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Protein

ATP-dependent RNA helicase HCA4

Gene

HCA4

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-dependent RNA helicase required for ribosome biogenesis. Involved in the release of U14 snoRNA in pre-ribosomal complexes. Required for pre-rRNA cleavage at site A2.4 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Kineticsi

  1. KM=0.24 mM for ATP1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi85 – 928ATP

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • ATP-dependent RNA helicase activity Source: SGD
    • RNA binding Source: UniProtKB-KW
    • RNA-dependent ATPase activity Source: SGD

    GO - Biological processi

    • RNA secondary structure unwinding Source: GO_Central
    • rRNA processing Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Helicase, Hydrolase

    Keywords - Biological processi

    Ribosome biogenesis, rRNA processing

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding, RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31500-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ATP-dependent RNA helicase HCA4 (EC:3.6.4.13)
    Alternative name(s):
    DEAD box protein 4
    Helicase CA4
    Helicase UF1
    Gene namesi
    Name:HCA4
    Synonyms:DBP4, ECM24
    Ordered Locus Names:YJL033W
    ORF Names:J1250
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome X

    Organism-specific databases

    EuPathDBiFungiDB:YJL033W.
    SGDiS000003570. HCA4.

    Subcellular locationi

    GO - Cellular componenti

    • nucleolus Source: SGD
    • small-subunit processome Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi91 – 911K → A or R: Lethal and prevents release of U14 snoRNA from pre-ribosomes. 1 Publication
    Mutagenesisi225 – 2251S → A: Lethal and prevents release of U14 snoRNA from pre-ribosomes; when associated with A-227. 1 Publication
    Mutagenesisi227 – 2271T → A: Lethal and prevents release of U14 snoRNA from pre-ribosomes; when associated with A-225. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 770770ATP-dependent RNA helicase HCA4PRO_0000055018Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei692 – 6921PhosphoserineCombined sources
    Modified residuei710 – 7101PhosphoserineCombined sources
    Modified residuei714 – 7141PhosphoserineCombined sources
    Modified residuei743 – 7431PhosphoserineCombined sources

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP20448.

    PTM databases

    iPTMnetiP20448.

    Interactioni

    Subunit structurei

    Interacts with the U3 and U14 snoRNAs. Associates with pre-ribosomal complexes.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    BFR2Q066315EBI-5612,EBI-36432
    ENP2P482343EBI-5612,EBI-23354

    Protein-protein interaction databases

    BioGridi33727. 86 interactions.
    DIPiDIP-6819N.
    IntActiP20448. 51 interactions.
    MINTiMINT-620511.

    Structurei

    3D structure databases

    ProteinModelPortaliP20448.
    SMRiP20448. Positions 17-442.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini72 – 246175Helicase ATP-bindingPROSITE-ProRule annotationAdd
    BLAST
    Domaini278 – 437160Helicase C-terminalPROSITE-ProRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi41 – 6929Q motifAdd
    BLAST
    Motifi194 – 1974DEAD box

    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

    GeneTreeiENSGT00550000074980.
    HOGENOMiHOG000268801.
    InParanoidiP20448.
    KOiK14776.
    OMAiYLGQRAF.
    OrthoDBiEOG7FR7R5.

    Family and domain databases

    Gene3Di3.40.50.300. 2 hits.
    InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
    IPR025313. DUF4217.
    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.
    PF13959. DUF4217. 1 hit.
    PF00271. Helicase_C. 1 hit.
    [Graphical view]
    SMARTiSM00487. DEXDc. 1 hit.
    SM01178. DUF4217. 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.

    P20448-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAKKNRLNTT QRKTLRQKED EYIENLKTKI DEYDPKITKA KFFKDLPISD
    60 70 80 90 100
    PTLKGLRESS FIKLTEIQAD SIPVSLQGHD VLAAAKTGSG KTLAFLVPVI
    110 120 130 140 150
    EKLYREKWTE FDGLGALIIS PTRELAMQIY EVLTKIGSHT SFSAGLVIGG
    160 170 180 190 200
    KDVKFELERI SRINILIGTP GRILQHLDQA VGLNTSNLQM LVLDEADRCL
    210 220 230 240 250
    DMGFKKTLDA IVSTLSPSRQ TLLFSATQSQ SVADLARLSL TDYKTVGTHD
    260 270 280 290 300
    VMDGSVNKEA STPETLQQFY IEVPLADKLD ILFSFIKSHL KCKMIVFLSS
    310 320 330 340 350
    SKQVHFVYET FRKMQPGISL MHLHGRQKQR ARTETLDKFN RAQQVCLFAT
    360 370 380 390 400
    DVVARGIDFP AVDWVVQVDC PEDVDTYIHR VGRCARYGKK GKSLIMLTPQ
    410 420 430 440 450
    EQEAFLKRLN ARKIEPGKLN IKQSKKKSIK PQLQSLLFKD PELKYLGQKA
    460 470 480 490 500
    FISYVRSIYV QKDKQVFKFD ELPTEEFAYS LGLPGAPKIK MKGMKTIEQA
    510 520 530 540 550
    KERKNAPRQL AFLSKANEDG EVIEDKSKQP RTKYDKMFER KNQTILSEHY
    560 570 580 590 600
    LNITKAQAQE DEDDDFISVK RKDHEINEAE LPALTLPTSR RAQKKALSKK
    610 620 630 640 650
    ASLASKGNAS KLIFDDEGEA HPVYELEDEE EFHKRGDAEV QKTEFLTKES
    660 670 680 690 700
    AVMADIDNID KQVAKEKKQE KKRKRLEAMR REMEAAMEEE ISGDEEEGKT
    710 720 730 740 750
    VAYLGTGNLS DDMSDGDMPD SEGHLKKKAR TVDYSHGHNP SNSVDDDIIE
    760 770
    VEEPQTLEDL ESLTAKLIQG
    Length:770
    Mass (Da):87,193
    Last modified:November 1, 1995 - v2
    Checksum:i0C9E4DEF5BFD640E
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti36 – 361K → R in AAT93137 (PubMed:17322287).Curated
    Sequence conflicti381 – 3811V → I no nucleotide entry (PubMed:2406722).Curated
    Sequence conflicti465 – 4651Q → E in AAB17005 (PubMed:9199348).Curated
    Sequence conflicti512 – 5121F → L in AAB17005 (PubMed:9199348).Curated
    Sequence conflicti668 – 6736KQEKKR → NKRRRG in AAB17005 (PubMed:9199348).Curated
    Sequence conflicti675 – 6751R → D in AAB17005 (PubMed:9199348).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U72149 Genomic DNA. Translation: AAB17005.1.
    Z49308 Genomic DNA. Translation: CAA89324.1.
    AY693118 Genomic DNA. Translation: AAT93137.1.
    BK006943 Genomic DNA. Translation: DAA08766.1.
    PIRiS56805.
    RefSeqiNP_012501.1. NM_001181467.1.

    Genome annotation databases

    EnsemblFungiiYJL033W; YJL033W; YJL033W.
    GeneIDi853419.
    KEGGisce:YJL033W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U72149 Genomic DNA. Translation: AAB17005.1.
    Z49308 Genomic DNA. Translation: CAA89324.1.
    AY693118 Genomic DNA. Translation: AAT93137.1.
    BK006943 Genomic DNA. Translation: DAA08766.1.
    PIRiS56805.
    RefSeqiNP_012501.1. NM_001181467.1.

    3D structure databases

    ProteinModelPortaliP20448.
    SMRiP20448. Positions 17-442.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi33727. 86 interactions.
    DIPiDIP-6819N.
    IntActiP20448. 51 interactions.
    MINTiMINT-620511.

    PTM databases

    iPTMnetiP20448.

    Proteomic databases

    MaxQBiP20448.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYJL033W; YJL033W; YJL033W.
    GeneIDi853419.
    KEGGisce:YJL033W.

    Organism-specific databases

    EuPathDBiFungiDB:YJL033W.
    SGDiS000003570. HCA4.

    Phylogenomic databases

    GeneTreeiENSGT00550000074980.
    HOGENOMiHOG000268801.
    InParanoidiP20448.
    KOiK14776.
    OMAiYLGQRAF.
    OrthoDBiEOG7FR7R5.

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31500-MONOMER.

    Miscellaneous databases

    PROiP20448.

    Family and domain databases

    Gene3Di3.40.50.300. 2 hits.
    InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
    IPR025313. DUF4217.
    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.
    PF13959. DUF4217. 1 hit.
    PF00271. Helicase_C. 1 hit.
    [Graphical view]
    SMARTiSM00487. DEXDc. 1 hit.
    SM01178. DUF4217. 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. "The rRNA-processing function of the yeast U14 small nucleolar RNA can be rescued by a conserved RNA helicase-like protein."
      Liang W.-Q., Clark J.A., Fournier M.J.
      Mol. Cell. Biol. 17:4124-4132(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
    2. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
      Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
      , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
      EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. "Identification of five putative yeast RNA helicase genes."
      Chang T.-H., Arenas J., Abelson J.
      Proc. Natl. Acad. Sci. U.S.A. 87:1571-1575(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 192-382.
    6. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    8. "The putative RNA helicase Dbp4p is required for release of the U14 snoRNA from preribosomes in Saccharomyces cerevisiae."
      Kos M., Tollervey D.
      Mol. Cell 20:53-64(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH THE U3 AND U14 SNORNAS, ASSOCIATION WITH THE PRE-RIBOSOMAL COMPLEX, MUTAGENESIS OF LYS-91; SER-225 AND THR-227.
    9. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-692, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    10. "Differential RNA-dependent ATPase activities of four rRNA processing yeast DEAD-box proteins."
      Garcia I., Uhlenbeck O.C.
      Biochemistry 47:12562-12573(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, RNA-BINDING, BIOPHYSICOCHEMICAL PROPERTIES.
    11. "Quantitative analysis of snoRNA association with pre-ribosomes and release of snR30 by Rok1 helicase."
      Bohnsack M.T., Kos M., Tollervey D.
      EMBO Rep. 9:1230-1236(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    12. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-692, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-710; SER-714 AND SER-743, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiDBP4_YEAST
    AccessioniPrimary (citable) accession number: P20448
    Secondary accession number(s): D6VWF0, Q6B1G2, Q92329
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1991
    Last sequence update: November 1, 1995
    Last modified: July 6, 2016
    This is version 158 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 7900 molecules/cell in log phase SD medium.1 Publication

    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 X
      Yeast (Saccharomyces cerevisiae) chromosome X: 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.