NOP53_YEAST
ID NOP53_YEAST Reviewed; 455 AA.
AC Q12080; D6W3M3;
DT 26-SEP-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 169.
DE RecName: Full=Ribosome biogenesis protein NOP53 {ECO:0000305};
DE AltName: Full=Nucleolar protein 53;
GN Name=NOP53 {ECO:0000312|SGD:S000006067}; OrderedLocusNames=YPL146C;
GN ORFNames=LPI2C, P2610;
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 204511 / S288c / AB972;
RX PubMed=8948103;
RX DOI=10.1002/(sici)1097-0061(199611)12:14<1483::aid-yea34>3.0.co;2-o;
RA Purnelle B., Coster F., Goffeau A.;
RT "The sequence of 55 kb on the left arm of yeast chromosome XVI identifies a
RT small nuclear RNA, a new putative protein kinase and two new putative
RT regulators.";
RL Yeast 12:1483-1492(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
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 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 [5]
RP FUNCTION, INTERACTION WITH CBF5, FPR3, FPR4 AND NOP2, SUBCELLULAR LOCATION,
RP DISRUPTION PHENOTYPE, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=15686447; DOI=10.1042/bj20041297;
RA Sydorskyy Y., Dilworth D.J., Halloran B., Yi E.C., Makhnevych T.,
RA Wozniak R.W., Aitchison J.D.;
RT "Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein.";
RL Biochem. J. 388:819-826(2005).
RN [6]
RP FUNCTION, INTERACTION WITH PIH1, PRE-RIBOSOMAL RNAS AND 5.8S RIBOSOMAL RNA,
RP SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=16128814; DOI=10.1111/j.1742-4658.2005.04861.x;
RA Granato D.C., Gonzales F.A., Luz J.S., Cassiola F., Machado-Santelli G.M.,
RA Oliveira C.C.;
RT "Nop53p, an essential nucleolar protein that interacts with Nop17p and
RT Nip7p, is required for pre-rRNA processing in Saccharomyces cerevisiae.";
RL FEBS J. 272:4450-4463(2005).
RN [7]
RP FUNCTION, INTERACTION WITH PRE-60S RIBOSOMAL COMPLEXES, SUBCELLULAR
RP LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=16043506; DOI=10.1261/rna.2720205;
RA Thomson E., Tollervey D.;
RT "Nop53p is required for late 60S ribosome subunit maturation and nuclear
RT export in yeast.";
RL RNA 11:1215-1224(2005).
RN [8]
RP FUNCTION, INTERACTION WITH RRN3, RRP6, PAP2 AND RIBOSOMAL RNAS, SUBCELLULAR
RP LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=18631361; DOI=10.1111/j.1742-4658.2008.06565.x;
RA Granato D.C., Machado-Santelli G.M., Oliveira C.C.;
RT "Nop53p interacts with 5.8S rRNA co-transcriptionally, and regulates
RT processing of pre-rRNA by the exosome.";
RL FEBS J. 275:4164-4178(2008).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-31, 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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-31, AND IDENTIFICATION BY
RP 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: Late-acting factor in the nuclear maturation of 60S ribosomal
CC subunits, which is required for normal acquisition of export
CC competence. Required for the export of the large subunit. Acts to
CC stimulate the RNase activity of the exosome complex, and may recruit
CC the exosome to 7S pre-rRNA for processing. Associates with numerous
CC RNAs including the 27S and 7S pre-rRNAs and the box H/ACA snoRNA snR37.
CC Also interacts (via N-terminal region) with the mature 25S rRNA and the
CC mature 5.8S rRNA. {ECO:0000269|PubMed:15686447,
CC ECO:0000269|PubMed:16043506, ECO:0000269|PubMed:16128814,
CC ECO:0000269|PubMed:18631361}.
CC -!- SUBUNIT: Interacts with CBF5, FPR3, FPR4, NOP2, PIH1, RRN3, RRP6 and
CC PAP2. Interacts with pre-60S ribosomal particles.
CC {ECO:0000269|PubMed:15686447, ECO:0000269|PubMed:16043506,
CC ECO:0000269|PubMed:16128814, ECO:0000269|PubMed:18631361}.
CC -!- INTERACTION:
CC Q12080; Q03862: ARX1; NbExp=3; IntAct=EBI-29395, EBI-31385;
CC Q12080; P38911: FPR3; NbExp=3; IntAct=EBI-29395, EBI-6951;
CC Q12080; P43586: LOC1; NbExp=3; IntAct=EBI-29395, EBI-22906;
CC Q12080; P25582: SPB1; NbExp=3; IntAct=EBI-29395, EBI-17814;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:15686447,
CC ECO:0000269|PubMed:16043506, ECO:0000269|PubMed:16128814}. Nucleus,
CC nucleoplasm {ECO:0000269|PubMed:16043506}. Note=Does not shuttle from
CC the nucleus to the cytoplasm (PubMed:16043506).
CC {ECO:0000269|PubMed:16043506}.
CC -!- DISRUPTION PHENOTYPE: Inhibition of cell growth. Defects in processing
CC of the rRNA components of the 60S ribosomal subunit and accumulation of
CC the corresponding polyadenylated pre-rRNAs. Some delay in the
CC maturation of the 35S primary transcript and 32S pre-rRNA. Delay in 20S
CC pre-rRNA formation and a severe delay in mature 25S and 5.8S rRNA
CC formation, with accumulation of the 35S, 32S, 27S, 26S and 7S pre-rRNAs
CC and a 5' extended form of the 25S rRNA. Complete loss of synthesis of
CC the mature 25S rRNA. Appearance at a low level of aberrant 23S species.
CC Shorter 18S and 5.8S rRNA at the 5' end. Imbalance in the 40S:60S ratio
CC and defects in progression beyond the 27S stage of 25S rRNA maturation
CC during 60S biogenesis. Decreased ribosomes and polysomes and presence
CC of halfmers. {ECO:0000269|PubMed:15686447, ECO:0000269|PubMed:16043506,
CC ECO:0000269|PubMed:16128814, ECO:0000269|PubMed:18631361}.
CC -!- MISCELLANEOUS: Present with 1600 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the NOP53 family. {ECO:0000305}.
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DR EMBL; U43703; AAB68216.1; -; Genomic_DNA.
DR EMBL; X96770; CAA65547.1; -; Genomic_DNA.
DR EMBL; Z73502; CAA97850.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11289.1; -; Genomic_DNA.
DR PIR; S65157; S65157.
DR RefSeq; NP_015179.1; NM_001183960.1.
DR PDB; 3JCT; EM; 3.08 A; q=1-455.
DR PDB; 5OOQ; X-ray; 3.20 A; C/D=59-91.
DR PDB; 6M62; EM; 3.20 A; q=1-455.
DR PDB; 6YLX; EM; 3.90 A; q=1-455.
DR PDB; 6YLY; EM; 3.80 A; q=1-455.
DR PDB; 7BTB; EM; 3.22 A; q=1-455.
DR PDB; 7OHQ; EM; 3.10 A; q=1-455.
DR PDBsum; 3JCT; -.
DR PDBsum; 5OOQ; -.
DR PDBsum; 6M62; -.
DR PDBsum; 6YLX; -.
DR PDBsum; 6YLY; -.
DR PDBsum; 7BTB; -.
DR PDBsum; 7OHQ; -.
DR AlphaFoldDB; Q12080; -.
DR SMR; Q12080; -.
DR BioGRID; 36037; 347.
DR DIP; DIP-993N; -.
DR IntAct; Q12080; 17.
DR MINT; Q12080; -.
DR STRING; 4932.YPL146C; -.
DR iPTMnet; Q12080; -.
DR MaxQB; Q12080; -.
DR PaxDb; Q12080; -.
DR PRIDE; Q12080; -.
DR EnsemblFungi; YPL146C_mRNA; YPL146C; YPL146C.
DR GeneID; 855957; -.
DR KEGG; sce:YPL146C; -.
DR SGD; S000006067; NOP53.
DR VEuPathDB; FungiDB:YPL146C; -.
DR eggNOG; KOG2823; Eukaryota.
DR GeneTree; ENSGT00390000017267; -.
DR HOGENOM; CLU_035888_1_1_1; -.
DR InParanoid; Q12080; -.
DR OMA; WRKTDIQ; -.
DR BioCyc; YEAST:G3O-34043-MON; -.
DR PRO; PR:Q12080; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q12080; protein.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); IMP:SGD.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0008097; F:5S rRNA binding; IBA:GO_Central.
DR GO; GO:0019843; F:rRNA binding; IDA:SGD.
DR GO; GO:0000460; P:maturation of 5.8S rRNA; IMP:CACAO.
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:0000027; P:ribosomal large subunit assembly; ISS:UniProtKB.
DR GO; GO:0000055; P:ribosomal large subunit export from nucleus; IMP:SGD.
DR GO; GO:0006364; P:rRNA processing; IMP:SGD.
DR InterPro; IPR011687; Nop53/GLTSCR2.
DR PANTHER; PTHR14211; PTHR14211; 1.
DR Pfam; PF07767; Nop53; 1.
DR PIRSF; PIRSF017302; Gltscr2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Nucleus; Phosphoprotein; Reference proteome;
KW Ribosome biogenesis; RNA-binding; rRNA processing.
FT CHAIN 1..455
FT /note="Ribosome biogenesis protein NOP53"
FT /id="PRO_0000218965"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 264..333
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 271..294
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 31
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956,
FT ECO:0007744|PubMed:19779198"
FT STRAND 61..63
FT /evidence="ECO:0007829|PDB:5OOQ"
SQ SEQUENCE 455 AA; 52556 MW; 9B761BB0318EFFC8 CRC64;
MAPTNLTKKP SQYKQSSRKG KKAWRKNIDL SDVEQYMEKK IDHEITHGTS DITSLQNDAL
FHVDVEGDEI LKNKLIKRKQ IKKVLKSKEI LDAVKTNSKI AALNHHKNSS GNPNKIQGVS
KHELKKLMAL AGRVHGESKI KNRVAKDGLV KTTAGDLWGE ESNSKKQKVK LPSGIKLDVE
KKDQIPEELL KKSTTSWSTA SVRPSTLDIE PIAVKEFTEI PHAGKSYNPN NKAWSELINK
EYKEEKARED ERIALEKYKE RIRHLMETLD DNEEEESSSN EEEEEEEEEN ENENESTQCS
GSDKEIKLSI NKPVKNKKKT KYQRNKAKRH EEKVKLQQEL KELRQRVKDL EEVINSEETE
ILSAIESDSN KVKKSKKNKK HKLGTKYSVI DERLEIKFSD ELSDSLRKLK PEGNLLYDTV
RKLQSSGKVE TRVPVRKGRK YKQKITEKWT HKDFK
