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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)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi50 – 578ATPUniRule annotation

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi157 – 1571E → 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 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved2 Publications
Chaini2 – 629628ATP-dependent RNA helicase DeaDPRO_0000055101Add
BLAST

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 interactions.
DIPiDIP-35752N.
IntActiP0A9P6. 84 interactions.
MINTiMINT-1219396.
STRINGi511145.b3162.

Structurei

3D structure databases

ProteinModelPortaliP0A9P6.
SMRiP0A9P6. Positions 8-379.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini37 – 208172Helicase ATP-bindingUniRule annotationAdd
BLAST
Domaini232 – 379148Helicase C-terminalUniRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi6 – 3429Q motifAdd
BLAST
Motifi156 – 1594DEAD box

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi568 – 62962Arg/Glu/Gly-richAdd
BLAST

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.
OrthoDBiEOG6GBMBM.
PhylomeDBiP0A9P6.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00964. DEAD_helicase_DeaD.
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 AAA23674.1 differs from that shown. Reason: Frameshift at positions 536 and 565. Curated
The sequence AAA23674.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence AAA57965.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti444 – 4441A → G in AAA23674 (PubMed:2045359).Curated

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. Positions 8-379.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262429. 117 interactions.
DIPiDIP-35752N.
IntActiP0A9P6. 84 interactions.
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.
OrthoDBiEOG6GBMBM.
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.
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...

Publicationsi

« Hide 'large scale' publications
  1. "deaD, a new Escherichia coli gene encoding a presumed ATP-dependent RNA helicase, can suppress a mutation in rpsB, the gene encoding ribosomal protein S2."
    Toone W.M., Rudd K.E., Friesen J.D.
    J. Bacteriol. 173:3291-3302(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUPPRESSION OF RPSB MUTATION, GENE NAME.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "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.
  4. "Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli."
    Jones P.G., Mitta M., Kim Y., Jiang W., Inouye M.
    Proc. Natl. Acad. Sci. U.S.A. 93:76-80(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-21, FUNCTION IN HELIX-DESTABILIZING, INTERACTION WITH RIBOSOME, SUBCELLULAR LOCATION, INDUCTION, DISRUPTION PHENOTYPE.
  5. "Molecular characterization of a prokaryotic translation factor homologous to the eukaryotic initiation factor eIF4A."
    Lu J., Aoki H., Ganoza M.C.
    Int. J. Biochem. Cell Biol. 31:215-229(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-16, FUNCTION AS A TRANSLATION FACTOR.
  6. "Nucleotide sequence and expression in Escherichia coli of the Klebsiella pneumoniae deaD gene."
    Peng H.L., Hsieh M.J., Zao C.L., Chang H.-Y.
    J. Biochem. 115:409-414(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 519-629.
    Strain: K12 / JM101 / ATCC 33876 / DSM 3948 / NCIMB 11926.
  7. "Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia coli."
    Yamanaka K., Ogura T., Koonin E.V., Niki H., Hiraga S.
    Mol. Gen. Genet. 243:9-16(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUPPRESSION OF PYRH MUTATION.
  8. "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, CATALYTIC ACTIVITY.
  9. "Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'."
    Prud'homme-Genereux A., Beran R.K., Iost I., Ramey C.S., Mackie G.A., Simons R.W.
    Mol. Microbiol. 54:1409-1421(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN MRNA DECAY, INTERACTION WITH RNASE E.
    Strain: CF881.
  10. "CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit."
    Charollais J., Dreyfus M., Iost I.
    Nucleic Acids Res. 32:2751-2759(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN 50S RIBOSOME BIOGENESIS, INTERACTION WITH 50S SUBUNIT, DISRUPTION PHENOTYPE.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  11. "Mutational analysis of the Escherichia coli DEAD box protein CsdA."
    Turner A.-M.W., Love C.F., Alexander R.W., Jones P.G.
    J. Bacteriol. 189:2769-2776(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-157.

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: April 13, 2016
This is version 102 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.