DBP6_YEAST
ID DBP6_YEAST Reviewed; 629 AA.
AC P53734; D6W1L4;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 185.
DE RecName: Full=ATP-dependent RNA helicase DBP6;
DE EC=3.6.4.13;
DE AltName: Full=DEAD box protein 6;
GN Name=DBP6; OrderedLocusNames=YNR038W; ORFNames=N3302;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169873;
RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT evolutionary implications.";
RL Nature 387:93-98(1997).
RN [2]
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 [3]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=9528757; DOI=10.1128/mcb.18.4.1855;
RA Kressler D., de la Cruz J., Rojo M., Linder P.;
RT "Dbp6p is an essential putative ATP-dependent RNA helicase required for
RT 60S-ribosomal-subunit assembly in Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 18:1855-1865(1998).
RN [4]
RP FUNCTION.
RX PubMed=10567587; DOI=10.1128/mcb.19.12.8633;
RA Kressler D., Doere M., Rojo M., Linder P.;
RT "Synthetic lethality with conditional dbp6 alleles identifies Rsa1p, a
RT nucleoplasmic protein involved in the assembly of 60S ribosomal subunits.";
RL Mol. Cell. Biol. 19:8633-8645(1999).
RN [5]
RP FUNCTION, AND INTERACTION WITH DBP9.
RX PubMed=11565753; DOI=10.1017/s1355838201010640;
RA Daugeron M.-C., Kressler D., Linder P.;
RT "Dbp9p, a putative ATP-dependent RNA helicase involved in 60S-ribosomal-
RT subunit biogenesis, functionally interacts with Dbp6p.";
RL RNA 7:1317-1334(2001).
RN [6]
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 [7]
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 [8]
RP FUNCTION, INTERACTION WITH RSA3, AND ASSOCIATION WITH PRE-RIBOSOMAL
RP PARTICLES.
RX PubMed=15126390; DOI=10.1534/genetics.166.4.1687;
RA de la Cruz J., Lacombe T., Deloche O., Linder P., Kressler D.;
RT "The putative RNA helicase Dbp6p functionally interacts with Rpl3p, Nop8p
RT and the novel trans-acting Factor Rsa3p during biogenesis of 60S ribosomal
RT subunits in Saccharomyces cerevisiae.";
RL Genetics 166:1687-1699(2004).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-73; SER-77 AND SER-78, AND
RP IDENTIFICATION BY 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 [10]
RP IDENTIFICATION IN A COMPLEX WITH NOP8; RSA3; URB1 AND URB2.
RX PubMed=17145778; DOI=10.1128/mcb.01523-06;
RA Rosado I.V., Dez C., Lebaron S., Caizergues-Ferrer M., Henry Y.,
RA de la Cruz J.;
RT "Characterization of Saccharomyces cerevisiae Npa2p (Urb2p) reveals a Low-
RT molecular-mass complex containing Dbp6p, Npa1p (Urb1p), Nop8p, and Rsa3p
RT involved in early steps of 60S ribosomal subunit biogenesis.";
RL Mol. Cell. Biol. 27:1207-1221(2007).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-73; SER-77 AND SER-78, 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-binding RNA helicase involved in the biogenesis of 60S
CC ribosomal subunits and is required for the normal formation of 25S and
CC 5.8S rRNAs. {ECO:0000269|PubMed:10567587, ECO:0000269|PubMed:11565753,
CC ECO:0000269|PubMed:15126390, ECO:0000269|PubMed:9528757}.
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 -!- SUBUNIT: Associated with pre-ribosomal particles. Interacts with DBP9
CC and RSA3. Together with NOP8, URB1, URB2 and RSA3, forms an RNA-
CC independent complex, which is required during early maturation of
CC nascent 60S ribosomal subunits. {ECO:0000269|PubMed:11565753,
CC ECO:0000269|PubMed:15126390, ECO:0000269|PubMed:17145778}.
CC -!- INTERACTION:
CC P53734; Q05942: RSA3; NbExp=3; IntAct=EBI-5625, EBI-33602;
CC P53734; P34241: URB1; NbExp=4; IntAct=EBI-5625, EBI-26595;
CC P53734; P47108: URB2; NbExp=4; IntAct=EBI-5625, EBI-25492;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:9528757}.
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 12700 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX51/DBP6
CC subfamily. {ECO:0000305}.
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DR EMBL; Z71653; CAA96318.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10580.1; -; Genomic_DNA.
DR PIR; S63369; S63369.
DR RefSeq; NP_014436.1; NM_001183215.1.
DR AlphaFoldDB; P53734; -.
DR SMR; P53734; -.
DR BioGRID; 35864; 267.
DR ComplexPortal; CPX-1421; NOP8 60s ribosome pre-assembly complex.
DR IntAct; P53734; 43.
DR MINT; P53734; -.
DR STRING; 4932.YNR038W; -.
DR iPTMnet; P53734; -.
DR MaxQB; P53734; -.
DR PaxDb; P53734; -.
DR PRIDE; P53734; -.
DR EnsemblFungi; YNR038W_mRNA; YNR038W; YNR038W.
DR GeneID; 855774; -.
DR KEGG; sce:YNR038W; -.
DR SGD; S000005321; DBP6.
DR VEuPathDB; FungiDB:YNR038W; -.
DR eggNOG; KOG0350; Eukaryota.
DR GeneTree; ENSGT00550000075141; -.
DR HOGENOM; CLU_003041_15_2_1; -.
DR InParanoid; P53734; -.
DR OMA; HLEWLVI; -.
DR BioCyc; YEAST:G3O-33348-MON; -.
DR PRO; PR:P53734; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P53734; protein.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
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:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003724; F:RNA helicase activity; ISS:SGD.
DR GO; GO:0000466; P:maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0000463; P:maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0042273; P:ribosomal large subunit biogenesis; IC:ComplexPortal.
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.
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..629
FT /note="ATP-dependent RNA helicase DBP6"
FT /id="PRO_0000055036"
FT DOMAIN 221..401
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 437..603
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..129
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 197..205
FT /note="Q motif"
FT MOTIF 341..344
FT /note="DEAD box"
FT COMPBIAS 90..106
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 234..241
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 73
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 77
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 78
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
SQ SEQUENCE 629 AA; 70362 MW; 64A04A2D88F44072 CRC64;
MFASRFDPSQ LTAPAASAPE GIVGTTPPAI VPLKRQATES DNEEYGSHQD SDESSNSSSE
EDEDRMQVDY GASEEDSSEV EEEESKPSTH STVLSRFKQT VSLQERLGAS DIAESKEDEG
IEDEAASTHQ LKQIPQPEFV KNPMNLNTNS LQFKSTGWLN TEKIYYDNSL IKPFSDYANE
LEAKLLQNIC KNFSTNTFPI QSIILDSILP VLNFTLNVSK RNFTRRIGDI LVNAATGSGK
TLAYSIPIVQ TLFKRQINRL RCIIIVPTKL LINQVYTTLT KLTQGTSLIV SIAKLENSLK
DEHKKLSNLE PDILITTPGR LVDHLNMKSI NLKNLKFLII DEADRLLNQS FQGWCPKLMS
HLKTDKLDTL PGNVIKMIFS ATLTTNTEKL NGLNLYKPKL FLKQTDKLYQ LPNKLNEFNI
NIPTAKSVYK PLILLYSICQ FMAHSPIAAK ILIFVKSNES SIRLSKLLQL ICESRSQSSV
LKNLQNLAVS INSVNSNNSK AENKKIVANF SHHSESAGIT ILITTDIMSR GIDINDITQV
INYDPPMSSQ QYVHRVGRTA RANELGSAYN LLVGRGERTF FDDLNKDLDR DGKSVQPLEL
DFTLLESDSE LYTSSLESLK NYHNNTAQA
