SPB4_YEAST
ID SPB4_YEAST Reviewed; 606 AA.
AC P25808; D6VTM9;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1992, sequence version 1.
DT 03-AUG-2022, entry version 190.
DE RecName: Full=ATP-dependent rRNA helicase SPB4 {ECO:0000305};
DE EC=3.6.4.13 {ECO:0000269|PubMed:2408148};
DE AltName: Full=Suppressor of PAB1 protein 4 {ECO:0000303|PubMed:2408148};
GN Name=SPB4 {ECO:0000303|PubMed:2408148};
GN OrderedLocusNames=YFL002C {ECO:0000312|SGD:S000001894};
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], FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=2408148; DOI=10.1126/science.2408148;
RA Sachs A.B., Davis R.W.;
RT "Translation initiation and ribosomal biogenesis: involvement of a putative
RT rRNA helicase and RPL46.";
RL Science 247:1077-1079(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204511 / S288c / AB972;
RX PubMed=8789262;
RX DOI=10.1002/(sici)1097-0061(199601)12:1<77::aid-yea887>3.0.co;2-5;
RA Naitou M., Ozawa M., Sasanuma S., Kobayashi M., Hagiwara H., Shibata T.,
RA Hanaoka F., Watanabe K., Ono A., Yamazaki M., Tashiro H., Eki T.,
RA Murakami Y.;
RT "Sequencing of a 23 kb fragment from Saccharomyces cerevisiae chromosome
RT VI.";
RL Yeast 12:77-84(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7670463; DOI=10.1038/ng0795-261;
RA Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S.,
RA Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K., Yamazaki M., Tashiro H.,
RA Eki T.;
RT "Analysis of the nucleotide sequence of chromosome VI from Saccharomyces
RT cerevisiae.";
RL Nat. Genet. 10:261-268(1995).
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 FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=9769101; DOI=10.1017/s1355838298981158;
RA de la Cruz J., Kressler D., Rojo M., Tollervey D., Linder P.;
RT "Spb4p, an essential putative RNA helicase, is required for a late step in
RT the assembly of 60S ribosomal subunits in Saccharomyces cerevisiae.";
RL RNA 4:1268-1281(1998).
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 PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-254, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [9]
RP FUNCTION, IDENTIFICATION IN PRE-60S RIBOSOMAL COMPLEXES, AND MUTAGENESIS OF
RP ARG-360.
RX PubMed=21825077; DOI=10.1128/mcb.05436-11;
RA Garcia-Gomez J.J., Lebaron S., Froment C., Monsarrat B., Henry Y.,
RA de la Cruz J.;
RT "Dynamics of the putative RNA helicase Spb4 during ribosome assembly in
RT Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 31:4156-4164(2011).
RN [10]
RP FUNCTION, AND IDENTIFICATION IN PRE-60S RIBOSOMAL COMPLEXES.
RX PubMed=22735702; DOI=10.1093/nar/gks609;
RA Talkish J., Zhang J., Jakovljevic J., Horsey E.W., Woolford J.L. Jr.;
RT "Hierarchical recruitment into nascent ribosomes of assembly factors
RT required for 27SB pre-rRNA processing in Saccharomyces cerevisiae.";
RL Nucleic Acids Res. 40:8646-8661(2012).
RN [11]
RP IDENTIFICATION IN PRE-60S RIBOSOMAL COMPLEXES.
RX PubMed=23874617; DOI=10.1371/journal.pone.0068412;
RA Ohmayer U., Gamalinda M., Sauert M., Ossowski J., Poell G., Linnemann J.,
RA Hierlmeier T., Perez-Fernandez J., Kumcuoglu B., Leger-Silvestre I.,
RA Faubladier M., Griesenbeck J., Woolford J., Tschochner H., Milkereit P.;
RT "Studies on the assembly characteristics of large subunit ribosomal
RT proteins in S. cerevisae.";
RL PLoS ONE 8:E68412-E68412(2013).
RN [12]
RP FUNCTION, AND IDENTIFICATION IN PRE-60S RIBOSOMAL COMPLEXES.
RX PubMed=25579579; DOI=10.1007/978-1-4939-2214-7_4;
RA Garcia-Gomez J.J., Lebaron S., Henry Y., de la Cruz J.;
RT "Dynamics of the Spb4 interactome monitored by affinity purification.";
RL Methods Mol. Biol. 1259:49-67(2015).
CC -!- FUNCTION: ATP-binding RNA helicase involved in the biogenesis of 60S
CC ribosomal subunits (PubMed:2408148, PubMed:25579579). Binds 90S pre-
CC ribosomal particles and dissociates from pre-60S ribosomal particles
CC after processing of 27SB pre-rRNA (PubMed:21825077). Required for the
CC normal formation of 18S rRNA through the processing of pre-rRNAs at
CC sites A0, A1 and A2, and the normal formation of 25S and 5.8S rRNAs
CC through the processing of pre-rRNAs at sites C1 and C2
CC (PubMed:9769101). Also required for recruitment of NOG2 to pre-
CC ribosomes (PubMed:22735702). {ECO:0000269|PubMed:21825077,
CC ECO:0000269|PubMed:22735702, ECO:0000269|PubMed:2408148,
CC ECO:0000269|PubMed:25579579, ECO:0000269|PubMed:9769101}.
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 Evidence={ECO:0000269|PubMed:2408148};
CC -!- SUBUNIT: Component of pre-60S ribosomal complexes.
CC {ECO:0000269|PubMed:21825077, ECO:0000269|PubMed:22735702,
CC ECO:0000269|PubMed:23874617, ECO:0000269|PubMed:25579579}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:9769101}.
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 {ECO:0000305}.
CC -!- MISCELLANEOUS: Present with 5740 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX55/SPB4
CC subfamily. {ECO:0000305}.
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DR EMBL; X16147; CAA34272.1; -; Genomic_DNA.
DR EMBL; D50617; BAA09238.1; -; Genomic_DNA.
DR EMBL; BK006940; DAA12439.1; -; Genomic_DNA.
DR PIR; S14942; S14942.
DR RefSeq; NP_116654.1; NM_001179964.1.
DR AlphaFoldDB; P25808; -.
DR SMR; P25808; -.
DR BioGRID; 31147; 681.
DR DIP; DIP-5423N; -.
DR IntAct; P25808; 36.
DR MINT; P25808; -.
DR STRING; 4932.YFL002C; -.
DR iPTMnet; P25808; -.
DR MaxQB; P25808; -.
DR PaxDb; P25808; -.
DR PRIDE; P25808; -.
DR EnsemblFungi; YFL002C_mRNA; YFL002C; YFL002C.
DR GeneID; 850549; -.
DR KEGG; sce:YFL002C; -.
DR SGD; S000001894; SPB4.
DR VEuPathDB; FungiDB:YFL002C; -.
DR eggNOG; KOG0345; Eukaryota.
DR GeneTree; ENSGT00550000074969; -.
DR HOGENOM; CLU_003041_26_4_1; -.
DR InParanoid; P25808; -.
DR OMA; DRAIHDK; -.
DR BioCyc; YEAST:G3O-30452-MON; -.
DR PRO; PR:P25808; -.
DR Proteomes; UP000002311; Chromosome VI.
DR RNAct; P25808; protein.
DR GO; GO:0030686; C:90S preribosome; IDA:SGD.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; 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:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003724; F:RNA helicase activity; ISS:SGD.
DR GO; GO:1902626; P:assembly of large subunit precursor of preribosome; IMP:SGD.
DR GO; GO:0000470; P:maturation of LSU-rRNA; IMP:SGD.
DR GO; GO:0000027; P:ribosomal large subunit assembly; 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; Coiled coil; Helicase; Hydrolase; Nucleotide-binding; Nucleus;
KW Phosphoprotein; Reference proteome; Ribosome biogenesis; RNA-binding;
KW rRNA processing.
FT CHAIN 1..606
FT /note="ATP-dependent rRNA helicase SPB4"
FT /id="PRO_0000055065"
FT DOMAIN 38..224
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 248..404
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT COILED 539..582
FT /evidence="ECO:0000255"
FT MOTIF 7..35
FT /note="Q motif"
FT /evidence="ECO:0000305"
FT MOTIF 172..175
FT /note="DEAD box"
FT /evidence="ECO:0000305"
FT BINDING 51..58
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 254
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358"
FT MUTAGEN 360
FT /note="R->G: Leads to accumulation of 35S and 27SB pre-
FT rRNAs and a net 40S ribosomal subunit defect."
FT /evidence="ECO:0000269|PubMed:21825077"
SQ SEQUENCE 606 AA; 69422 MW; B2EC8B8B5E34AA10 CRC64;
MSKSLEWDNL GFSLLPWIRT GLDVMGFETM TPVQASTIPM LAGNKDVVVD SVTGSGKTAA
FVIPVLEKVV KEEANTSKFK KAHFHSLIIA PTRELSRQIE SVVLSFLEHY PSDLFPIKCQ
LLVGTNEATV RDDVSNFLRN RPQILIGTPG RVLDFLQMPA VKTSACSMVV MDEADRLLDM
SFIKDTEKIL RLLPKQRRTG LFSATMRSAG SDIFKTGLRN PVRITVNSKN QAPSSLKLNY
CVVNPAEKLQ LLVSILNNYK FKKCIVYFPT CVSVSYFYSF IQYLGKRNIL VNEVEIFSLH
GKLQTSARTK TLTAFTDSLS NSVLFTTDVA ARGIDIPDVD LVIQLDPPTN TDMFMHRCGR
TGRANRVGKA ITFLNEGREE DFIPFMQVKN VELEELDLEV KGITTNFYED FRNWILEDRD
RFDKGVKAYV AFIKYYSNHS ATSIFRLQSL DYVGIAKLYG LFRLPRMPEI TKYLATEKQE
GIFPGNWLVD PPVNMDEYKY KDKKREKERQ ETLKNISLIN DKKKLKSELK KKNLAWSDKT
LTKERKLERK EKMSLKRKAI EEELKAEELD ENAEEERIKE DWKEIVLQNK RKKVSSKAIQ
GNFDDL
