YMR1_YEAST
ID YMR1_YEAST Reviewed; 688 AA.
AC P47147; D6VWS9; Q12388;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1996, sequence version 1.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=Phosphoinositide 3-phosphatase {ECO:0000303|PubMed:10900271};
DE EC=3.1.3.64 {ECO:0000269|PubMed:10900271};
DE AltName: Full=Yeast myotubularin-related protein 1 {ECO:0000303|PubMed:10900271};
GN Name=YMR1 {ECO:0000303|PubMed:10900271}; OrderedLocusNames=YJR110W;
GN ORFNames=J2007;
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=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL EMBO J. 15:2031-2049(1996).
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] OF 1-88.
RX PubMed=2689869; DOI=10.1128/mcb.9.11.4882-4888.1989;
RA Kinney D.M., Lusty C.J.;
RT "Arginine restriction induced by delta-N-(phosphonacetyl)-L-ornithine
RT signals increased expression of HIS3, TRP5, CPA1, and CPA2 in Saccharomyces
RT cerevisiae.";
RL Mol. Cell. Biol. 9:4882-4888(1989).
RN [4]
RP FUNCTION, DISRUPTION PHENOTYPE, AND CATALYTIC ACTIVITY.
RX PubMed=10900271; DOI=10.1073/pnas.160255697;
RA Taylor G.S., Maehama T., Dixon J.E.;
RT "Myotubularin, a protein tyrosine phosphatase mutated in myotubular
RT myopathy, dephosphorylates the lipid second messenger, phosphatidylinositol
RT 3-phosphate.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:8910-8915(2000).
RN [5]
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 [6]
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 [7]
RP FUNCTION.
RX PubMed=15169871; DOI=10.1091/mbc.e04-03-0209;
RA Parrish W.R., Stefan C.J., Emr S.D.;
RT "Essential role for the myotubularin-related phosphatase Ymr1p and the
RT synaptojanin-like phosphatases Sjl2p and Sjl3p in regulation of
RT phosphatidylinositol 3-phosphate in yeast.";
RL Mol. Biol. Cell 15:3567-3579(2004).
CC -!- FUNCTION: Lipid phosphatase which dephosphorylates phosphatidylinositol
CC 3-monophosphate (PI3P). Involved in the control of PI3P-dependent
CC signaling and in the maintenance of endosomal system integrity.
CC {ECO:0000269|PubMed:10900271, ECO:0000269|PubMed:15169871}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-
CC phosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-
CC inositol) + phosphate; Xref=Rhea:RHEA:12316, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57880, ChEBI:CHEBI:58088; EC=3.1.3.64;
CC Evidence={ECO:0000269|PubMed:10900271};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
CC -!- DISRUPTION PHENOTYPE: Exhibits increased phosphatidylinositol 3-
CC monophosphate (PI3P) level. {ECO:0000269|PubMed:10900271}.
CC -!- MISCELLANEOUS: Present with 1080 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Non-
CC receptor class myotubularin subfamily. {ECO:0000305}.
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DR EMBL; Z49610; CAA89640.1; -; Genomic_DNA.
DR EMBL; M30466; AAA66903.1; -; Genomic_DNA.
DR EMBL; K01178; AAA66901.1; -; Genomic_DNA.
DR EMBL; BK006943; DAA08895.1; -; Genomic_DNA.
DR PIR; S57131; S57131.
DR RefSeq; NP_012644.1; NM_001181768.1.
DR AlphaFoldDB; P47147; -.
DR SMR; P47147; -.
DR BioGRID; 33866; 69.
DR DIP; DIP-5260N; -.
DR IntAct; P47147; 15.
DR MINT; P47147; -.
DR STRING; 4932.YJR110W; -.
DR iPTMnet; P47147; -.
DR MaxQB; P47147; -.
DR PaxDb; P47147; -.
DR PRIDE; P47147; -.
DR EnsemblFungi; YJR110W_mRNA; YJR110W; YJR110W.
DR GeneID; 853574; -.
DR KEGG; sce:YJR110W; -.
DR SGD; S000003871; YMR1.
DR VEuPathDB; FungiDB:YJR110W; -.
DR eggNOG; KOG1089; Eukaryota.
DR GeneTree; ENSGT00940000172348; -.
DR HOGENOM; CLU_001839_5_1_1; -.
DR InParanoid; P47147; -.
DR OMA; EKWFQIE; -.
DR BioCyc; YEAST:MON3O-76; -.
DR Reactome; R-SCE-1483248; Synthesis of PIPs at the ER membrane.
DR Reactome; R-SCE-1632852; Macroautophagy.
DR Reactome; R-SCE-1660499; Synthesis of PIPs at the plasma membrane.
DR Reactome; R-SCE-1660516; Synthesis of PIPs at the early endosome membrane.
DR Reactome; R-SCE-1660517; Synthesis of PIPs at the late endosome membrane.
DR PRO; PR:P47147; -.
DR Proteomes; UP000002311; Chromosome X.
DR RNAct; P47147; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0003729; F:mRNA binding; IDA:SGD.
DR GO; GO:0004438; F:phosphatidylinositol-3-phosphatase activity; IMP:UniProtKB.
DR GO; GO:0046856; P:phosphatidylinositol dephosphorylation; IMP:UniProtKB.
DR Gene3D; 2.30.29.30; -; 1.
DR InterPro; IPR010569; Myotubularin-like_Pase_dom.
DR InterPro; IPR030564; Myotubularin_fam.
DR InterPro; IPR011993; PH-like_dom_sf.
DR InterPro; IPR029021; Prot-tyrosine_phosphatase-like.
DR InterPro; IPR016130; Tyr_Pase_AS.
DR PANTHER; PTHR10807; PTHR10807; 1.
DR Pfam; PF06602; Myotub-related; 1.
DR SUPFAM; SSF52799; SSF52799; 1.
DR PROSITE; PS51339; PPASE_MYOTUBULARIN; 1.
DR PROSITE; PS00383; TYR_PHOSPHATASE_1; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Hydrolase; Reference proteome.
FT CHAIN 1..688
FT /note="Phosphoinositide 3-phosphatase"
FT /id="PRO_0000094948"
FT DOMAIN 155..637
FT /note="Myotubularin phosphatase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00669"
FT REGION 647..672
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 647..669
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 397
FT /note="Phosphocysteine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10044"
FT CONFLICT 85
FT /note="Q -> H (in Ref. 3; AAA66903/AAA66901)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 688 AA; 80152 MW; A097F4B98B626C01 CRC64;
MEYIKIAKVS NVVLHRRGTA TQGTLHLTTH HLIFESPQLS TEFWFPYPLI YGVHKNPGST
LLSKLTSTNQ IQLEGTDSQN YKLYQGKDLW SFVNIKVIGK DYAVFSLDFG GDLHLQARKV
YDSILNLTVL SNITQLYAFI YISNNLERKL PSPDSWDIYD PIKEFRRQGL DSKDETCPWR
LSTVNEHYEF CPTYPSKLFV PRSTSDILLK HASKFRSQKR IPVLTYHHKA TDCNILRSSQ
PLPGLINQRS IQDEKLVWES FNSFCNKDIR RTKHVIVDAR PRTNALAQMA LGGGTENMDN
YNFFLADNNM GVDKSLKLPT VTRLFLGIDN IHIVSNTAAY MTEVICQGGD LNLPLEQNLI
RSQKFSNWLK LNTLILKSVD MLLKSIIFNH SNVLVHCSDG WDRTSQVVSL LEICLDPFYR
TFEGFMILVE KDWCSFGHRF LERSGHLNSD IRFHDNTMHS NFNDVDTNGD DLDIGVNTQD
DYAEDDEGGE DETNLINLSR ISKKFNENFK LNKKSLKFVS PVFQQFLDCV YQLLTQNPDL
FEFNERFLRR LVYHLYSCQY GTFLSNSEKE KFQQNLPNKT KSVWDYFRSR RKQFINPNFI
QRKRSGMNEH DQNLEEEEKV EWISPDLKKV QWWWQLYGRK DSEMNDELRH KRDSVPISVD
KKSKEHSNSD GGKGLNLSIF GFDMFNRK
