosphate | 2 | |
Regioni | 404 – 407 | Required for zinc-mediated homotetramerization and catalytic activity | 4 | |
Regioni | 833 – 850 | Interaction with enolaseAdd BLAST | 18 | |
Regioni | 1021 – 1061 | Interaction with PNPaseAdd BLAST | 41 |
Domaini
The N-terminal S1 motif binds RNA, and can also bind single-stranded DNA (in vitro). The C-terminal region interacts with the other degradosomal components.2 Publications
Sequence similaritiesi
Phylogenomic databases
eggNOGi | COG1530, Bacteria |
HOGENOMi | CLU_003468_1_2_6 |
InParanoidi | P21513 |
Family and domain databases
DisProti | DP00207 |
HAMAPi | MF_00970, RNase_E, 1 hit |
InterProi | View protein in InterPro IPR012340, NA-bd_OB-fold IPR021968, PNPase_C IPR019307, RNA-bd_AU-1/RNase_E/G IPR028878, RNase_E IPR004659, RNase_E/G IPR022967, S1_dom IPR003029, S1_domain |
Pfami | View protein in Pfam PF12111, PNPase_C, 1 hit PF10150, RNase_E_G, 1 hit PF00575, S1, 1 hit |
SMARTi | View protein in SMART SM00316, S1, 1 hit |
SUPFAMi | SSF50249, SSF50249, 1 hit |
TIGRFAMsi | TIGR00757, RNaseEG, 1 hit |
PROSITEi | View protein in PROSITE PS50126, S1, 1 hit |
i Sequence
Sequence statusi: Complete.
P21513-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MKRMLINATQ QEELRVALVD GQRLYDLDIE SPGHEQKKAN IYKGKITRIE
60 70 80 90 100
PSLEAAFVDY GAERHGFLPL KEIAREYFPA NYSAHGRPNI KDVLREGQEV
110 120 130 140 150
IVQIDKEERG NKGAALTTFI SLAGSYLVLM PNNPRAGGIS RRIEGDDRTE
160 170 180 190 200
LKEALASLEL PEGMGLIVRT AGVGKSAEAL QWDLSFRLKH WEAIKKAAES
210 220 230 240 250
RPAPFLIHQE SNVIVRAFRD YLRQDIGEIL IDNPKVLELA RQHIAALGRP
260 270 280 290 300
DFSSKIKLYT GEIPLFSHYQ IESQIESAFQ REVRLPSGGS IVIDSTEALT
310 320 330 340 350
AIDINSARAT RGGDIEETAF NTNLEAADEI ARQLRLRDLG GLIVIDFIDM
360 370 380 390 400
TPVRHQRAVE NRLREAVRQD RARIQISHIS RFGLLEMSRQ RLSPSLGESS
410 420 430 440 450
HHVCPRCSGT GTVRDNESLS LSILRLIEEE ALKENTQEVH AIVPVPIASY
460 470 480 490 500
LLNEKRSAVN AIETRQDGVR CVIVPNDQME TPHYHVLRVR KGEETPTLSY
510 520 530 540 550
MLPKLHEEAM ALPSEEEFAE RKRPEQPALA TFAMPDVPPA PTPAEPAAPV
560 570 580 590 600
VAPAPKAAPA TPAAPAQPGL LSRFFGALKA LFSGGEETKP TEQPAPKAEA
610 620 630 640 650
KPERQQDRRK PRQNNRRDRN ERRDTRSERT EGSDNREENR RNRRQAQQQT
660 670 680 690 700
AETRESRQQA EVTEKARTAD EQQAPRRERS RRRNDDKRQA QQEAKALNVE
710 720 730 740 750
EQSVQETEQE ERVRPVQPRR KQRQLNQKVR YEQSVAEEAV VAPVVEETVA
760 770 780 790 800
AEPIVQEAPA PRTELVKVPL PVVAQTAPEQ QEENNADNRD NGGMPRRSRR
810 820 830 840 850
SPRHLRVSGQ RRRRYRDERY PTQSPMPLTV ACASPELASG KVWIRYPIVR
860 870 880 890 900
PQDVQVEEQR EQEEVHVQPM VTEVPVAAAI EPVVSAPVVE EVAGVVEAPV
910 920 930 940 950
QVAEPQPEVV ETTHPEVIAA AVTEQPQVIT ESDVAVAQEV AEQAEPVVEP
960 970 980 990 1000
QEETADIEEV VETAEVVVAE PEVVAQPAAP VVAEVAAEVE TVAAVEPEVT
1010 1020 1030 1040 1050
VEHNHATAPM TRAPAPEYVP EAPRHSDWQR PTFAFEGKGA AGGHTATHHA
1060
SAAPARPQPV E
Sequence cautioni
The sequence AAA23443 differs from that shown. Reason: Frameshift.Curated
The sequence CAA38206 differs from that shown. Reason: Frameshift.Curated
The sequence CAA47818 differs from that shown. Reason: Frameshift.Curated
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 390 | Q → H in AAA23443 (PubMed:1704367).Curated | 1 | |
Sequence conflicti | 487 | L → V in CAA47818 (PubMed:1447789).Curated | 1 | |
Sequence conflicti | 487 | L → V in AAA23443 (PubMed:1704367).Curated | 1 | |
Sequence conflicti | 564 | A → R in CAA47818 (PubMed:1447789).Curated | 1 | |
Sequence conflicti | 784 | N → K in CAA47818 (PubMed:1447789).Curated | 1 | |
Sequence conflicti | 838 | A → R in AAA23443 (PubMed:1704367).Curated | 1 | |
Sequence conflicti | 905 | P → R in CAA47818 (PubMed:1447789).Curated | 1 | |
Sequence conflicti | 1048 | H → R in AAA03347 (PubMed:8415644).Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U00096 Genomic DNA Translation: AAC74168.1 AP009048 Genomic DNA Translation: BAA35893.1 X67470 Genomic DNA Translation: CAA47818.1 Frameshift. M62747 Genomic DNA Translation: AAA23443.1 Frameshift. X54309 Genomic DNA Translation: CAA38206.1 Frameshift. L23942 Genomic DNA Translation: AAA03347.1 |
PIRi | A64852, S27311 |
RefSeqi | NP_415602.1, NC_000913.3 WP_000827360.1, NZ_LN832404.1 |
Genome annotation databases
EnsemblBacteriai | AAC74168; AAC74168; b1084 BAA35893; BAA35893; BAA35893 |
GeneIDi | 57731871 945641 |
KEGGi | ecj:JW1071 eco:b1084 |
PATRICi | fig|1411691.4.peg.1184 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U00096 Genomic DNA Translation: AAC74168.1 AP009048 Genomic DNA Translation: BAA35893.1 X67470 Genomic DNA Translation: CAA47818.1 Frameshift. M62747 Genomic DNA Translation: AAA23443.1 Frameshift. X54309 Genomic DNA Translation: CAA38206.1 Frameshift. L23942 Genomic DNA Translation: AAA03347.1 |
PIRi | A64852, S27311 |
RefSeqi | NP_415602.1, NC_000913.3 WP_000827360.1, NZ_LN832404.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1SLJ | NMR | - | A | 35-125 | [»] | |
1SMX | X-ray | 1.80 | A/B | 35-125 | [»] | |
1SN8 | X-ray | 2.00 | A/B | 35-125 | [»] | |
2BX2 | X-ray | 2.85 | L | 1-510 | [»] | |
2C0B | X-ray | 3.18 | L | 1-510 | [»] | |
2C4R | X-ray | 3.60 | L | 1-510 | [»] | |
2FYM | X-ray | 1.60 | B/E | 833-850 | [»] | |
2VMK | X-ray | 3.30 | A/B/C/D | 1-515 | [»] | |
2VRT | X-ray | 3.50 | A/B/C/D | 1-509 | [»] | |
3GCM | X-ray | 2.50 | D/E/F | 1021-1061 | [»] | |
3GME | X-ray | 2.40 | D | 1021-1061 | [»] | |
3H1C | X-ray | 3.57 | D/E/F/H/J/L/N/P/S/U/W/Y | 1021-1061 | [»] | |
3H8A | X-ray | 1.90 | E/F | 823-850 | [»] | |
5F6C | X-ray | 3.00 | A | 1-510 | [»] | |
B | 1-511 | [»] | ||||
6G63 | X-ray | 3.95 | A/G/L/N | 1-510 | [»] | |
BMRBi | P21513 | |||||
SASBDBi | P21513 | |||||
SMRi | P21513 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4261023, 251 interactors 850013, 1 interactor |
ComplexPortali | CPX-403, RNA degradosome |
DIPi | DIP-10727N |
IntActi | P21513, 63 interactors |
MINTi | P21513 |
STRINGi | 511145.b1084 |
Proteomic databases
jPOSTi | P21513 |
PaxDbi | P21513 |
PRIDEi | P21513 |
Genome annotation databases
EnsemblBacteriai | AAC74168; AAC74168; b1084 BAA35893; BAA35893; BAA35893 |
GeneIDi | 57731871 945641 |
KEGGi | ecj:JW1071 eco:b1084 |
PATRICi | fig|1411691.4.peg.1184 |
Organism-specific databases
EchoBASEi | EB0852 |
Phylogenomic databases
eggNOGi | COG1530, Bacteria |
HOGENOMi | CLU_003468_1_2_6 |
InParanoidi | P21513 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10859-MONOMER MetaCyc:EG10859-MONOMER |
BRENDAi | 3.1.26.12, 2026 |
Miscellaneous databases
EvolutionaryTracei | P21513 |
PROi | PR:P21513 |
Family and domain databases
DisProti | DP00207 |
HAMAPi | MF_00970, RNase_E, 1 hit |
InterProi | View protein in InterPro IPR012340, NA-bd_OB-fold IPR021968, PNPase_C IPR019307, RNA-bd_AU-1/RNase_E/G IPR028878, RNase_E IPR004659, RNase_E/G IPR022967, S1_dom IPR003029, S1_domain |
Pfami | View protein in Pfam PF12111, PNPase_C, 1 hit PF10150, RNase_E_G, 1 hit PF00575, S1, 1 hit |
SMARTi | View protein in SMART SM00316, S1, 1 hit |
SUPFAMi | SSF50249, SSF50249, 1 hit |
TIGRFAMsi | TIGR00757, RNaseEG, 1 hit |
PROSITEi | View protein in PROSITE PS50126, S1, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | RNE_ECOLI | |
Accessioni | P21513Primary (citable) accession number: P21513 Secondary accession number(s): P77591 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | May 1, 1991 |
Last sequence update: | August 29, 2003 | |
Last modified: | April 7, 2021 | |
This is version 202 of the entry and version 6 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families