ID YTM1_SCHPO Reviewed; 440 AA.
AC Q9URY0;
DT 24-MAY-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 27-MAR-2024, entry version 141.
DE RecName: Full=Ribosome biogenesis protein ytm1 {ECO:0000255|HAMAP-Rule:MF_03029};
GN Name=ytm1; ORFNames=SPAC890.04c;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=972 / ATCC 24843;
RA Matsumoto S.;
RT "Schizosaccharomyces pombe homolog of the Saccharomyces cerevisiae YTM1.";
RL Submitted (FEB-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [3]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-140 AND SER-242, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=18257517; DOI=10.1021/pr7006335;
RA Wilson-Grady J.T., Villen J., Gygi S.P.;
RT "Phosphoproteome analysis of fission yeast.";
RL J. Proteome Res. 7:1088-1097(2008).
CC -!- FUNCTION: Component of the NOP7 complex, which is required for
CC maturation of the 25S and 5.8S ribosomal RNAs and formation of the 60S
CC ribosome. {ECO:0000255|HAMAP-Rule:MF_03029}.
CC -!- SUBUNIT: Component of the NOP7 complex, composed of erb1, ppp1/nop7 and
CC ytm1. The complex is held together by erb1, which interacts with
CC ppp1/nop7 via its N-terminal domain and with ytm1 via a high-affinity
CC interaction between the seven-bladed beta-propeller domains of the 2
CC proteins. The NOP7 complex associates with the 66S pre-ribosome.
CC Interacts (via UBL domain) with mdn1 (via VWFA/MIDAS domain).
CC {ECO:0000255|HAMAP-Rule:MF_03029}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000255|HAMAP-
CC Rule:MF_03029}. Nucleus, nucleoplasm {ECO:0000255|HAMAP-Rule:MF_03029}.
CC -!- SIMILARITY: Belongs to the WD repeat WDR12/YTM1 family.
CC {ECO:0000255|HAMAP-Rule:MF_03029}.
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DR EMBL; AF237708; AAF40218.1; -; mRNA.
DR EMBL; CU329670; CAB63495.1; -; Genomic_DNA.
DR PIR; T50260; T50260.
DR RefSeq; NP_594822.1; NM_001020251.2.
DR PDB; 8ESQ; EM; 2.80 A; p=1-440.
DR PDB; 8ESR; EM; 3.20 A; p=1-440.
DR PDB; 8ETG; EM; 3.40 A; p=1-440.
DR PDB; 8EUG; EM; 2.80 A; p=1-440.
DR PDB; 8EUI; EM; 3.10 A; p=1-440.
DR PDBsum; 8ESQ; -.
DR PDBsum; 8ESR; -.
DR PDBsum; 8ETG; -.
DR PDBsum; 8EUG; -.
DR PDBsum; 8EUI; -.
DR AlphaFoldDB; Q9URY0; -.
DR SMR; Q9URY0; -.
DR BioGRID; 279966; 8.
DR STRING; 284812.Q9URY0; -.
DR iPTMnet; Q9URY0; -.
DR MaxQB; Q9URY0; -.
DR PaxDb; 4896-SPAC890-04c-1; -.
DR EnsemblFungi; SPAC890.04c.1; SPAC890.04c.1:pep; SPAC890.04c.
DR GeneID; 2543549; -.
DR KEGG; spo:SPAC890.04c; -.
DR PomBase; SPAC890.04c; ytm1.
DR VEuPathDB; FungiDB:SPAC890.04c; -.
DR eggNOG; KOG0313; Eukaryota.
DR HOGENOM; CLU_000288_57_0_1; -.
DR InParanoid; Q9URY0; -.
DR OMA; YMAPQPE; -.
DR PhylomeDB; Q9URY0; -.
DR Reactome; R-SPO-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR Reactome; R-SPO-983168; Antigen processing: Ubiquitination & Proteasome degradation.
DR PRO; PR:Q9URY0; -.
DR Proteomes; UP000002485; Chromosome I.
DR GO; GO:0000785; C:chromatin; HDA:PomBase.
DR GO; GO:0005730; C:nucleolus; IDA:PomBase.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; HDA:PomBase.
DR GO; GO:0070545; C:PeBoW complex; IBA:GO_Central.
DR GO; GO:0030687; C:preribosome, large subunit precursor; IBA:GO_Central.
DR GO; GO:0043021; F:ribonucleoprotein complex binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000466; P:maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IEA:UniProtKB-UniRule.
DR GO; GO:0000463; P:maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IEA:UniProtKB-UniRule.
DR GO; GO:0042273; P:ribosomal large subunit biogenesis; IBA:GO_Central.
DR Gene3D; 2.130.10.10; YVTN repeat-like/Quinoprotein amine dehydrogenase; 1.
DR HAMAP; MF_03029; WDR12; 1.
DR InterPro; IPR020472; G-protein_beta_WD-40_rep.
DR InterPro; IPR012972; NLE.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR019775; WD40_repeat_CS.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR InterPro; IPR001680; WD40_rpt.
DR InterPro; IPR028599; WDR12/Ytm1.
DR PANTHER; PTHR19855:SF11; RIBOSOME BIOGENESIS PROTEIN WDR12; 1.
DR PANTHER; PTHR19855; WD40 REPEAT PROTEIN 12, 37; 1.
DR Pfam; PF08154; NLE; 1.
DR Pfam; PF00400; WD40; 4.
DR PRINTS; PR00320; GPROTEINBRPT.
DR SMART; SM00320; WD40; 7.
DR SUPFAM; SSF50978; WD40 repeat-like; 1.
DR PROSITE; PS00678; WD_REPEATS_1; 1.
DR PROSITE; PS50082; WD_REPEATS_2; 4.
DR PROSITE; PS50294; WD_REPEATS_REGION; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Nucleus; Phosphoprotein; Reference proteome; Repeat;
KW Ribosome biogenesis; rRNA processing; WD repeat.
FT CHAIN 1..440
FT /note="Ribosome biogenesis protein ytm1"
FT /id="PRO_0000051465"
FT REPEAT 102..139
FT /note="WD 1"
FT REPEAT 141..180
FT /note="WD 2"
FT REPEAT 195..234
FT /note="WD 3"
FT REPEAT 267..306
FT /note="WD 4"
FT REPEAT 308..347
FT /note="WD 5"
FT REPEAT 353..393
FT /note="WD 6"
FT REPEAT 403..440
FT /note="WD 7"
FT REGION 11..90
FT /note="Ubiquitin-like (UBL) domain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03029"
FT MOD_RES 140
FT /note="Phosphothreonine"
FT /evidence="ECO:0000269|PubMed:18257517"
FT MOD_RES 242
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18257517"
FT STRAND 96..102
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 107..112
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 117..121
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 126..129
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 131..133
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 135..138
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 146..153
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 156..162
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 165..171
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 188..194
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 207..215
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 219..229
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 262..266
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 272..277
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 283..288
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 291..297
FT /evidence="ECO:0007829|PDB:8ETG"
FT TURN 298..300
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 302..308
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 313..319
FT /evidence="ECO:0007829|PDB:8ETG"
FT TURN 320..323
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 324..329
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 332..337
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 348..352
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 358..363
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 370..375
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 378..386
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 392..396
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 408..414
FT /evidence="ECO:0007829|PDB:8ETG"
FT TURN 415..417
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 418..423
FT /evidence="ECO:0007829|PDB:8ETG"
FT STRAND 427..432
FT /evidence="ECO:0007829|PDB:8ETG"
SQ SEQUENCE 440 AA; 48334 MW; 825FDB62CDAFA1D8 CRC64;
MDAQSAPSGQ VQVRFTTRNE DLAVGDTPIF VPTSLKRYGL SQIVNHLLKT EKPTPFDFLV
QGQLLKTTLD EYIVQNGLST ESILDIEYIQ STLPPAYLAS FSHDDWISGI QLTSDTILTS
SYDGIARVWD KSGEIKFQST GCGSSLKSAS WHIPNQSFLT ASLDQKIFHW VIEEPESMLD
AEKKSSGILQ TLFVGHKDIV ERVRSLESSS VFISASADNT VGIWDFERSP ETTLESFSSS
ISKKRRRKNA EFTPQAGARS PLILCEGHTG PVMDIVFSDD PSVAYSVGQD HTIKTWDLIT
GQNVDSKITK APLLCVEKLT DLHLVICGSS ARHIVVHDPR AGSDKIVSHT LSGHKNLVSG
LSASPENPYM FASVSHDNTC RVWDVRATSG SIYTISRAEK TGSQWDKLFA VDWNKSIGIV
TGGTDKQLQI NQSSSFGKSE
//
