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Protein

ATP-dependent RNA helicase DeaD

Gene

deaD

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 various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. Exhibits RNA-stimulated ATP hydrolysis and RNA unwinding activity at low temperature. Involved in 50S ribosomal subunit assembly, acting after SrmB, and could also play a role in the biogenesis of the 30S ribosomal subunit. In addition, is involved in mRNA decay, via formation of a cold-shock degradosome with RNase E. Also stimulates translation of some mRNAs, probably at the level of initiation.UniRule annotation6 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.UniRule annotation2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi50 – 57ATPUniRule annotation8

GO - Molecular functioni

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

GO - Biological processi

  • cellular response to cold Source: EcoCyc
  • mRNA stabilization Source: CACAO
  • positive regulation of translation Source: EcoCyc
  • ribosomal large subunit assembly Source: EcoCyc
  • RNA catabolic process Source: EcoCyc
  • RNA secondary structure unwinding Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Stress response

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10215-MONOMER.
ECOL316407:JW5531-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DeaDUniRule annotation (EC:3.6.4.13UniRule annotation)
Alternative name(s):
Cold-shock DEAD box protein AUniRule annotation
Translation factor W2
Gene namesi
Name:deaDUniRule annotation
Synonyms:csdA, mssB, rhlD
Ordered Locus Names:b3162, JW5531
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10215. deaD.

Subcellular locationi

  • Cytoplasm UniRule annotation1 Publication

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene grow very poorly at 15-20 degrees Celsius and accumulate an abnormal large ribosomal subunit.2 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi157E → Q: Abolishes ATPase activity, drastically reduces helicase activity. In vivo acts as a dominant negative mutation in the presence of the wild-type protein at low temperature. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved2 Publications
ChainiPRO_00000551012 – 629ATP-dependent RNA helicase DeaDAdd BLAST628

Proteomic databases

EPDiP0A9P6.
PaxDbiP0A9P6.
PRIDEiP0A9P6.

2D gel databases

SWISS-2DPAGEP0A9P6.

Expressioni

Inductioni

In response to low temperature.1 Publication

Interactioni

Subunit structurei

Interacts with the 50S ribosomal subunit upon shifting to 15 degrees Celsius. Also found associated with the RNA degradosome at 15 degrees Celsius; binds RNase E (rne).3 Publications

Protein-protein interaction databases

BioGridi4262429. 117 interactors.
DIPiDIP-35752N.
IntActiP0A9P6. 84 interactors.
MINTiMINT-1219396.
STRINGi511145.b3162.

Structurei

3D structure databases

ProteinModelPortaliP0A9P6.
SMRiP0A9P6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini37 – 208Helicase ATP-bindingUniRule annotationAdd BLAST172
Domaini232 – 379Helicase C-terminalUniRule annotationAdd BLAST148

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi6 – 34Q motifAdd BLAST29
Motifi156 – 159DEAD box4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi568 – 629Arg/Glu/Gly-richAdd BLAST62

Sequence similaritiesi

Belongs to the DEAD box helicase family. DeaD 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.
HOGENOMiHOG000268810.
InParanoidiP0A9P6.
KOiK05592.
OMAiTEGNATY.
PhylomeDBiP0A9P6.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00964. DEAD_helicase_DeaD. 1 hit.
InterProiIPR021046. Cold-shock_DEAD_Abox_C.
IPR005580. DbpA_RNA-bd_dom.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR028618. DEAD_helicase_DeaD.
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.
PF12343. DEADboxA. 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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A9P6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAEFETTFAD LGLKAPILEA LNDLGYEKPS PIQAECIPHL LNGRDVLGMA
60 70 80 90 100
QTGSGKTAAF SLPLLQNLDP ELKAPQILVL APTRELAVQV AEAMTDFSKH
110 120 130 140 150
MRGVNVVALY GGQRYDVQLR ALRQGPQIVV GTPGRLLDHL KRGTLDLSKL
160 170 180 190 200
SGLVLDEADE MLRMGFIEDV ETIMAQIPEG HQTALFSATM PEAIRRITRR
210 220 230 240 250
FMKEPQEVRI QSSVTTRPDI SQSYWTVWGM RKNEALVRFL EAEDFDAAII
260 270 280 290 300
FVRTKNATLE VAEALERNGY NSAALNGDMN QALREQTLER LKDGRLDILI
310 320 330 340 350
ATDVAARGLD VERISLVVNY DIPMDSESYV HRIGRTGRAG RAGRALLFVE
360 370 380 390 400
NRERRLLRNI ERTMKLTIPE VELPNAELLG KRRLEKFAAK VQQQLESSDL
410 420 430 440 450
DQYRALLSKI QPTAEGEELD LETLAAALLK MAQGERTLIV PPDAPMRPKR
460 470 480 490 500
EFRDRDDRGP RDRNDRGPRG DREDRPRRER RDVGDMQLYR IEVGRDDGVE
510 520 530 540 550
VRHIVGAIAN EGDISSRYIG NIKLFASHST IELPKGMPGE VLQHFTRTRI
560 570 580 590 600
LNKPMNMQLL GDAQPHTGGE RRGGGRGFGG ERREGGRNFS GERREGGRGD
610 620
GRRFSGERRE GRAPRRDDST GRRRFGGDA
Length:629
Mass (Da):70,546
Last modified:January 23, 2007 - v2
Checksum:i9DB692D41C38D17C
GO

Sequence cautioni

The sequence AAA23674 differs from that shown. Reason: Frameshift at positions 536 and 565.Curated
The sequence AAA23674 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence AAA57965 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti444A → G in AAA23674 (PubMed:2045359).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M63288 Genomic DNA. Translation: AAA23674.1. Sequence problems.
U18997 Genomic DNA. Translation: AAA57965.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76196.2.
AP009048 Genomic DNA. Translation: BAE77208.1.
U03750 Genomic DNA. Translation: AAA03626.1.
PIRiF65106.
RefSeqiNP_417631.2. NC_000913.3.
WP_001295553.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76196; AAC76196; b3162.
BAE77208; BAE77208; BAE77208.
GeneIDi947674.
KEGGiecj:JW5531.
eco:b3162.
PATRICi32121742. VBIEscCol129921_3257.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M63288 Genomic DNA. Translation: AAA23674.1. Sequence problems.
U18997 Genomic DNA. Translation: AAA57965.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76196.2.
AP009048 Genomic DNA. Translation: BAE77208.1.
U03750 Genomic DNA. Translation: AAA03626.1.
PIRiF65106.
RefSeqiNP_417631.2. NC_000913.3.
WP_001295553.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP0A9P6.
SMRiP0A9P6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262429. 117 interactors.
DIPiDIP-35752N.
IntActiP0A9P6. 84 interactors.
MINTiMINT-1219396.
STRINGi511145.b3162.

2D gel databases

SWISS-2DPAGEP0A9P6.

Proteomic databases

EPDiP0A9P6.
PaxDbiP0A9P6.
PRIDEiP0A9P6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76196; AAC76196; b3162.
BAE77208; BAE77208; BAE77208.
GeneIDi947674.
KEGGiecj:JW5531.
eco:b3162.
PATRICi32121742. VBIEscCol129921_3257.

Organism-specific databases

EchoBASEiEB0211.
EcoGeneiEG10215. deaD.

Phylogenomic databases

eggNOGiENOG4105C1J. Bacteria.
COG0513. LUCA.
HOGENOMiHOG000268810.
InParanoidiP0A9P6.
KOiK05592.
OMAiTEGNATY.
PhylomeDBiP0A9P6.

Enzyme and pathway databases

BioCyciEcoCyc:EG10215-MONOMER.
ECOL316407:JW5531-MONOMER.

Miscellaneous databases

PROiP0A9P6.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00964. DEAD_helicase_DeaD. 1 hit.
InterProiIPR021046. Cold-shock_DEAD_Abox_C.
IPR005580. DbpA_RNA-bd_dom.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR028618. DEAD_helicase_DeaD.
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.
PF12343. DEADboxA. 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 nameiDEAD_ECOLI
AccessioniPrimary (citable) accession number: P0A9P6
Secondary accession number(s): P23304, Q2M948, Q8FD90
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 105 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

When overexpressed suppresses cold-sensitive mutants of rpsB (ribosomal protein S2) (PubMed:2045359) and pyrH/smbA2 (uridylate kinase) (PubMed:8190075).2 Publications

Caution

It is unclear whether it requires ATP: according to PubMed:8552679 and PubMed:10216955, it does not require ATP, while according to PubMed:15196029, PubMed:15554978 and PubMed:17259309, it requires ATP.Curated

Keywords - Technical termi

Complete proteome, Direct protein sequencing, 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.