TPMT2_ARATH
ID TPMT2_ARATH Reviewed; 228 AA.
AC Q6NKR2; F4K7Q7; Q9FJU7;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=Phosphatidylglycerophosphate phosphatase PTPMT2 {ECO:0000303|PubMed:29476828};
DE EC=3.1.3.27 {ECO:0000305|PubMed:29476828};
DE AltName: Full=Protein TYROSINE PHOSPHATASE LOCALIZED TO THE MITOCHONDRION 2 {ECO:0000303|PubMed:29476828};
DE AltName: Full=Putative dual specificity protein phosphatase PTPMT2 {ECO:0000305};
DE EC=3.1.3.16 {ECO:0000250|UniProtKB:P0C089};
DE EC=3.1.3.48 {ECO:0000255|PROSITE-ProRule:PRU10044};
GN Name=PTPMT2 {ECO:0000312|EMBL:AED96787.1};
GN Synonyms=PTP133 {ECO:0000303|Ref.1};
GN OrderedLocusNames=At5g56610 {ECO:0000312|Araport:AT5G56610};
GN ORFNames=MIK19.6 {ECO:0000312|EMBL:BAB09879.1};
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 [GENOMIC DNA].
RA Gao Z., Zhang J., Jia W.;
RL Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9734815; DOI=10.1093/dnares/5.3.203;
RA Kotani H., Nakamura Y., Sato S., Asamizu E., Kaneko T., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence
RT features of the regions of 1,367,185 bp covered by 19 physically assigned
RT P1 and TAC clones.";
RL DNA Res. 5:203-216(1998).
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] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Shinn P., Chen H., Cheuk R.F., Kim C.J., Carninci P., Hayashizaki Y.,
RA Ishida J., Kamiya A., Kawai J., Narusaka M., Sakurai T., Satou M., Seki M.,
RA Shinozaki K., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAY-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1; Synonyms=PTPMT2.1 {ECO:0000303|PubMed:29476828};
CC IsoId=Q6NKR2-1; Sequence=Displayed;
CC Name=2; Synonyms=PTPMT2.2 {ECO:0000303|PubMed:29476828};
CC IsoId=Q6NKR2-2; Sequence=VSP_060573;
CC -!- TISSUE SPECIFICITY: [Isoform 1]: Expressed in roots, leaves, stems and
CC flowers. {ECO:0000269|PubMed:29476828}.
CC -!- TISSUE SPECIFICITY: [Isoform 2]: Expressed at low levels in stems and
CC flowers. {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=BAB09879.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; FJ605096; ACU43460.1; -; Genomic_DNA.
DR EMBL; AB013392; BAB09879.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED96787.1; -; Genomic_DNA.
DR EMBL; CP002688; AED96788.1; -; Genomic_DNA.
DR EMBL; BT012631; AAT06450.1; -; mRNA.
DR EMBL; AK221735; BAD93755.1; -; mRNA.
DR RefSeq; NP_001032084.1; NM_001037007.1. [Q6NKR2-2]
DR RefSeq; NP_200472.2; NM_125044.4. [Q6NKR2-1]
DR AlphaFoldDB; Q6NKR2; -.
DR SMR; Q6NKR2; -.
DR STRING; 3702.AT5G56610.1; -.
DR PaxDb; Q6NKR2; -.
DR PRIDE; Q6NKR2; -.
DR ProteomicsDB; 181061; -. [Q6NKR2-1]
DR ProteomicsDB; 228499; -.
DR EnsemblPlants; AT5G56610.1; AT5G56610.1; AT5G56610. [Q6NKR2-1]
DR EnsemblPlants; AT5G56610.2; AT5G56610.2; AT5G56610. [Q6NKR2-2]
DR GeneID; 835762; -.
DR Gramene; AT5G56610.1; AT5G56610.1; AT5G56610. [Q6NKR2-1]
DR Gramene; AT5G56610.2; AT5G56610.2; AT5G56610. [Q6NKR2-2]
DR KEGG; ath:AT5G56610; -.
DR Araport; AT5G56610; -.
DR TAIR; locus:2165016; AT5G56610.
DR eggNOG; KOG1719; Eukaryota.
DR HOGENOM; CLU_047330_0_1_1; -.
DR InParanoid; Q6NKR2; -.
DR OMA; KISSRRW; -.
DR OrthoDB; 1386941at2759; -.
DR PhylomeDB; Q6NKR2; -.
DR BRENDA; 3.1.3.27; 399.
DR UniPathway; UPA00084; UER00504.
DR PRO; PR:Q6NKR2; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q6NKR2; 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:0004439; F:phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity; IBA:GO_Central.
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:0006655; P:phosphatidylglycerol biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006470; P:protein dephosphorylation; IEA:InterPro.
DR GO; GO:0048364; P:root development; IMP:UniProtKB.
DR CDD; cd14524; PTPMT1; 1.
DR Gene3D; 3.90.190.10; -; 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 Pfam; PF00782; DSPc; 1.
DR SMART; SM00195; DSPc; 1.
DR SUPFAM; SSF52799; SSF52799; 1.
DR PROSITE; PS00383; TYR_PHOSPHATASE_1; 1.
DR PROSITE; PS50056; TYR_PHOSPHATASE_2; 1.
DR PROSITE; PS50054; TYR_PHOSPHATASE_DUAL; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Hydrolase; Lipid biosynthesis; Lipid metabolism;
KW Phospholipid biosynthesis; Phospholipid metabolism; Protein phosphatase;
KW Reference proteome.
FT CHAIN 1..228
FT /note="Phosphatidylglycerophosphate phosphatase PTPMT2"
FT /id="PRO_0000449815"
FT DOMAIN 66..213
FT /note="Tyrosine-protein phosphatase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00160"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 157..163
FT /note="Glucan phosphatase signature motif CXAGXGR"
FT /evidence="ECO:0000250|UniProtKB:Q9FEB5"
FT COMPBIAS 7..30
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 157
FT /note="Phosphocysteine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00160"
FT BINDING 48
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9FEB5"
FT BINDING 126
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9FEB5"
FT BINDING 158..163
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9FEB5"
FT VAR_SEQ 73..113
FT /note="Missing (in isoform 2)"
FT /id="VSP_060573"
SQ SEQUENCE 228 AA; 25726 MW; FA6B196784943CE4 CRC64;
MTDETEEDDT TQQRSSRNDG VSKNKGKGFK GDKAKRALIG AGGRILFYPT LLYNLVRFKL
QSQFRWWDQI DEYLLMGAVP FRKDVPRLKK LGVGGVITLN EPYETLVPSS LYSAYEMEHL
VIPTRDYLFA PSIVDITLAV NFIHKNALLG KTTYVHCKAG RGRSTTVVLC YLIEHKSMTV
AAAFEHVRSI RPRVLLHPSQ RKVVEEFSRL QSPLSESTFI ATSGDIVS
