DBP3_YEAST
ID DBP3_YEAST Reviewed; 523 AA.
AC P20447; D6VU66;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 03-AUG-2022, entry version 194.
DE RecName: Full=ATP-dependent RNA helicase DBP3;
DE EC=3.6.4.13;
DE AltName: Full=DEAD box protein 3;
DE AltName: Full=Helicase CA3;
GN Name=DBP3; OrderedLocusNames=YGL078C;
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].
RC STRAIN=ATCC 204508 / S288c;
RA Johnston M., Nogae I.;
RL Submitted (DEC-1991) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9290212;
RX DOI=10.1002/(sici)1097-0061(19970915)13:11<1077::aid-yea152>3.0.co;2-y;
RA Rieger M., Brueckner M., Schaefer M., Mueller-Auer S.;
RT "Sequence analysis of 203 kilobases from Saccharomyces cerevisiae
RT chromosome VII.";
RL Yeast 13:1077-1090(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(1997).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 260-448.
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 FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=9032262; DOI=10.1128/mcb.17.3.1354;
RA Weaver P.L., Sun C., Chang T.-H.;
RT "Dbp3p, a putative RNA helicase in Saccharomyces cerevisiae, is required
RT for efficient pre-rRNA processing predominantly at site A3.";
RL Mol. Cell. Biol. 17:1354-1365(1997).
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 IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: ATP-dependent RNA helicase required for 60S ribosomal subunit
CC synthesis. Involved in efficient pre-rRNA processing, predominantly at
CC site A3, which is necessary for the normal formation of 25S and 5.8S
CC rRNAs. {ECO:0000269|PubMed:9032262}.
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 -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:9032262}.
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 38900 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX5/DBP2
CC subfamily. {ECO:0000305}.
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DR EMBL; M80437; AAA73137.1; -; Genomic_DNA.
DR EMBL; Z72600; CAA96783.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08027.1; -; Genomic_DNA.
DR PIR; S30805; S30805.
DR RefSeq; NP_011437.3; NM_001180943.3.
DR AlphaFoldDB; P20447; -.
DR SMR; P20447; -.
DR BioGRID; 33172; 274.
DR DIP; DIP-2668N; -.
DR IntAct; P20447; 13.
DR MINT; P20447; -.
DR STRING; 4932.YGL078C; -.
DR MaxQB; P20447; -.
DR PaxDb; P20447; -.
DR PRIDE; P20447; -.
DR EnsemblFungi; YGL078C_mRNA; YGL078C; YGL078C.
DR GeneID; 852802; -.
DR KEGG; sce:YGL078C; -.
DR SGD; S000003046; DBP3.
DR VEuPathDB; FungiDB:YGL078C; -.
DR eggNOG; KOG0331; Eukaryota.
DR HOGENOM; CLU_003041_1_5_1; -.
DR InParanoid; P20447; -.
DR OMA; KKKTHDM; -.
DR BioCyc; YEAST:G3O-30579-MON; -.
DR SABIO-RK; P20447; -.
DR PRO; PR:P20447; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P20447; protein.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0030687; C:preribosome, large subunit precursor; IDA: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:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IDA:SGD.
DR GO; GO:0000464; P:endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0006364; P:rRNA processing; IBA:GO_Central.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
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 Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 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 Reference proteome; Ribosome biogenesis; RNA-binding; rRNA processing.
FT CHAIN 1..523
FT /note="ATP-dependent RNA helicase DBP3"
FT /id="PRO_0000055017"
FT DOMAIN 143..315
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 344..493
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..71
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 114..140
FT /note="Q motif"
FT MOTIF 262..265
FT /note="DEAD box"
FT COMPBIAS 1..23
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 24..48
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 49..68
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 156..163
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 441
FT /note="E -> A (in Ref. 5; no nucleotide entry)"
FT /evidence="ECO:0000305"
FT CONFLICT 444
FT /note="V -> I (in Ref. 5; no nucleotide entry)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 523 AA; 58827 MW; C198CF4E8D5BAFAA CRC64;
MTKEEIADKK RKVVDEEVIE KKKSKKHKKD KKDKKEKKDK KHKKHKKEKK GEKEVEVPEK
ESEKKPEPTS AVASEFYVQS EALTSLPQSD IDEYFKENEI AVEDSLDLAL RPLLSFDYLS
LDSSIQAEIS KFPKPTPIQA VAWPYLLSGK DVVGVAETGS GKTFAFGVPA ISHLMNDQKK
RGIQVLVISP TRELASQIYD NLIVLTDKVG MQCCCVYGGV PKDEQRIQLK KSQVVVATPG
RLLDLLQEGS VDLSQVNYLV LDEADRMLEK GFEEDIKNII RETDASKRQT LMFTATWPKE
VRELASTFMN NPIKVSIGNT DQLTANKRIT QIVEVVDPRG KERKLLELLK KYHSGPKKNE
KVLIFALYKK EAARVERNLK YNGYNVAAIH GDLSQQQRTQ ALNEFKSGKS NLLLATDVAA
RGLDIPNVKT VINLTFPLTV EDYVHRIGRT GRAGQTGTAH TLFTEQEKHL AGGLVNVLNG
ANQPVPEDLI KFGTHTKKKE HSAYGSFFKD VDLTKKPKKI TFD
