YTM1_YEAST
ID YTM1_YEAST Reviewed; 460 AA.
AC Q12024; D6W2X2;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 194.
DE RecName: Full=Ribosome biogenesis protein YTM1 {ECO:0000255|HAMAP-Rule:MF_03029};
DE AltName: Full=Microtubule-associated protein YTM1 {ECO:0000303|Ref.1};
GN Name=YTM1 {ECO:0000255|HAMAP-Rule:MF_03029, ECO:0000303|Ref.1};
GN OrderedLocusNames=YOR272W {ECO:0000312|SGD:S000005798};
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=SM201;
RA Matsumoto S., Yahara I.;
RT "YTM1, a suppressor of beta-tubulin mutation, encodes a novel microtubule-
RT interacting protein and is essential for G1/S transition in Saccharomyces
RT cerevisiae.";
RL Submitted (APR-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8896271;
RX DOI=10.1002/(sici)1097-0061(199609)12:10b%3c1059::aid-yea994%3e3.0.co;2-7;
RA Cheret G., Bernardi A., Sor F.J.;
RT "DNA sequence analysis of the VPH1-SNF2 region on chromosome XV of
RT Saccharomyces cerevisiae.";
RL Yeast 12:1059-1064(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
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 IDENTIFICATION BY MASS SPECTROMETRY, AND IDENTIFICATION IN THE NOP7 COMPLEX
RP WITH ERB1 AND NOP7.
RX PubMed=12110181; DOI=10.1016/s0092-8674(02)00773-0;
RA Du Y.-C.N., Stillman B.;
RT "Yph1p, an ORC-interacting protein: potential links between cell
RT proliferation control, DNA replication, and ribosome biogenesis.";
RL Cell 109:835-848(2002).
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, IDENTIFICATION IN THE NOP7 COMPLEX WITH ERB1 AND NOP7,
RP ASSOCIATION OF THE NOP7 COMPLEX WITH THE 66S PRE-RIBOSOME, AND MUTAGENESIS
RP OF GLY-398 AND SER-442.
RX PubMed=16287855; DOI=10.1128/mcb.25.23.10419-10432.2005;
RA Miles T.D., Jakovljevic J., Horsey E.W., Harnpicharnchai P., Tang L.,
RA Woolford J.L. Jr.;
RT "Ytm1, Nop7, and Erb1 form a complex necessary for maturation of yeast 66S
RT preribosomes.";
RL Mol. Cell. Biol. 25:10419-10432(2005).
RN [9]
RP FUNCTION, CHARACTERIZATION OF THE NOP7 COMPLEX, AND SUBCELLULAR LOCATION.
RX PubMed=18448671; DOI=10.1091/mbc.e07-12-1281;
RA Tang L., Sahasranaman A., Jakovljevic J., Schleifman E., Woolford J.L. Jr.;
RT "Interactions among Ytm1, Erb1, and Nop7 required for assembly of the Nop7-
RT subcomplex in yeast preribosomes.";
RL Mol. Biol. Cell 19:2844-2856(2008).
RN [10]
RP IDENTIFICATION BY 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 [11]
RP FUNCTION, SUBUNIT, AND INTERACTION WITH MDN1.
RX PubMed=20542003; DOI=10.1016/j.molcel.2010.05.024;
RA Bassler J., Kallas M., Pertschy B., Ulbrich C., Thoms M., Hurt E.;
RT "The AAA-ATPase Rea1 drives removal of biogenesis factors during multiple
RT stages of 60S ribosome assembly.";
RL Mol. Cell 38:712-721(2010).
RN [12]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [13]
RP INTERACTION WITH ERB1, AND MUTAGENESIS OF ASP-104; TYR-123 AND HIS-310.
RX PubMed=26657628; DOI=10.1093/nar/gkv1365;
RA Thoms M., Ahmed Y.L., Maddi K., Hurt E., Sinning I.;
RT "Concerted removal of the Erb1-Ytm1 complex in ribosome biogenesis relies
RT on an elaborate interface.";
RL Nucleic Acids Res. 44:926-939(2016).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 5-92.
RX PubMed=26601951; DOI=10.1074/jbc.m115.693259;
RA Romes E.M., Sobhany M., Stanley R.E.;
RT "The crystal structure of the ubiquitin-like domain of ribosome assembly
RT factor Ytm1 and characterization of its interaction with the AAA-ATPase
RT Midasin.";
RL J. Biol. Chem. 291:882-893(2016).
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 ECO:0000269|PubMed:16287855, ECO:0000269|PubMed:18448671,
CC ECO:0000269|PubMed:20542003}.
CC -!- SUBUNIT: Component of the NOP7 complex, composed of ERB1, NOP7 and
CC YTM1. The complex is held together by ERB1, which interacts with NOP7
CC via its N-terminal domain and with YTM1 via a high-affinity interaction
CC between the seven-bladed beta-propeller domains of the 2 proteins. The
CC NOP7 complex associates with the 66S pre-ribosome (PubMed:12110181,
CC PubMed:16287855, PubMed:26657628). Interacts (via UBL domain) with MDN1
CC (via VWFA/MIDAS domain) (By similarity) (PubMed:20542003,
CC PubMed:26601951). {ECO:0000255|HAMAP-Rule:MF_03029,
CC ECO:0000269|PubMed:12110181, ECO:0000269|PubMed:16287855,
CC ECO:0000269|PubMed:20542003, ECO:0000269|PubMed:26601951,
CC ECO:0000269|PubMed:26657628}.
CC -!- INTERACTION:
CC Q12024; Q04660: ERB1; NbExp=12; IntAct=EBI-29589, EBI-28098;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:14562095}.
CC Nucleus, nucleoplasm {ECO:0000305|PubMed:18448671}.
CC -!- MISCELLANEOUS: Present with 6670 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the WD repeat WDR12/YTM1 family.
CC {ECO:0000255|HAMAP-Rule:MF_03029}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U92821; AAB51396.1; -; Genomic_DNA.
DR EMBL; X89633; CAA61778.1; -; Genomic_DNA.
DR EMBL; Z75180; CAA99497.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA11038.1; -; Genomic_DNA.
DR PIR; S67174; S67174.
DR RefSeq; NP_014915.3; NM_001183691.3.
DR PDB; 5DTC; X-ray; 1.70 A; A/B=5-92.
DR PDB; 6ELZ; EM; 3.30 A; p=1-460.
DR PDB; 6EM5; EM; 4.30 A; p=1-460.
DR PDB; 7OHR; EM; 4.72 A; p=1-460.
DR PDB; 7OHV; EM; 3.90 A; p=1-460.
DR PDBsum; 5DTC; -.
DR PDBsum; 6ELZ; -.
DR PDBsum; 6EM5; -.
DR PDBsum; 7OHR; -.
DR PDBsum; 7OHV; -.
DR AlphaFoldDB; Q12024; -.
DR SMR; Q12024; -.
DR BioGRID; 34661; 263.
DR ComplexPortal; CPX-1862; PeBoW complex.
DR DIP; DIP-6484N; -.
DR IntAct; Q12024; 65.
DR MINT; Q12024; -.
DR STRING; 4932.YOR272W; -.
DR iPTMnet; Q12024; -.
DR MaxQB; Q12024; -.
DR PaxDb; Q12024; -.
DR PRIDE; Q12024; -.
DR EnsemblFungi; YOR272W_mRNA; YOR272W; YOR272W.
DR GeneID; 854446; -.
DR KEGG; sce:YOR272W; -.
DR SGD; S000005798; YTM1.
DR VEuPathDB; FungiDB:YOR272W; -.
DR eggNOG; KOG0313; Eukaryota.
DR GeneTree; ENSGT00930000150950; -.
DR HOGENOM; CLU_000288_57_0_1; -.
DR InParanoid; Q12024; -.
DR OMA; VDCTRTK; -.
DR BioCyc; YEAST:G3O-33762-MON; -.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR PRO; PR:Q12024; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q12024; protein.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0070545; C:PeBoW complex; IDA:SGD.
DR GO; GO:0030687; C:preribosome, large subunit precursor; IDA:SGD.
DR GO; GO:0043021; F:ribonucleoprotein complex binding; IEA:UniProtKB-UniRule.
DR GO; GO:0051276; P:chromosome organization; IMP:SGD.
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:0110136; P:protein-RNA complex remodeling; IDA:SGD.
DR GO; GO:0042273; P:ribosomal large subunit biogenesis; IDA:ComplexPortal.
DR GO; GO:0006364; P:rRNA processing; IDA:ComplexPortal.
DR Gene3D; 2.130.10.10; -; 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; IPR001680; WD40_repeat.
DR InterPro; IPR019775; WD40_repeat_CS.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR InterPro; IPR028599; WDR12/Ytm1.
DR Pfam; PF08154; NLE; 1.
DR Pfam; PF00400; WD40; 4.
DR PRINTS; PR00320; GPROTEINBRPT.
DR SMART; SM00320; WD40; 7.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS00678; WD_REPEATS_1; 2.
DR PROSITE; PS50082; WD_REPEATS_2; 5.
DR PROSITE; PS50294; WD_REPEATS_REGION; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Nucleus; Reference proteome; Repeat; Ribosome biogenesis;
KW rRNA processing; WD repeat.
FT CHAIN 1..460
FT /note="Ribosome biogenesis protein YTM1"
FT /id="PRO_0000051466"
FT REPEAT 101..140
FT /note="WD 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03029"
FT REPEAT 142..180
FT /note="WD 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03029"
FT REPEAT 206..244
FT /note="WD 3"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03029"
FT REPEAT 285..325
FT /note="WD 4"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03029"
FT REPEAT 327..366
FT /note="WD 5"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03029"
FT REPEAT 373..413
FT /note="WD 6"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03029"
FT REPEAT 424..460
FT /note="WD 7"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03029"
FT REGION 8..89
FT /note="Ubiquitin-like (UBL) domain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03029,
FT ECO:0000305|PubMed:26601951"
FT REGION 99..460
FT /note="Sufficient for interaction with ERB1 and association
FT with 66S pre-ribosomes"
FT /evidence="ECO:0000269|PubMed:18448671,
FT ECO:0000269|PubMed:26657628"
FT MUTAGEN 104
FT /note="D->R: Weakens the interaction with ERB1, leading to
FT mostly ribosome-unbound YTM1 and defects in 60S maturation.
FT Disrupts the interaction with YTM1 and cannot sustain
FT growth; when associated with E-310."
FT /evidence="ECO:0000269|PubMed:26657628"
FT MUTAGEN 123
FT /note="Y->A: Disrupts the interaction with YTM1 and cannot
FT sustain growth; when associated with E-310."
FT /evidence="ECO:0000269|PubMed:26657628"
FT MUTAGEN 310
FT /note="H->E: Disrupts the interaction with YTM1 and cannot
FT sustain growth; when associated with R-104 or A-123."
FT /evidence="ECO:0000269|PubMed:26657628"
FT MUTAGEN 398
FT /note="G->D: In ytm1-1; abrogates binding to ERB1 and
FT impairs 27S pre-rRNA processing and 66S pre-ribosome
FT maturation; when associated with N-442."
FT /evidence="ECO:0000269|PubMed:16287855"
FT MUTAGEN 442
FT /note="S->N: In ytm1-1; abrogates binding to ERB1 and
FT impairs 27S pre-rRNA processing and 66S pre-ribosome
FT maturation; when associated with D-398."
FT /evidence="ECO:0000269|PubMed:16287855"
SQ SEQUENCE 460 AA; 51359 MW; DBC26738651433C4 CRC64;
MTEDKSQVKI RFFTREKDEL LHVQDTPMYA PISLKRYGLS EIVNHLLGSE KPVPFDFLIE
GELLRTSLHD YLTKKGLSSE ASLNVEYTRA ILPPSYLNSF SNEDWVSSLD VGDGSKHIIS
GSYDGIVRTW DLSGNVQKQY SGHSGPIRAV KYISNTRLVS AGNDRTLRLW KTKNDDLKLT
SQQQAQEDDD DEVNIEDGKT LAILEGHKAP VVSIDVSDNS RILSASYDNS IGFWSTIYKE
MTVVDPLEDI NNPNNKISTA ARKRRKLTMK DGTIRRRAPL SLLESHTAPV EQVIFDSTDN
TVGYSVSQDH TIKTWDLVTA RCIDTRTTSY SLLSIAQLST LNLLACGSSA RHITLHDPRV
GASSKVTQQQ LIGHKNFVSS LDTCPENEYI LCSGSHDGTV KVWDVRSTSP MYTITREDKS
VQKGVNDKVF AVKWAEKVGI ISAGQDKKIQ INKGDNIFKN
