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Protein

Ribonuclease E

Gene

rne

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

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.UniRule annotation9 Publications

Catalytic activityi

Endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions.UniRule annotation3 Publications

Cofactori

Protein has several cofactor binding sites:

Enzyme regulationi

Binding to the membrane stabilizes protein structure and increases affinity for the substrate.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi303Magnesium; catalytic1 Publication1
Metal bindingi346Magnesium; catalytic1 Publication1
Metal bindingi404Zinc; shared with dimeric partner2 Publications1
Metal bindingi407Zinc; shared with dimeric partner2 Publications1

GO - Molecular functioni

GO - Biological processi

  • mRNA catabolic process Source: UniProtKB-HAMAP
  • RNA catabolic process Source: EcoCyc
  • rRNA 5'-end processing Source: EcoCyc
  • tRNA processing Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

rRNA processing, tRNA processing

Keywords - Ligandi

Magnesium, Metal-binding, RNA-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10859-MONOMER.
ECOL316407:JW1071-MONOMER.
MetaCyc:EG10859-MONOMER.
BRENDAi3.1.26.12. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease EUniRule annotation (EC:3.1.26.12UniRule annotation)
Short name:
RNase EUniRule annotation
Gene namesi
Name:rneUniRule annotation
Synonyms:ams, hmp1
Ordered Locus Names:b1084, JW1071
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10859. rne.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: EcoCyc
  • cytoplasmic side of plasma membrane Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Cytoplasm, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi57F → A: Reduces RNA cleavage by over 98%. 1 Publication1
Mutagenesisi66G → S: Disrupts folding of the S1 motif. 1 Publication1
Mutagenesisi67F → A: Reduces RNA cleavage by over 98%. 1 Publication1
Mutagenesisi112K → A: Reduces RNA cleavage by 98%. 1 Publication1
Mutagenesisi170T → V: Abolishes enzyme activity toward RNA substrates with a 5' monophosphate (PubMed:16237448). Strongly reduces enzyme activity toward cspA mRNA (PubMed:19889093). 2 Publications1
Mutagenesisi303D → N: Reduces RNA cleavage by over 96%. 1 Publication1
Mutagenesisi305N → D or L: Reduces RNA cleavage by over 96%. 1 Publication1
Mutagenesisi346D → N: Reduces RNA cleavage by over 96%. 1 Publication1
Mutagenesisi373R → A or D: Reduces RNA cleavage by 89%. 1 Publication1
Mutagenesisi404C → A: Reduces zinc-binding. Abolishes homotetramerization and enzyme activity. 1 Publication1
Mutagenesisi407C → A: Reduces zinc-binding. Abolishes homotetramerization and enzyme activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000973731 – 1061Ribonuclease EAdd BLAST1061

Proteomic databases

EPDiP21513.
PaxDbiP21513.
PRIDEiP21513.

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 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
dnaKP0A6Y89EBI-549958,EBI-542092
enoP0A6P915EBI-549958,EBI-368855
pnpP0505511EBI-549958,EBI-548080
rhlBP0A8J816EBI-549958,EBI-555806

Protein-protein interaction databases

BioGridi4261023. 189 interactors.
DIPiDIP-10727N.
IntActiP21513. 61 interactors.
MINTiMINT-1220086.
STRINGi511145.b1084.

Structurei

Secondary structure

11061
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 7Combined sources6
Beta strandi10 – 12Combined sources3
Beta strandi14 – 20Combined sources7
Beta strandi23 – 30Combined sources8
Beta strandi32 – 34Combined sources3
Beta strandi36 – 39Combined sources4
Beta strandi42 – 50Combined sources9
Helixi51 – 53Combined sources3
Beta strandi55 – 64Combined sources10
Beta strandi66 – 69Combined sources4
Helixi70 – 72Combined sources3
Helixi75 – 77Combined sources3
Beta strandi84 – 86Combined sources3
Helixi90 – 92Combined sources3
Beta strandi99 – 106Combined sources8
Beta strandi110 – 112Combined sources3
Beta strandi115 – 118Combined sources4
Beta strandi125 – 130Combined sources6
Beta strandi134 – 136Combined sources3
Turni145 – 148Combined sources4
Helixi151 – 155Combined sources5
Beta strandi165 – 168Combined sources4
Helixi170 – 174Combined sources5
Helixi177 – 199Combined sources23
Beta strandi205 – 208Combined sources4
Beta strandi210 – 212Combined sources3
Helixi213 – 221Combined sources9
Beta strandi226 – 232Combined sources7
Helixi234 – 246Combined sources13
Helixi250 – 255Combined sources6
Beta strandi256 – 258Combined sources3
Helixi265 – 268Combined sources4
Helixi272 – 277Combined sources6
Beta strandi281 – 284Combined sources4
Beta strandi290 – 295Combined sources6
Beta strandi300 – 305Combined sources6
Helixi315 – 336Combined sources22
Beta strandi341 – 346Combined sources6
Helixi353 – 366Combined sources14
Turni367 – 369Combined sources3
Beta strandi374 – 379Combined sources6
Beta strandi383 – 389Combined sources7
Helixi396 – 400Combined sources5
Beta strandi405 – 411Combined sources7
Helixi416 – 432Combined sources17
Beta strandi436 – 443Combined sources8
Helixi445 – 451Combined sources7
Turni452 – 455Combined sources4
Helixi456 – 465Combined sources10
Turni466 – 468Combined sources3
Beta strandi470 – 475Combined sources6
Beta strandi485 – 490Combined sources6
Turni491 – 493Combined sources3
Helixi499 – 501Combined sources3
Helixi502 – 506Combined sources5
Turni507 – 509Combined sources3
Helixi831 – 833Combined sources3
Helixi835 – 838Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SLJNMR-A35-125[»]
1SMXX-ray1.80A/B35-125[»]
1SN8X-ray2.00A/B35-125[»]
2BX2X-ray2.85L1-510[»]
2C0BX-ray3.18L1-510[»]
2C4RX-ray3.60L1-510[»]
2FYMX-ray1.60B/E833-850[»]
2VMKX-ray3.30A/B/C/D1-515[»]
2VRTX-ray3.50A/B/C/D1-509[»]
3GCMX-ray2.50D/E/F1021-1061[»]
3GMEX-ray2.40D1021-1061[»]
3H1CX-ray3.57D/E/F/H/J/L/N/P/S/U/W/Y1021-1061[»]
3H8AX-ray1.90E/F823-850[»]
DisProtiDP00207.
ProteinModelPortaliP21513.
SMRiP21513.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP21513.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini39 – 119S1 motifUniRule annotationAdd BLAST81

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni57 – 112Interaction with RNAAdd BLAST56
Regioni169 – 170Interaction with RNA 5'-terminal monophosphate2
Regioni404 – 407Required for zinc-mediated homotetramerization and catalytic activity4
Regioni833 – 850Interaction with enolaseAdd BLAST18
Regioni1021 – 1061Interaction with PNPaseAdd BLAST41

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

Belongs to the RNase E/G family. RNase E subfamily.UniRule annotation
Contains 1 S1 motif domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107QQB. Bacteria.
COG1530. LUCA.
HOGENOMiHOG000258027.
InParanoidiP21513.
KOiK08300.
OMAiEYFPSNY.

Family and domain databases

HAMAPiMF_00970. RNase_E. 1 hit.
InterProiIPR012340. 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.
[Graphical view]
PfamiPF12111. PNPase_C. 1 hit.
PF10150. RNase_E_G. 1 hit.
PF00575. S1. 1 hit.
[Graphical view]
SMARTiSM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00757. RNaseEG. 1 hit.
PROSITEiPS50126. S1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P21513-1 [UniParc]FASTAAdd to basket

« Hide

        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
Length:1,061
Mass (Da):118,197
Last modified:August 29, 2003 - v6
Checksum:iD4066D80E1DE7D37
GO

Sequence cautioni

The sequence AAA23443 differs from that shown. Reason: Frameshift at position 796.Curated
The sequence CAA38206 differs from that shown. Reason: Frameshift at several positions.Curated
The sequence CAA47818 differs from that shown. Reason: Frameshift at position 1003.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti390Q → H in AAA23443 (PubMed:1704367).Curated1
Sequence conflicti487L → V in CAA47818 (PubMed:1447789).Curated1
Sequence conflicti487L → V in AAA23443 (PubMed:1704367).Curated1
Sequence conflicti564A → R in CAA47818 (PubMed:1447789).Curated1
Sequence conflicti784N → K in CAA47818 (PubMed:1447789).Curated1
Sequence conflicti838A → R in AAA23443 (PubMed:1704367).Curated1
Sequence conflicti905P → R in CAA47818 (PubMed:1447789).Curated1
Sequence conflicti1048H → R in AAA03347 (PubMed:8415644).Curated1

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.
PIRiA64852. S27311.
RefSeqiNP_415602.1. NC_000913.3.
WP_000827360.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74168; AAC74168; b1084.
BAA35893; BAA35893; BAA35893.
GeneIDi945641.
KEGGiecj:JW1071.
eco:b1084.
PATRICi32117409. VBIEscCol129921_1127.

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.
PIRiA64852. S27311.
RefSeqiNP_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 entryMethodResolution (Å)ChainPositionsPDBsum
1SLJNMR-A35-125[»]
1SMXX-ray1.80A/B35-125[»]
1SN8X-ray2.00A/B35-125[»]
2BX2X-ray2.85L1-510[»]
2C0BX-ray3.18L1-510[»]
2C4RX-ray3.60L1-510[»]
2FYMX-ray1.60B/E833-850[»]
2VMKX-ray3.30A/B/C/D1-515[»]
2VRTX-ray3.50A/B/C/D1-509[»]
3GCMX-ray2.50D/E/F1021-1061[»]
3GMEX-ray2.40D1021-1061[»]
3H1CX-ray3.57D/E/F/H/J/L/N/P/S/U/W/Y1021-1061[»]
3H8AX-ray1.90E/F823-850[»]
DisProtiDP00207.
ProteinModelPortaliP21513.
SMRiP21513.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261023. 189 interactors.
DIPiDIP-10727N.
IntActiP21513. 61 interactors.
MINTiMINT-1220086.
STRINGi511145.b1084.

Proteomic databases

EPDiP21513.
PaxDbiP21513.
PRIDEiP21513.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74168; AAC74168; b1084.
BAA35893; BAA35893; BAA35893.
GeneIDi945641.
KEGGiecj:JW1071.
eco:b1084.
PATRICi32117409. VBIEscCol129921_1127.

Organism-specific databases

EchoBASEiEB0852.
EcoGeneiEG10859. rne.

Phylogenomic databases

eggNOGiENOG4107QQB. Bacteria.
COG1530. LUCA.
HOGENOMiHOG000258027.
InParanoidiP21513.
KOiK08300.
OMAiEYFPSNY.

Enzyme and pathway databases

BioCyciEcoCyc:EG10859-MONOMER.
ECOL316407:JW1071-MONOMER.
MetaCyc:EG10859-MONOMER.
BRENDAi3.1.26.12. 2026.

Miscellaneous databases

EvolutionaryTraceiP21513.
PROiP21513.

Family and domain databases

HAMAPiMF_00970. RNase_E. 1 hit.
InterProiIPR012340. 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.
[Graphical view]
PfamiPF12111. PNPase_C. 1 hit.
PF10150. RNase_E_G. 1 hit.
PF00575. S1. 1 hit.
[Graphical view]
SMARTiSM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00757. RNaseEG. 1 hit.
PROSITEiPS50126. S1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRNE_ECOLI
AccessioniPrimary (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: November 30, 2016
This is version 165 of the entry and version 6 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.