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Protein

ATP-dependent RNA helicase RhlE

Gene

rhlE

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

Functioni

DEAD-box RNA helicase involved in ribosome assembly. Has RNA-dependent ATPase activity and unwinds double-stranded RNA. May play a role in the interconversion of ribosomal RNA-folding intermediates that are further processed by DeaD or SrmB during ribosome maturation.UniRule annotation2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.UniRule annotation1 Publication

Enzyme regulationi

ATPase activity is stimulated by both long RNAs and short oligoribonucleotides.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi45 – 528ATPUniRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • ATP-dependent RNA helicase activity Source: EcoCyc
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

  • response to heat Source: EcoCyc
  • ribosome assembly Source: EcoCyc
  • RNA secondary structure unwinding Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Ribosome biogenesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11235-MONOMER.
ECOL316407:JW0781-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase RhlEUniRule annotation (EC:3.6.4.13UniRule annotation)
Gene namesi
Name:rhlEUniRule annotation
Ordered Locus Names:b0797, JW0781
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11235. rhlE.

Subcellular locationi

  • Cytoplasm UniRule annotation1 Publication

  • Note: Ribosome-associated. Can either bind to the intact 70S ribosome or to individual ribosomal subunits.

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 454454ATP-dependent RNA helicase RhlEPRO_0000055108Add
BLAST

Proteomic databases

PaxDbiP25888.
PRIDEiP25888.

Expressioni

Inductioni

Transiently induced by cold shock in a PNPase-dependent fashion.1 Publication

Interactioni

Subunit structurei

Interacts with PcnB. Interacts in vitro with RNase E.2 Publications

Protein-protein interaction databases

BioGridi4259962. 77 interactions.
DIPiDIP-10697N.
IntActiP25888. 35 interactions.
MINTiMINT-1313387.
STRINGi511145.b0797.

Structurei

3D structure databases

ProteinModelPortaliP25888.
SMRiP25888. Positions 1-371.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini32 – 208177Helicase ATP-bindingUniRule annotationAdd
BLAST
Domaini219 – 381163Helicase C-terminalUniRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi1 – 2929Q motifAdd
BLAST
Motifi156 – 1594DEAD box

Sequence similaritiesi

Belongs to the DEAD box helicase family. RhlE subfamily.UniRule annotation
Contains 1 helicase ATP-binding domain.UniRule annotation
Contains 1 helicase C-terminal domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C1J. Bacteria.
COG0513. LUCA.
HOGENOMiHOG000268807.
InParanoidiP25888.
KOiK11927.
OMAiCAPDETR.
OrthoDBiEOG6GBMBM.
PhylomeDBiP25888.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00968. DEAD_helicase_RhlE.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR028622. DEAD_helicase_RhlE.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P25888-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSFDSLGLSP DILRAVAEQG YREPTPIQQQ AIPAVLEGRD LMASAQTGTG
60 70 80 90 100
KTAGFTLPLL QHLITRQPHA KGRRPVRALI LTPTRELAAQ IGENVRDYSK
110 120 130 140 150
YLNIRSLVVF GGVSINPQMM KLRGGVDVLV ATPGRLLDLE HQNAVKLDQV
160 170 180 190 200
EILVLDEADR MLDMGFIHDI RRVLTKLPAK RQNLLFSATF SDDIKALAEK
210 220 230 240 250
LLHNPLEIEV ARRNTASDQV TQHVHFVDKK RKRELLSHMI GKGNWQQVLV
260 270 280 290 300
FTRTKHGANH LAEQLNKDGI RSAAIHGNKS QGARTRALAD FKSGDIRVLV
310 320 330 340 350
ATDIAARGLD IEELPHVVNY ELPNVPEDYV HRIGRTGRAA ATGEALSLVC
360 370 380 390 400
VDEHKLLRDI EKLLKKEIPR IAIPGYEPDP SIKAEPIQNG RQQRGGGGRG
410 420 430 440 450
QGGGRGQQQP RRGEGGAKSA SAKPAEKPSR RLGDAKPAGE QQRRRRPRKP

AAAQ
Length:454
Mass (Da):49,989
Last modified:June 1, 1994 - v3
Checksum:i7576B35B7901671F
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti55 – 551F → G in X56307 (PubMed:1931833).Curated
Sequence conflicti107 – 1071L → R in X56307 (PubMed:1931833).Curated
Sequence conflicti210 – 2101V → A in X56307 (PubMed:1931833).Curated
Sequence conflicti230 – 2301K → E in X56307 (PubMed:1931833).Curated
Sequence conflicti239 – 2391M → L in X56307 (PubMed:1931833).Curated
Sequence conflicti258 – 2581A → G in X56307 (PubMed:1931833).Curated
Sequence conflicti286 – 2872RA → LS in X56307 (PubMed:1931833).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L02123 Genomic DNA. Translation: AAA53653.1.
U00096 Genomic DNA. Translation: AAC73884.1.
AP009048 Genomic DNA. Translation: BAA35457.1.
X56307 Genomic DNA. No translation available.
PIRiE64816.
RefSeqiNP_415318.1. NC_000913.3.
WP_000007101.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73884; AAC73884; b0797.
BAA35457; BAA35457; BAA35457.
GeneIDi945425.
KEGGiecj:JW0781.
eco:b0797.
PATRICi32116795. VBIEscCol129921_0823.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L02123 Genomic DNA. Translation: AAA53653.1.
U00096 Genomic DNA. Translation: AAC73884.1.
AP009048 Genomic DNA. Translation: BAA35457.1.
X56307 Genomic DNA. No translation available.
PIRiE64816.
RefSeqiNP_415318.1. NC_000913.3.
WP_000007101.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP25888.
SMRiP25888. Positions 1-371.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259962. 77 interactions.
DIPiDIP-10697N.
IntActiP25888. 35 interactions.
MINTiMINT-1313387.
STRINGi511145.b0797.

Proteomic databases

PaxDbiP25888.
PRIDEiP25888.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73884; AAC73884; b0797.
BAA35457; BAA35457; BAA35457.
GeneIDi945425.
KEGGiecj:JW0781.
eco:b0797.
PATRICi32116795. VBIEscCol129921_0823.

Organism-specific databases

EchoBASEiEB1217.
EcoGeneiEG11235. rhlE.

Phylogenomic databases

eggNOGiENOG4105C1J. Bacteria.
COG0513. LUCA.
HOGENOMiHOG000268807.
InParanoidiP25888.
KOiK11927.
OMAiCAPDETR.
OrthoDBiEOG6GBMBM.
PhylomeDBiP25888.

Enzyme and pathway databases

BioCyciEcoCyc:EG11235-MONOMER.
ECOL316407:JW0781-MONOMER.

Miscellaneous databases

PROiP25888.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00968. DEAD_helicase_RhlE.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR028622. DEAD_helicase_RhlE.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Structural analysis of the rhlE gene of Escherichia coli."
    Ohmori H.
    Jpn. J. Genet. 69:1-12(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Erratum
    Ohmori H.
    Jpn. J. Genet. 69:425-425(1994)
    Cited for: SEQUENCE REVISION TO C-TERMINUS.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "rhlB, a new Escherichia coli K-12 gene with an RNA helicase-like protein sequence motif, one of at least five such possible genes in a prokaryote."
    Kalman M., Murphy H., Cashel M.
    New Biol. 3:886-895(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 50-335.
    Strain: K12.
  7. "Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation."
    Raynal L.C., Carpousis A.J.
    Mol. Microbiol. 32:765-775(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH PCNB.
  8. "Changes in Escherichia coli transcriptome during acclimatization at low temperature."
    Polissi A., De Laurentis W., Zangrossi S., Briani F., Longhi V., Pesole G., Deho G.
    Res. Microbiol. 154:573-580(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION BY COLD SHOCK.
    Strain: K12 / MG1655 / ATCC 47076.
  9. "Studies on three E. coli DEAD-box helicases point to an unwinding mechanism different from that of model DNA helicases."
    Bizebard T., Ferlenghi I., Iost I., Dreyfus M.
    Biochemistry 43:7857-7866(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS RNA-HELICASE, FUNCTION AS ATPASE, CATALYTIC ACTIVITY, ENZYME REGULATION.
  10. "The RNase E of Escherichia coli has at least two binding sites for DEAD-box RNA helicases: functional replacement of RhlB by RhlE."
    Khemici V., Toesca I., Poljak L., Vanzo N.F., Carpousis A.J.
    Mol. Microbiol. 54:1422-1430(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RNASE E.
  11. "The E. coli RhlE RNA helicase regulates the function of related RNA helicases during ribosome assembly."
    Jain C.
    RNA 14:381-389(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN RIBOSOME ASSEMBLY, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiRHLE_ECOLI
AccessioniPrimary (citable) accession number: P25888
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: June 1, 1994
Last modified: April 13, 2016
This is version 134 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

In vitro, can replace RhlB in degradosome and facilitate the degradation of RNA by PNPase.1 Publication

Keywords - Technical termi

Complete proteome, 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.