DBP4_YEAST
ID DBP4_YEAST Reviewed; 770 AA.
AC P20448; D6VWF0; Q6B1G2; Q92329;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 2.
DT 03-AUG-2022, entry version 199.
DE RecName: Full=ATP-dependent RNA helicase HCA4;
DE EC=3.6.4.13;
DE AltName: Full=DEAD box protein 4;
DE AltName: Full=Helicase CA4;
DE AltName: Full=Helicase UF1;
GN Name=HCA4; Synonyms=DBP4, ECM24; OrderedLocusNames=YJL033W; ORFNames=J1250;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RX PubMed=9199348; DOI=10.1128/mcb.17.7.4124;
RA Liang W.-Q., Clark J.A., Fournier M.J.;
RT "The rRNA-processing function of the yeast U14 small nucleolar RNA can be
RT rescued by a conserved RNA helicase-like protein.";
RL Mol. Cell. Biol. 17:4124-4132(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL EMBO J. 15:2031-2049(1996).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 192-382.
RX PubMed=2406722; DOI=10.1073/pnas.87.4.1571;
RA Chang T.-H., Arenas J., Abelson J.;
RT "Identification of five putative yeast RNA helicase genes.";
RL Proc. Natl. Acad. Sci. U.S.A. 87:1571-1575(1990).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=14690591; DOI=10.1016/s1097-2765(03)00476-3;
RA Hazbun T.R., Malmstroem L., Anderson S., Graczyk B.J., Fox B., Riffle M.,
RA Sundin B.A., Aranda J.D., McDonald W.H., Chiu C.-H., Snydsman B.E.,
RA Bradley P., Muller E.G.D., Fields S., Baker D., Yates J.R. III, Davis T.N.;
RT "Assigning function to yeast proteins by integration of technologies.";
RL Mol. Cell 12:1353-1365(2003).
RN [7]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [8]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [9]
RP FUNCTION, INTERACTION WITH THE U3 AND U14 SNORNAS, ASSOCIATION WITH THE
RP PRE-RIBOSOMAL COMPLEX, AND MUTAGENESIS OF LYS-91; SER-225 AND THR-227.
RX PubMed=16209945; DOI=10.1016/j.molcel.2005.08.022;
RA Kos M., Tollervey D.;
RT "The putative RNA helicase Dbp4p is required for release of the U14 snoRNA
RT from preribosomes in Saccharomyces cerevisiae.";
RL Mol. Cell 20:53-64(2005).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-692, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [11]
RP FUNCTION, RNA-BINDING, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=18975973; DOI=10.1021/bi8016119;
RA Garcia I., Uhlenbeck O.C.;
RT "Differential RNA-dependent ATPase activities of four rRNA processing yeast
RT DEAD-box proteins.";
RL Biochemistry 47:12562-12573(2008).
RN [12]
RP FUNCTION.
RX PubMed=18833290; DOI=10.1038/embor.2008.184;
RA Bohnsack M.T., Kos M., Tollervey D.;
RT "Quantitative analysis of snoRNA association with pre-ribosomes and release
RT of snR30 by Rok1 helicase.";
RL EMBO Rep. 9:1230-1236(2008).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-692, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-710; SER-714 AND SER-743, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: ATP-dependent RNA helicase required for ribosome biogenesis.
CC Involved in the release of U14 snoRNA in pre-ribosomal complexes.
CC Required for pre-rRNA cleavage at site A2.
CC {ECO:0000269|PubMed:16209945, ECO:0000269|PubMed:18833290,
CC ECO:0000269|PubMed:18975973, ECO:0000269|PubMed:9199348}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.24 mM for ATP {ECO:0000269|PubMed:18975973};
CC -!- SUBUNIT: Interacts with the U3 and U14 snoRNAs. Associates with pre-
CC ribosomal complexes. {ECO:0000269|PubMed:16209945}.
CC -!- INTERACTION:
CC P20448; Q06631: BFR2; NbExp=5; IntAct=EBI-5612, EBI-36432;
CC P20448; P15790: CKA1; NbExp=2; IntAct=EBI-5612, EBI-9533;
CC P20448; P48234: ENP2; NbExp=3; IntAct=EBI-5612, EBI-23354;
CC P20448; Q06344: ESF1; NbExp=3; IntAct=EBI-5612, EBI-34121;
CC P20448; P53743: ESF2; NbExp=2; IntAct=EBI-5612, EBI-28537;
CC P20448; Q03532: HAS1; NbExp=3; IntAct=EBI-5612, EBI-8170;
CC P20448; P20448: HCA4; NbExp=2; IntAct=EBI-5612, EBI-5612;
CC P20448; Q12136: SAS10; NbExp=3; IntAct=EBI-5612, EBI-36084;
CC P20448; P53254: UTP22; NbExp=3; IntAct=EBI-5612, EBI-1878;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:14562095}.
CC -!- DOMAIN: The Q motif is unique to and characteristic of the DEAD box
CC family of RNA helicases and controls ATP binding and hydrolysis.
CC -!- MISCELLANEOUS: Present with 7900 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX10/DBP4
CC subfamily. {ECO:0000305}.
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DR EMBL; U72149; AAB17005.1; -; Genomic_DNA.
DR EMBL; Z49308; CAA89324.1; -; Genomic_DNA.
DR EMBL; AY693118; AAT93137.1; -; Genomic_DNA.
DR EMBL; BK006943; DAA08766.1; -; Genomic_DNA.
DR PIR; S56805; S56805.
DR RefSeq; NP_012501.1; NM_001181467.1.
DR AlphaFoldDB; P20448; -.
DR SMR; P20448; -.
DR BioGRID; 33727; 220.
DR ComplexPortal; CPX-1604; Small ribosomal subunit processome, variant 1.
DR ComplexPortal; CPX-1607; Small ribosomal subunit processome, variant 2.
DR ComplexPortal; CPX-1608; Small ribosomal subunit processome, variant 3.
DR DIP; DIP-6819N; -.
DR IntAct; P20448; 62.
DR MINT; P20448; -.
DR STRING; 4932.YJL033W; -.
DR iPTMnet; P20448; -.
DR MaxQB; P20448; -.
DR PaxDb; P20448; -.
DR PRIDE; P20448; -.
DR EnsemblFungi; YJL033W_mRNA; YJL033W; YJL033W.
DR GeneID; 853419; -.
DR KEGG; sce:YJL033W; -.
DR SGD; S000003570; HCA4.
DR VEuPathDB; FungiDB:YJL033W; -.
DR eggNOG; KOG0343; Eukaryota.
DR GeneTree; ENSGT00550000074980; -.
DR HOGENOM; CLU_003041_26_1_1; -.
DR InParanoid; P20448; -.
DR OMA; YDKMFER; -.
DR BioCyc; YEAST:G3O-31500-MON; -.
DR SABIO-RK; P20448; -.
DR PRO; PR:P20448; -.
DR Proteomes; UP000002311; Chromosome X.
DR RNAct; P20448; protein.
DR GO; GO:0005730; C:nucleolus; IDA:ComplexPortal.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0032040; C:small-subunit processome; IMP:SGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0008186; F:ATP-dependent activity, acting on RNA; IDA:SGD.
DR GO; GO:0034512; F:box C/D RNA binding; IDA:SGD.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0003724; F:RNA helicase activity; IDA:SGD.
DR GO; GO:0034511; F:U3 snoRNA binding; IDA:SGD.
DR GO; GO:0030490; P:maturation of SSU-rRNA; IC:ComplexPortal.
DR GO; GO:0006364; P:rRNA processing; IMP:SGD.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR025313; DUF4217.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR000629; RNA-helicase_DEAD-box_CS.
DR InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF13959; DUF4217; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM01178; DUF4217; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS00039; DEAD_ATP_HELICASE; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Helicase; Hydrolase; Nucleotide-binding; Nucleus;
KW Phosphoprotein; Reference proteome; Ribosome biogenesis; RNA-binding;
KW rRNA processing.
FT CHAIN 1..770
FT /note="ATP-dependent RNA helicase HCA4"
FT /id="PRO_0000055018"
FT DOMAIN 72..246
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 278..437
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 705..724
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 41..69
FT /note="Q motif"
FT MOTIF 194..197
FT /note="DEAD box"
FT BINDING 85..92
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT MOD_RES 692
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956"
FT MOD_RES 710
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 714
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 743
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MUTAGEN 91
FT /note="K->A,R: Lethal and prevents release of U14 snoRNA
FT from pre-ribosomes."
FT /evidence="ECO:0000269|PubMed:16209945"
FT MUTAGEN 225
FT /note="S->A: Lethal and prevents release of U14 snoRNA from
FT pre-ribosomes; when associated with A-227."
FT /evidence="ECO:0000269|PubMed:16209945"
FT MUTAGEN 227
FT /note="T->A: Lethal and prevents release of U14 snoRNA from
FT pre-ribosomes; when associated with A-225."
FT /evidence="ECO:0000269|PubMed:16209945"
FT CONFLICT 36
FT /note="K -> R (in Ref. 4; AAT93137)"
FT /evidence="ECO:0000305"
FT CONFLICT 381
FT /note="V -> I (in Ref. 5; no nucleotide entry)"
FT /evidence="ECO:0000305"
FT CONFLICT 465
FT /note="Q -> E (in Ref. 1; AAB17005)"
FT /evidence="ECO:0000305"
FT CONFLICT 512
FT /note="F -> L (in Ref. 1; AAB17005)"
FT /evidence="ECO:0000305"
FT CONFLICT 668..673
FT /note="KQEKKR -> NKRRRG (in Ref. 1; AAB17005)"
FT /evidence="ECO:0000305"
FT CONFLICT 675
FT /note="R -> D (in Ref. 1; AAB17005)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 770 AA; 87193 MW; 0C9E4DEF5BFD640E CRC64;
MAKKNRLNTT QRKTLRQKED EYIENLKTKI DEYDPKITKA KFFKDLPISD PTLKGLRESS
FIKLTEIQAD SIPVSLQGHD VLAAAKTGSG KTLAFLVPVI EKLYREKWTE FDGLGALIIS
PTRELAMQIY EVLTKIGSHT SFSAGLVIGG KDVKFELERI SRINILIGTP GRILQHLDQA
VGLNTSNLQM LVLDEADRCL DMGFKKTLDA IVSTLSPSRQ TLLFSATQSQ SVADLARLSL
TDYKTVGTHD VMDGSVNKEA STPETLQQFY IEVPLADKLD ILFSFIKSHL KCKMIVFLSS
SKQVHFVYET FRKMQPGISL MHLHGRQKQR ARTETLDKFN RAQQVCLFAT DVVARGIDFP
AVDWVVQVDC PEDVDTYIHR VGRCARYGKK GKSLIMLTPQ EQEAFLKRLN ARKIEPGKLN
IKQSKKKSIK PQLQSLLFKD PELKYLGQKA FISYVRSIYV QKDKQVFKFD ELPTEEFAYS
LGLPGAPKIK MKGMKTIEQA KERKNAPRQL AFLSKANEDG EVIEDKSKQP RTKYDKMFER
KNQTILSEHY LNITKAQAQE DEDDDFISVK RKDHEINEAE LPALTLPTSR RAQKKALSKK
ASLASKGNAS KLIFDDEGEA HPVYELEDEE EFHKRGDAEV QKTEFLTKES AVMADIDNID
KQVAKEKKQE KKRKRLEAMR REMEAAMEEE ISGDEEEGKT VAYLGTGNLS DDMSDGDMPD
SEGHLKKKAR TVDYSHGHNP SNSVDDDIIE VEEPQTLEDL ESLTAKLIQG
