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Protein

ATP-dependent RNA helicase DED1

Gene

DED1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

ATP-binding RNA helicase involved in translation initiation. Remodels RNA in response to ADP and ATP concentrations by facilitating disruption, but also formation of RNA duplexes. Has weak ATP-dependent affinity for dsRNA, but strong ATP-dependent affinity for ssRNA. Acts as a virus host factor involved in the replication of the MBV and the L-A viruses by promoting the negative-strand RNA synthesis. May be involved in recognition of the preinitiation complex and DNA binding of the RNA polymerase III and play a role in mRNA splicing.12 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Kineticsi

  1. KM=0.34 mM for ATP2 Publications

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi186 – 193ATP8

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • ATP-dependent RNA helicase activity Source: SGD
    • RNA strand annealing activity Source: SGD
    • translation initiation factor activity Source: UniProtKB-KW

    GO - Biological processi

    • chromosome segregation Source: GO_Central
    • regulation of gene expression Source: GO_Central
    • RNA secondary structure unwinding Source: GO_Central
    • spliceosomal complex disassembly Source: SGD
    • translational initiation Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Helicase, Hydrolase, Initiation factor

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding, RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-33708-MONOMER.
    BRENDAi3.6.4.13. 984.
    ReactomeiR-SCE-6798695. Neutrophil degranulation.
    SABIO-RKP06634.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ATP-dependent RNA helicase DED1 (EC:3.6.4.13)
    Alternative name(s):
    DEAD box protein 1
    Gene namesi
    Name:DED1
    Synonyms:SPP81
    Ordered Locus Names:YOR204W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome XV

    Organism-specific databases

    EuPathDBiFungiDB:YOR204W.
    SGDiS000005730. DED1.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: SGD
    • cytoplasmic ribonucleoprotein granule Source: GO_Central
    • cytoplasmic stress granule Source: SGD
    • nucleus Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi108G → D in DED1-120; impairs protein synthesis at 15 degrees Celsius; when associated with D-494. 1 Publication1
    Mutagenesisi144F → A: Slow growth at 18 and 30 degrees Celsius and no growth at 16 degrees Celsius. 1 Publication1
    Mutagenesisi144F → D or E: Lethal. 1 Publication1
    Mutagenesisi162F → A: Lethal in vivo and inhibits ATPase and helicase activities in vitro. 1 Publication1
    Mutagenesisi162F → C: Slow growth at 18 degrees Celsius. 1 Publication1
    Mutagenesisi162F → L: Reduces RNA-helicase activity about 5-fold in vitro. 1 Publication1
    Mutagenesisi166T → A: Reduces RNA-helicase activity about 2.5-fold in vitro. 1 Publication1
    Mutagenesisi166T → S: Slow growth at 18 and 36 degrees Celsius in vivo, and reduces RNA-helicase activity about 5-fold in vitro. 1 Publication1
    Mutagenesisi169Q → A or E: Lethal in vivo and impairs ATPase and RNA-helicase activities in vitro. 1 Publication1
    Mutagenesisi169Q → C, D, F, G, H, K, L, M, N, S or T: Lethal. 1 Publication1
    Mutagenesisi192K → A: Impairs RNA-helicase activity in vitro. 1 Publication1
    Mutagenesisi237L → M in DED1-18; impairs BMV RNA synthesis; when associated with D-317. 1 Publication1
    Mutagenesisi307E → A: Lethal in vivo and impairs ATPase and RNA-helicase activities in vitro. 1 Publication1
    Mutagenesisi317E → D in DED1-18; impairs BMV RNA synthesis; when associated with M-237. 1 Publication1
    Mutagenesisi368G → D in DED1-199; impairs protein synthesis at 15 degrees Celsius. 1 Publication1
    Mutagenesisi405F → Y, M, L, A or W: Reduces strongly ATPase activity and strand displacement activity. 1 Publication1
    Mutagenesisi486R → A: Reduces ATPase activity. 1 Publication1
    Mutagenesisi494G → D in DED1-120; impairs protein synthesis at 15 degrees Celsius; when associated with D-108. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemovedCombined sources
    ChainiPRO_00000550432 – 604ATP-dependent RNA helicase DED1Add BLAST603

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei2N-acetylalanineCombined sources1
    Modified residuei62Dimethylated arginine1 Publication1
    Cross-linki158Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei215PhosphoserineCombined sources1
    Modified residuei218PhosphoserineCombined sources1
    Modified residuei263PhosphoserineCombined sources1
    Modified residuei535PhosphoserineCombined sources1
    Modified residuei539PhosphoserineCombined sources1
    Modified residuei543PhosphoserineCombined sources1
    Modified residuei572PhosphoserineCombined sources1
    Modified residuei576PhosphoserineCombined sources1
    Modified residuei598PhosphoserineCombined sources1

    Keywords - PTMi

    Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiP06634.
    PRIDEiP06634.

    PTM databases

    iPTMnetiP06634.

    Interactioni

    Subunit structurei

    Interacts with the L-A virus GAG protein and the whole L-A virus particles.1 Publication

    Protein-protein interaction databases

    BioGridi34599. 184 interactors.
    DIPiDIP-5820N.
    IntActiP06634. 85 interactors.
    MINTiMINT-697363.

    Structurei

    3D structure databases

    ProteinModelPortaliP06634.
    SMRiP06634.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini173 – 362Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST190
    Domaini373 – 533Helicase C-terminalPROSITE-ProRule annotationAdd BLAST161

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi142 – 170Q motifAdd BLAST29
    Motifi306 – 309DEAD box4

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi10 – 75Asn-richAdd BLAST66

    Domaini

    The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.

    Sequence similaritiesi

    Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
    Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

    Phylogenomic databases

    GeneTreeiENSGT00770000120531.
    HOGENOMiHOG000268804.
    InParanoidiP06634.
    KOiK11594.
    OMAiFFNSENS.
    OrthoDBiEOG092C1B4A.

    Family and domain databases

    Gene3Di3.40.50.300. 2 hits.
    InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
    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.

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

    P06634-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAELSEQVQN LSINDNNENG YVPPHLRGKP RSARNNSSNY NNNNGGYNGG
    60 70 80 90 100
    RGGGSFFSNN RRGGYGNGGF FGGNNGGSRS NGRSGGRWID GKHVPAPRNE
    110 120 130 140 150
    KAEIAIFGVP EDPNFQSSGI NFDNYDDIPV DASGKDVPEP ITEFTSPPLD
    160 170 180 190 200
    GLLLENIKLA RFTKPTPVQK YSVPIVANGR DLMACAQTGS GKTGGFLFPV
    210 220 230 240 250
    LSESFKTGPS PQPESQGSFY QRKAYPTAVI MAPTRELATQ IFDEAKKFTY
    260 270 280 290 300
    RSWVKACVVY GGSPIGNQLR EIERGCDLLV ATPGRLNDLL ERGKISLANV
    310 320 330 340 350
    KYLVLDEADR MLDMGFEPQI RHIVEDCDMT PVGERQTLMF SATFPADIQH
    360 370 380 390 400
    LARDFLSDYI FLSVGRVGST SENITQKVLY VENQDKKSAL LDLLSASTDG
    410 420 430 440 450
    LTLIFVETKR MADQLTDFLI MQNFRATAIH GDRTQSERER ALAAFRSGAA
    460 470 480 490 500
    TLLVATAVAA RGLDIPNVTH VINYDLPSDV DDYVHRIGRT GRAGNTGLAT
    510 520 530 540 550
    AFFNSENSNI VKGLHEILTE ANQEVPSFLK DAMMSAPGSR SNSRRGGFGR
    560 570 580 590 600
    NNNRDYRKAG GASAGGWGSS RSRDNSFRGG SGWGSDSKSS GWGNSGGSNN

    SSWW
    Length:604
    Mass (Da):65,553
    Last modified:March 1, 1992 - v2
    Checksum:iB6722D94C03BFA4B
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti37S → M in CAA27004 (PubMed:9169874).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X57278 Genomic DNA. Translation: CAA40546.1.
    Z75110 Genomic DNA. Translation: CAA99419.1.
    X03245 Genomic DNA. Translation: CAA27004.1.
    BK006948 Genomic DNA. Translation: DAA10976.1.
    PIRiS13653.
    RefSeqiNP_014847.3. NM_001183623.3.

    Genome annotation databases

    EnsemblFungiiYOR204W; YOR204W; YOR204W.
    GeneIDi854379.
    KEGGisce:YOR204W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X57278 Genomic DNA. Translation: CAA40546.1.
    Z75110 Genomic DNA. Translation: CAA99419.1.
    X03245 Genomic DNA. Translation: CAA27004.1.
    BK006948 Genomic DNA. Translation: DAA10976.1.
    PIRiS13653.
    RefSeqiNP_014847.3. NM_001183623.3.

    3D structure databases

    ProteinModelPortaliP06634.
    SMRiP06634.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi34599. 184 interactors.
    DIPiDIP-5820N.
    IntActiP06634. 85 interactors.
    MINTiMINT-697363.

    PTM databases

    iPTMnetiP06634.

    Proteomic databases

    MaxQBiP06634.
    PRIDEiP06634.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYOR204W; YOR204W; YOR204W.
    GeneIDi854379.
    KEGGisce:YOR204W.

    Organism-specific databases

    EuPathDBiFungiDB:YOR204W.
    SGDiS000005730. DED1.

    Phylogenomic databases

    GeneTreeiENSGT00770000120531.
    HOGENOMiHOG000268804.
    InParanoidiP06634.
    KOiK11594.
    OMAiFFNSENS.
    OrthoDBiEOG092C1B4A.

    Enzyme and pathway databases

    BioCyciYEAST:G3O-33708-MONOMER.
    BRENDAi3.6.4.13. 984.
    ReactomeiR-SCE-6798695. Neutrophil degranulation.
    SABIO-RKP06634.

    Miscellaneous databases

    PROiP06634.

    Family and domain databases

    Gene3Di3.40.50.300. 2 hits.
    InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
    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...

    Entry informationi

    Entry nameiDED1_YEAST
    AccessioniPrimary (citable) accession number: P06634
    Secondary accession number(s): D6W2R0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1988
    Last sequence update: March 1, 1992
    Last modified: November 30, 2016
    This is version 175 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    3. Yeast chromosome XV
      Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

    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.