DBP9_YEAST
ID DBP9_YEAST Reviewed; 594 AA.
AC Q06218; D6VYS3; Q66R46;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 181.
DE RecName: Full=ATP-dependent RNA helicase DBP9;
DE EC=3.6.4.13;
DE AltName: Full=DEAD box protein 9;
GN Name=DBP9; OrderedLocusNames=YLR276C; ORFNames=L9328.3;
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=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(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 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 [4]
RP FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH DBP6.
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 [5]
RP FUNCTION, AND MUTAGENESIS OF ARG-413.
RX PubMed=15028736; DOI=10.1074/jbc.m400231200;
RA Kikuma T., Ohtsu M., Utsugi T., Koga S., Okuhara K., Eki T., Fujimori F.,
RA Murakami Y.;
RT "Dbp9p, a member of the DEAD box protein family, exhibits DNA helicase
RT activity.";
RL J. Biol. Chem. 279:20692-20698(2004).
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:11565753, ECO:0000269|PubMed:15028736}.
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: Interacts with DBP6. {ECO:0000269|PubMed:11565753}.
CC -!- INTERACTION:
CC Q06218; P10962: MAK16; NbExp=4; IntAct=EBI-5640, EBI-10937;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:11565753}.
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 -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX56/DBP9
CC subfamily. {ECO:0000305}.
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DR EMBL; U17245; AAB67366.1; -; Genomic_DNA.
DR EMBL; AY723847; AAU09764.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09589.1; -; Genomic_DNA.
DR PIR; S51412; S51412.
DR RefSeq; NP_013378.1; NM_001182163.1.
DR AlphaFoldDB; Q06218; -.
DR SMR; Q06218; -.
DR BioGRID; 31544; 306.
DR DIP; DIP-4771N; -.
DR IntAct; Q06218; 13.
DR MINT; Q06218; -.
DR STRING; 4932.YLR276C; -.
DR CarbonylDB; Q06218; -.
DR MaxQB; Q06218; -.
DR PaxDb; Q06218; -.
DR PRIDE; Q06218; -.
DR EnsemblFungi; YLR276C_mRNA; YLR276C; YLR276C.
DR GeneID; 850982; -.
DR KEGG; sce:YLR276C; -.
DR SGD; S000004266; DBP9.
DR VEuPathDB; FungiDB:YLR276C; -.
DR eggNOG; KOG0346; Eukaryota.
DR GeneTree; ENSGT00550000074946; -.
DR HOGENOM; CLU_003041_17_1_1; -.
DR InParanoid; Q06218; -.
DR OMA; GYEKDFK; -.
DR BioCyc; YEAST:G3O-32375-MON; -.
DR BRENDA; 3.6.4.12; 984.
DR PRO; PR:Q06218; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; Q06218; protein.
DR GO; GO:0005730; C:nucleolus; 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:0003678; F:DNA helicase activity; IDA:SGD.
DR GO; GO:0033677; F:DNA/RNA helicase activity; IDA:SGD.
DR GO; GO:0003729; F:mRNA binding; HDA:SGD.
DR GO; GO:0003724; F:RNA helicase activity; IDA:SGD.
DR GO; GO:0000463; P:maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
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; IPR014014; RNA_helicase_DEAD_Q_motif.
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; 2.
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..594
FT /note="ATP-dependent RNA helicase DBP9"
FT /id="PRO_0000055039"
FT DOMAIN 49..233
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 246..476
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 339..377
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 558..594
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 17..45
FT /note="Q motif"
FT MOTIF 179..182
FT /note="DEAD box"
FT COMPBIAS 348..377
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 564..581
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 62..69
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MUTAGEN 413
FT /note="R->A,K,T: Impairs helicase activity in vitro."
FT /evidence="ECO:0000269|PubMed:15028736"
FT CONFLICT 24
FT /note="L -> F (in Ref. 3; AAU09764)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 594 AA; 68060 MW; CCE8E0AF8B4071D7 CRC64;
MSYEKKSVEG AYIDDSTTFE AFHLDSRLLQ AIKNIGFQYP TLIQSHAIPL ALQQKRDIIA
KAATGSGKTL AYLIPVIETI LEYKKTIDNG EENGTLGIIL VPTRELAQQV YNVLEKLVLY
CSKDIRTLNI SSDMSDSVLS TLLMDQPEII VGTPGKLLDL LQTKINSISL NELKFLVVDE
VDLVLTFGYQ DDLNKIGEYL PLKKNLQTFL MSATLNDDIQ ALKQKFCRSP AILKFNDEEI
NKNQNKLLQY YVKVSEFDKF LLCYVIFKLN LIKGKTLIFV NNIDRGYRLK LVMEQFGIKS
CILNSELPVN SRQHIVDQFN KNVYQLLIAT DDTEYIKEED DEIEEGHNTE NQEEKSLEGE
PENDKKPSKK KKVQVKKDKE YGVSRGVDFK NVACVLNFDL PTTAKSYVHR VGRTARGGKT
GTAISFVVPL KEFGKHKPSM LQTAKKDERI LSRIIKQQSK LGLELQPYKF DQKQVEAFRY
RMEDGFRAVT QVAIREARVK ELKQELLASE KLKRHFEENP KELQSLRHDK ELHPARVQQH
LKRVPDYLLP ESARGNGTKV KFVPFHNAKK RHSHKKGRVS KPKNGKVDPL KNFK
