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Protein

ATP-dependent RNA helicase DbpA

Gene

dbpA

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 the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes. Requires a single-stranded RNA loading site on the 3' side of the substrate helix.UniRule annotation9 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.UniRule annotation4 Publications

Enzyme regulationi

Requires hairpin 92 of 23S rRNA for optimal activity. ATPase activity is stimulated by interaction of the N-terminal domain with RNA.3 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi47 – 54ATPUniRule annotation8

GO - Molecular functioni

  • ADP binding Source: EcoCyc
  • ATPase activity Source: EcoliWiki
  • ATP binding Source: EcoCyc
  • ATP-dependent 3'-5' RNA helicase activity Source: EcoCyc
  • DNA/RNA helicase activity Source: EcoliWiki
  • RNA helicase activity Source: EcoliWiki
  • rRNA binding Source: EcoCyc

GO - Biological processi

  • ribosomal large subunit 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:EG10210-MONOMER.
ECOL316407:JW1337-MONOMER.
MetaCyc:EG10210-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DbpAUniRule annotation (EC:3.6.4.13UniRule annotation)
Gene namesi
Name:dbpAUniRule annotation
Ordered Locus Names:b1343, JW1337
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10210. dbpA.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi53K → A: Shows accumulation of partially-assembled 45S particles. 1 Publication1
Mutagenesisi154E → A: Shows accumulation of partially-assembled 45S particles. 1 Publication1
Mutagenesisi331R → A: Shows accumulation of partially-assembled 45S particles. Binds rRNA normally but is severely impaired in ATPase and helicase activities. Overexpression confers a dominant slow growth and cold-sensitive phenotype. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000550961 – 457ATP-dependent RNA helicase DbpAAdd BLAST457

Proteomic databases

PaxDbiP21693.
PRIDEiP21693.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi4262985. 62 interactors.
IntActiP21693. 6 interactors.
STRINGi511145.b1343.

Structurei

3D structure databases

ProteinModelPortaliP21693.
SMRiP21693.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini34 – 205Helicase ATP-bindingUniRule annotationAdd BLAST172
Domaini230 – 376Helicase C-terminalUniRule annotationAdd BLAST147

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni383 – 457Involved in 23S rRNA bindingUniRule annotationAdd BLAST75

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi3 – 31Q motifAdd BLAST29
Motifi153 – 156DEAD box4

Domaini

Contains an N-terminal domain that binds non-specifically to RNA and a C-terminal domain that binds specifically and tightly to hairpin 92 of 23S rRNA.UniRule annotation2 Publications

Sequence similaritiesi

Belongs to the DEAD box helicase family. DbpA 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.
HOGENOMiHOG000268809.
InParanoidiP21693.
KOiK05591.
OMAiKKSGQNR.
PhylomeDBiP21693.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00965. DEAD_helicase_DbpA. 1 hit.
InterProiIPR005580. DbpA_RNA-bd_dom.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR028619. DEAD_helicase_DbpA.
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]
PfamiPF03880. DbpA. 1 hit.
PF00270. 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.

P21693-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTAFSTLNVL PPAQLTNLNE LGYLTMTPVQ AAALPAILAG KDVRVQAKTG
60 70 80 90 100
SGKTAAFGLG LLQQIDASLF QTQALVLCPT RELADQVAGE LRRLARFLPN
110 120 130 140 150
TKILTLCGGQ PFGMQRDSLQ HAPHIIVATP GRLLDHLQKG TVSLDALNTL
160 170 180 190 200
VMDEADRMLD MGFSDAIDDV IRFAPASRQT LLFSATWPEA IAAISGRVQR
210 220 230 240 250
DPLAIEIDST DALPPIEQQF YETSSKGKIP LLQRLLSLHQ PSSCVVFCNT
260 270 280 290 300
KKDCQAVCDA LNEVGQSALS LHGDLEQRDR DQTLVRFANG SARVLVATDV
310 320 330 340 350
AARGLDIKSL ELVVNFELAW DPEVHVHRIG RTARAGNSGL AISFCAPEEA
360 370 380 390 400
QRANIISDML QIKLNWQTPP ANSSIATLEA EMATLCIDGG KKAKMRPGDV
410 420 430 440 450
LGALTGDIGL DGADIGKIAV HPAHVYVAVR QAVAHKAWKQ LQGGKIKGKT

CRVRLLK
Length:457
Mass (Da):49,188
Last modified:October 1, 1993 - v2
Checksum:iD9198B1FABA4D38A
GO

Sequence cautioni

The sequence CAA36872 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X52647 Genomic DNA. Translation: CAA36872.1. Different initiation.
U00096 Genomic DNA. Translation: AAC74425.1.
AP009048 Genomic DNA. Translation: BAA14946.1.
PIRiB64884.
RefSeqiNP_415859.1. NC_000913.3.
WP_000123737.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74425; AAC74425; b1343.
BAA14946; BAA14946; BAA14946.
GeneIDi947153.
KEGGiecj:JW1337.
eco:b1343.
PATRICi32117966. VBIEscCol129921_1403.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X52647 Genomic DNA. Translation: CAA36872.1. Different initiation.
U00096 Genomic DNA. Translation: AAC74425.1.
AP009048 Genomic DNA. Translation: BAA14946.1.
PIRiB64884.
RefSeqiNP_415859.1. NC_000913.3.
WP_000123737.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP21693.
SMRiP21693.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262985. 62 interactors.
IntActiP21693. 6 interactors.
STRINGi511145.b1343.

Proteomic databases

PaxDbiP21693.
PRIDEiP21693.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74425; AAC74425; b1343.
BAA14946; BAA14946; BAA14946.
GeneIDi947153.
KEGGiecj:JW1337.
eco:b1343.
PATRICi32117966. VBIEscCol129921_1403.

Organism-specific databases

EchoBASEiEB0206.
EcoGeneiEG10210. dbpA.

Phylogenomic databases

eggNOGiENOG4105C1J. Bacteria.
COG0513. LUCA.
HOGENOMiHOG000268809.
InParanoidiP21693.
KOiK05591.
OMAiKKSGQNR.
PhylomeDBiP21693.

Enzyme and pathway databases

BioCyciEcoCyc:EG10210-MONOMER.
ECOL316407:JW1337-MONOMER.
MetaCyc:EG10210-MONOMER.

Miscellaneous databases

PROiP21693.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00965. DEAD_helicase_DbpA. 1 hit.
InterProiIPR005580. DbpA_RNA-bd_dom.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR028619. DEAD_helicase_DbpA.
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]
PfamiPF03880. DbpA. 1 hit.
PF00270. 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...

Entry informationi

Entry nameiDBPA_ECOLI
AccessioniPrimary (citable) accession number: P21693
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: October 1, 1993
Last modified: November 2, 2016
This is version 137 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.