ID   TPMT1_ARATH             Reviewed;         337 AA.
AC   Q9ZQP1; Q8VZ64; Q940J5;
DT   16-MAY-2012, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2002, sequence version 2.
DT   24-JAN-2024, entry version 141.
DE   RecName: Full=Phosphatidylglycerophosphate phosphatase PTPMT1 {ECO:0000303|PubMed:29476828};
DE            EC=3.1.3.27 {ECO:0000305|PubMed:29476828};
DE   AltName: Full=Protein TYROSINE PHOSPHATASE LOCALIZED TO THE MITOCHONDRION 1 {ECO:0000303|PubMed:29476828};
DE   AltName: Full=Putative dual specificity protein phosphatase DSP8 {ECO:0000303|Ref.1};
DE            EC=3.1.3.16 {ECO:0000250|UniProtKB:P0C089};
DE            EC=3.1.3.48 {ECO:0000255|PROSITE-ProRule:PRU10044};
GN   Name=PTPMT1 {ECO:0000303|PubMed:29476828};
GN   Synonyms=DSP8 {ECO:0000303|Ref.1};
GN   OrderedLocusNames=At2g35680 {ECO:0000312|Araport:AT2G35680};
GN   ORFNames=T20F21.13 {ECO:0000312|EMBL:AAD15447.2};
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 [MRNA].
RC   STRAIN=cv. Columbia;
RA   Gupta R., Sokolov L.N., Luan S.;
RT   "A stress inducible dual-specific phosphatase that plays a role in ABA and
RT   sugar signaling.";
RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10617197; DOI=10.1038/45471;
RA   Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA   Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA   Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA   Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA   Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA   Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA   Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT   "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL   Nature 402:761-768(1999).
RN   [3]
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   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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   [5]
RP   FUNCTION, DISRUPTION PHENOTYPE, CATALYTIC ACTIVITY, TISSUE SPECIFICITY, AND
RP   PATHWAY.
RC   STRAIN=cv. Columbia;
RX   PubMed=29476828; DOI=10.1016/j.bbalip.2018.02.007;
RA   Lin Y.-C., Kobayashi K., Wada H., Nakamura Y.;
RT   "Phosphatidylglycerophosphate phosphatase is required for root growth in
RT   Arabidopsis.";
RL   Biochim. Biophys. Acta 1863:563-575(2018).
CC   -!- FUNCTION: Exhibits phosphatidylglycerophosphate phosphatase activity
CC       (PubMed:29476828). Involved in root growth and columella cells
CC       organization (PubMed:29476828). May possess protein phosphatase
CC       activity (By similarity). {ECO:0000250|UniProtKB:P0C089,
CC       ECO:0000269|PubMed:29476828}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] +
CC         phosphate; Xref=Rhea:RHEA:20629, Rhea:RHEA-COMP:9863, Rhea:RHEA-
CC         COMP:11604, ChEBI:CHEBI:15377, ChEBI:CHEBI:29999, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:83421; EC=3.1.3.16;
CC         Evidence={ECO:0000250|UniProtKB:P0C089};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] +
CC         phosphate; Xref=Rhea:RHEA:47004, Rhea:RHEA-COMP:11060, Rhea:RHEA-
CC         COMP:11605, ChEBI:CHEBI:15377, ChEBI:CHEBI:30013, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:61977; EC=3.1.3.16;
CC         Evidence={ECO:0000250|UniProtKB:P0C089};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] +
CC         phosphate; Xref=Rhea:RHEA:10684, Rhea:RHEA-COMP:10136, Rhea:RHEA-
CC         COMP:10137, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, ChEBI:CHEBI:46858,
CC         ChEBI:CHEBI:82620; EC=3.1.3.48; Evidence={ECO:0000255|PROSITE-
CC         ProRule:PRU10044};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycero-3'-phosphate) +
CC         H2O = 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + phosphate;
CC         Xref=Rhea:RHEA:33751, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:60110, ChEBI:CHEBI:64716; EC=3.1.3.27;
CC         Evidence={ECO:0000305|PubMed:29476828};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:33752;
CC         Evidence={ECO:0000305|PubMed:29476828};
CC   -!- PATHWAY: Phospholipid metabolism; phosphatidylglycerol biosynthesis;
CC       phosphatidylglycerol from CDP-diacylglycerol: step 2/2.
CC       {ECO:0000305|PubMed:29476828}.
CC   -!- TISSUE SPECIFICITY: Expressed in stems, roots, flowers, mature seeds
CC       and leaves. {ECO:0000269|PubMed:29476828}.
CC   -!- DISRUPTION PHENOTYPE: No visible phenotype in the double mutant ptpmt1-
CC       1 ptpmt2-1 (PubMed:29476828). But plants lacking PTPMT1, PTPMT2 and
CC       PGPP1 have strongly shorter roots associated with a defective order of
CC       columella cells in the root apices, with stronger effect than in the
CC       single mutant pgpp1-1 (PubMed:29476828). {ECO:0000269|PubMed:29476828}.
CC   -!- SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Non-
CC       receptor class dual specificity subfamily. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAK96749.1; Type=Frameshift; Evidence={ECO:0000305};
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DR   EMBL; AJ574761; CAE00415.1; -; mRNA.
DR   EMBL; AC006068; AAD15447.2; -; Genomic_DNA.
DR   EMBL; CP002685; AEC09144.1; -; Genomic_DNA.
DR   EMBL; AY054558; AAK96749.1; ALT_FRAME; mRNA.
DR   EMBL; AY065219; AAL38695.1; -; mRNA.
DR   EMBL; BT008574; AAP40401.1; -; mRNA.
DR   PIR; F84771; F84771.
DR   RefSeq; NP_565816.1; NM_129123.3.
DR   AlphaFoldDB; Q9ZQP1; -.
DR   SMR; Q9ZQP1; -.
DR   BioGRID; 3482; 1.
DR   STRING; 3702.Q9ZQP1; -.
DR   PaxDb; 3702-AT2G35680-1; -.
DR   ProteomicsDB; 224297; -.
DR   EnsemblPlants; AT2G35680.1; AT2G35680.1; AT2G35680.
DR   GeneID; 818137; -.
DR   Gramene; AT2G35680.1; AT2G35680.1; AT2G35680.
DR   KEGG; ath:AT2G35680; -.
DR   Araport; AT2G35680; -.
DR   TAIR; AT2G35680; PTPMT1.
DR   eggNOG; KOG1719; Eukaryota.
DR   HOGENOM; CLU_047330_6_0_1; -.
DR   InParanoid; Q9ZQP1; -.
DR   OMA; RHDHKLS; -.
DR   OrthoDB; 1046951at2759; -.
DR   PhylomeDB; Q9ZQP1; -.
DR   BRENDA; 3.1.3.27; 399.
DR   UniPathway; UPA00084; UER00504.
DR   PRO; PR:Q9ZQP1; -.
DR   Proteomes; UP000006548; Chromosome 2.
DR   ExpressionAtlas; Q9ZQP1; baseline and differential.
DR   GO; GO:0017018; F:myosin phosphatase activity; IEA:UniProtKB-EC.
DR   GO; GO:0008962; F:phosphatidylglycerophosphatase activity; IDA:TAIR.
DR   GO; GO:0004725; F:protein tyrosine phosphatase activity; IEA:UniProtKB-EC.
DR   GO; GO:0008138; F:protein tyrosine/serine/threonine phosphatase activity; IEA:InterPro.
DR   GO; GO:0016311; P:dephosphorylation; IEA:InterPro.
DR   GO; GO:0006655; P:phosphatidylglycerol biosynthetic process; IEA:UniProtKB-UniPathway.
DR   GO; GO:0048364; P:root development; IMP:UniProtKB.
DR   CDD; cd14524; PTPMT1; 1.
DR   Gene3D; 3.90.190.10; Protein tyrosine phosphatase superfamily; 1.
DR   InterPro; IPR000340; Dual-sp_phosphatase_cat-dom.
DR   InterPro; IPR029021; Prot-tyrosine_phosphatase-like.
DR   InterPro; IPR044596; PTPMT1-like.
DR   InterPro; IPR016130; Tyr_Pase_AS.
DR   InterPro; IPR000387; Tyr_Pase_dom.
DR   InterPro; IPR020422; TYR_PHOSPHATASE_DUAL_dom.
DR   PANTHER; PTHR46274:SF9; PHOSPHATIDYLGLYCEROPHOSPHATE PHOSPHATASE PTPMT1; 1.
DR   PANTHER; PTHR46274; PHOSPHATIDYLINOSITOL PHOSPHATASE; 1.
DR   Pfam; PF00782; DSPc; 1.
DR   SMART; SM00195; DSPc; 1.
DR   SUPFAM; SSF52799; (Phosphotyrosine protein) phosphatases II; 1.
DR   PROSITE; PS00383; TYR_PHOSPHATASE_1; 1.
DR   PROSITE; PS50056; TYR_PHOSPHATASE_2; 1.
DR   PROSITE; PS50054; TYR_PHOSPHATASE_DUAL; 1.
DR   Genevisible; Q9ZQP1; AT.
PE   1: Evidence at protein level;
KW   Hydrolase; Lipid biosynthesis; Lipid metabolism; Phospholipid biosynthesis;
KW   Phospholipid metabolism; Protein phosphatase; Reference proteome.
FT   CHAIN           1..337
FT                   /note="Phosphatidylglycerophosphate phosphatase PTPMT1"
FT                   /id="PRO_0000417332"
FT   DOMAIN          73..220
FT                   /note="Tyrosine-protein phosphatase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00160"
FT   REGION          1..20
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           164..170
FT                   /note="Glucan phosphatase signature motif CXAGXGR"
FT                   /evidence="ECO:0000250|UniProtKB:Q9FEB5"
FT   ACT_SITE        164
FT                   /note="Phosphocysteine intermediate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00160"
FT   BINDING         55
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250|UniProtKB:Q9FEB5"
FT   BINDING         133
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250|UniProtKB:Q9FEB5"
FT   BINDING         165..170
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250|UniProtKB:Q9FEB5"
SQ   SEQUENCE   337 AA;  37548 MW;  8A11D39F2772D2A2 CRC64;
     MYIKELTETD EEKRERSVED NVDDGDKAVL VSRGNVIVLT TKRALVGVGA RALFYPTLVY
     NVVRNKLESE FRWWDRVAEF ILLGAVPFPS DVPQLKELGV CGVITLNEPY ETLVPSSLYK
     SYCIDHLVIA TRDYCFAPSM EAICQAVEFI HRNASLGKTT YVHCKAGRGR STTIVICYLV
     QHKNMTPEAA YSYVRSIRPR VLLAAAQWKA VVEYYHVKVL NTQSCLTDAT SALIPRNVKQ
     VCSGNVVVFD DGSMVVVTHS DLEGYNDDDS RSRRSVKVNG NELWAAAADL SMVYRVKVVG
     QAAMARISCL WLGLREDQKL SGKNLSMGGI SVDISVY
//