MYTM1_ARATH
ID MYTM1_ARATH Reviewed; 840 AA.
AC F4J3T8; Q84W79; Q9CAF1; Q9LPP2;
DT 22-JAN-2014, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 75.
DE RecName: Full=Phosphatidylinositol-3-phosphatase myotubularin-1;
DE Short=AtMTM1;
DE AltName: Full=Phosphatidylinositol-3,5-bisphosphate 3-phosphatase;
DE EC=3.1.3.95 {ECO:0000269|PubMed:19901554, ECO:0000269|PubMed:22324391, ECO:0000305|PubMed:20967218};
DE AltName: Full=Phosphatidylinositol-3-phosphate phosphatase;
DE EC=3.1.3.64 {ECO:0000269|PubMed:19901554, ECO:0000269|PubMed:22324391};
GN Name=MTM1; OrderedLocusNames=At3g10550; ORFNames=F13M14.17, F18K10.13;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP GENE FAMILY.
RX PubMed=12068129; DOI=10.1104/pp.004002;
RA Kerk D., Bulgrien J., Smith D.W., Barsam B., Veretnik S., Gribskov M.;
RT "The complement of protein phosphatase catalytic subunits encoded in the
RT genome of Arabidopsis.";
RL Plant Physiol. 129:908-925(2002).
RN [5]
RP GENE FAMILY.
RX PubMed=18201690; DOI=10.1016/j.ydbio.2007.11.031;
RA Jiang S.Y., Ramamoorthy R., Ramachandran S.;
RT "Comparative transcriptional profiling and evolutionary analysis of the
RT GRAM domain family in eukaryotes.";
RL Dev. Biol. 314:418-432(2008).
RN [6]
RP INDUCTION BY DEHYDRATION, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP CATALYTIC ACTIVITY.
RX PubMed=19901554; DOI=10.4161/psb.4.11.10103;
RA Ding Y., Lapko H., Ndamukong I., Xia Y., Al-Abdallat A., Lalithambika S.,
RA Sadder M., Saleh A., Fromm M., Riethoven J.-J., Lu G., Avramova Z.;
RT "The Arabidopsis chromatin modifier ATX1, the myotubularin-like AtMTM and
RT the response to drought.";
RL Plant Signal. Behav. 4:1049-1058(2009).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, AND CATALYTIC ACTIVITY.
RX PubMed=20967218; DOI=10.1371/journal.pone.0013396;
RA Ndamukong I., Jones D.R., Lapko H., Divecha N., Avramova Z.;
RT "Phosphatidylinositol 5-phosphate links dehydration stress to the activity
RT of ARABIDOPSIS TRITHORAX-LIKE factor ATX1.";
RL PLoS ONE 5:E13396-E13396(2010).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY,
RP DEVELOPMENTAL STAGE, TISSUE SPECIFICITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=cv. Columbia;
RX PubMed=22324391; DOI=10.1111/j.1365-313x.2012.04936.x;
RA Ding Y., Ndamukong I., Zhao Y., Xia Y., Riethoven J.-J., Jones D.R.,
RA Divecha N., Avramova Z.;
RT "Divergent functions of the myotubularin (MTM) homologs AtMTM1 and AtMTM2
RT in Arabidopsis thaliana: evolution of the plant MTM family.";
RL Plant J. 70:866-878(2012).
CC -!- FUNCTION: Phosphatase with phosphoinositide 3'-phosphatase activity
CC that can use phosphatidylinositol-3-phosphate (PtdIns3P) and
CC phosphatidylinositol-3,5-diphosphate (PtdIns3,5P(2)) as substrates and
CC produces phosphatidylinositol-5-phosphate (PtdIns5P); participates in
CC pathway(s) that transfer gene regulatory signals to the nucleus.
CC Required for recovery after water deprivation, via the accumulation of
CC PtdIns5P upon dehydration; high PtdIns5P levels mediate ATX1
CC cytoplasmic localization, thus down-regulating the expression of ATX1-
CC dependent genes. Confers sensitivity to soil-water-deficit stress.
CC {ECO:0000269|PubMed:19901554, ECO:0000269|PubMed:20967218,
CC ECO:0000269|PubMed:22324391}.
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:19901554, ECO:0000269|PubMed:20967218,
CC ECO:0000269|PubMed:22324391};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3,5-
CC bisphosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-
CC inositol-5-phosphate) + phosphate; Xref=Rhea:RHEA:39019,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, ChEBI:CHEBI:57795,
CC ChEBI:CHEBI:57923; EC=3.1.3.95;
CC Evidence={ECO:0000269|PubMed:19901554, ECO:0000269|PubMed:22324391,
CC ECO:0000305|PubMed:20967218};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=201.7 uM for PtdIns3P {ECO:0000269|PubMed:19901554,
CC ECO:0000269|PubMed:22324391};
CC KM=146 uM for PtdIns3,5P(2) {ECO:0000269|PubMed:19901554,
CC ECO:0000269|PubMed:22324391};
CC Vmax=94.3 pmol/min/mg enzyme with PtdIns3P as substrate
CC {ECO:0000269|PubMed:19901554, ECO:0000269|PubMed:22324391};
CC Vmax=142.6 pmol/min/mg enzyme with PtdIns3,5P(2) as substrate
CC {ECO:0000269|PubMed:19901554, ECO:0000269|PubMed:22324391};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:22324391}. Endosome
CC membrane {ECO:0000269|PubMed:22324391}; Peripheral membrane protein
CC {ECO:0000269|PubMed:22324391}. Note=Present in granular particles of
CC varying abundance and size at the cell periphery and throughout the
CC cytoplasm.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=F4J3T8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4J3T8-2; Sequence=VSP_053569, VSP_053570;
CC -!- TISSUE SPECIFICITY: Mostly expressed in siliques and leaves (including
CC hydathodes), and, to a lower extent, in flowers and roots.
CC {ECO:0000269|PubMed:22324391}.
CC -!- DEVELOPMENTAL STAGE: Expressed in young seedlings, especially at the
CC tip of the growing shoot meristems. Later observed in roots and in
CC aerial parts. Weakly expressed in leaves with local higher levels in
CC the trichomes, hydathodes and in cotyledon veins. Present at low levels
CC in flowers with higher accumulation in cells at organ-stem junctions,
CC as well as in the septum and the funiculi of the developing siliques.
CC Also observed in a diffuse pattern, appearing as patches along the stem
CC but also concentrated at the peduncle. {ECO:0000269|PubMed:22324391}.
CC -!- INDUCTION: Accumulates upon dehydration. {ECO:0000269|PubMed:19901554}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype in normal conditions.
CC Impaired accumulation of PtdIns5P in response to stress such as
CC dehydration, leading to an increased resistance.
CC {ECO:0000269|PubMed:20967218, ECO:0000269|PubMed:22324391}.
CC -!- SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Non-
CC receptor class myotubularin subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF76357.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAG51396.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC011560; AAG51396.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC013428; AAF76357.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE74924.1; -; Genomic_DNA.
DR EMBL; BT004136; AAO42157.1; -; mRNA.
DR RefSeq; NP_187666.5; NM_111891.7. [F4J3T8-1]
DR AlphaFoldDB; F4J3T8; -.
DR SMR; F4J3T8; -.
DR STRING; 3702.AT3G10550.1; -.
DR iPTMnet; F4J3T8; -.
DR PaxDb; F4J3T8; -.
DR PRIDE; F4J3T8; -.
DR ProteomicsDB; 251190; -. [F4J3T8-1]
DR EnsemblPlants; AT3G10550.1; AT3G10550.1; AT3G10550. [F4J3T8-1]
DR GeneID; 820220; -.
DR Gramene; AT3G10550.1; AT3G10550.1; AT3G10550. [F4J3T8-1]
DR KEGG; ath:AT3G10550; -.
DR Araport; AT3G10550; -.
DR TAIR; locus:2075850; AT3G10550.
DR eggNOG; KOG4471; Eukaryota.
DR HOGENOM; CLU_017601_0_0_1; -.
DR InParanoid; F4J3T8; -.
DR OMA; VISWCDP; -.
DR PRO; PR:F4J3T8; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; F4J3T8; baseline and differential.
DR Genevisible; F4J3T8; AT.
DR GO; GO:0031410; C:cytoplasmic vesicle; IDA:UniProtKB.
DR GO; GO:0010008; C:endosome membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0052629; F:phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity; IDA:UniProtKB.
DR GO; GO:0004438; F:phosphatidylinositol-3-phosphatase activity; IDA:UniProtKB.
DR GO; GO:0004721; F:phosphoprotein phosphatase activity; IEA:UniProtKB-KW.
DR GO; GO:0042631; P:cellular response to water deprivation; IEP:UniProtKB.
DR GO; GO:0035556; P:intracellular signal transduction; IMP:UniProtKB.
DR GO; GO:0046856; P:phosphatidylinositol dephosphorylation; IBA:GO_Central.
DR GO; GO:2000070; P:regulation of response to water deprivation; IMP:UniProtKB.
DR Gene3D; 2.30.29.30; -; 1.
DR InterPro; IPR004182; GRAM.
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 SMART; SM00568; GRAM; 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 Alternative splicing; Coiled coil; Cytoplasm; Endosome; Hydrolase;
KW Lipid metabolism; Membrane; Protein phosphatase; Reference proteome.
FT CHAIN 1..840
FT /note="Phosphatidylinositol-3-phosphatase myotubularin-1"
FT /id="PRO_0000425083"
FT DOMAIN 45..112
FT /note="GRAM"
FT DOMAIN 199..650
FT /note="Myotubularin phosphatase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00669"
FT REGION 1..28
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 506..535
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 745..771
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 666..734
FT /evidence="ECO:0000255"
FT COMPBIAS 745..765
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 443
FT /note="Phosphocysteine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10044"
FT BINDING 332..335
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 357..358
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 443..449
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 489
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT VAR_SEQ 474..503
FT /note="LVEKDWLAFGHPFSDRVGMPNISGSGNFDF -> VFVCWKFPFISCASVFRI
FT SSLTIFKLFPWA (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_053569"
FT VAR_SEQ 504..840
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_053570"
FT CONFLICT 356
FT /note="D -> G (in Ref. 3; AAO42157)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 840 AA; 93378 MW; FFB4E238942B3C66 CRC64;
MTPPRPPSGR VRSLRDYSSE SEKMDGTGSW DTLEWTKLDS TSGSGSFSNL SCLLESERVI
VEGYGVVLIN TDEAGTLLVT NFRILFLSEG TRKVIPLGTI PLATIEKFNK MVLKVQSSPR
QSDKIPPRRL LQVTGKDMRI IVYGFRPRTK QRRNVFDALL KCTKPERVWD LYTFACGPSK
FGNANPKERL LNEYFRLLGK SSIRASMDMI EDGAFTLSNE LWRISDLNSN YNLCQTYPFA
FMIPKSISDA ELLQACSFRA RCRLPVITWC QPGSGAVIAR SSQPLVGLMM NMRSNLDEKL
VAAFCSQLPG AKGERRKLYI ADARPRKNAL ANGAMGGGSE SSSNYFQSEI VFFGIDNIHA
MRESFSRVRD YLDMHGTTSS DGRSSFLRHG GWTWGGGNLS SMSASVSLLG DSGWLIHIQS
VLAGAAWIAA RVAMESASVL VHCSDGWDRT TQLVSLACLL LDPYYRTFAG FQALVEKDWL
AFGHPFSDRV GMPNISGSGN FDFPRQSSSA GSFPSSPVRQ SSGSAASQSS SSSHGHNNYS
PIFMQWIDSV SQLMRMYPCA FEFSPTFLVD FMDCLLSCRF GNFLCNSEKE REQCGIADAC
GCLWAYLTDL RSFSATSHVH CNPFYDPLKY DGPLLPPAAS LAPTLWPQFH LRWACPEEAK
AADIGVQCRA MTVKYSEMQK EKEAAERRVD EISFAMESLS AELLRERHLS WVARESANRA
TKEYAALTRA VQSLGCKINF TTSDVEDDPR SSLENNPRRR NRHGNNSDVS VSISLMPEEN
TSGNPKGRVC EALCPLRTRE GVCRWPEVGC AHVGSQFVGL KANFDAFDRL AIYDSYFQPK
