PGPP1_ARATH
ID PGPP1_ARATH Reviewed; 348 AA.
AC Q9LXR9; A0A178VLA6; Q84VV0;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=Phosphatidylglycerophosphate phosphatase 1, chloroplastic/mitochondrial {ECO:0000303|PubMed:27541283, ECO:0000303|PubMed:27614107};
DE Short=AtPGPP1 {ECO:0000303|PubMed:27541283, ECO:0000303|PubMed:27614107};
DE Short=PGP phosphatase 1 {ECO:0000303|PubMed:27541283, ECO:0000303|PubMed:27614107};
DE EC=3.1.3.27 {ECO:0000269|PubMed:27541283, ECO:0000269|PubMed:27614107};
DE Flags: Precursor;
GN Name=PGPP1 {ECO:0000303|PubMed:27541283, ECO:0000303|PubMed:27614107};
GN OrderedLocusNames=At3g58830 {ECO:0000312|Araport:AT3G58830};
GN ORFNames=T20N10.180 {ECO:0000312|EMBL:CAB88300.1};
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 [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].
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, CATALYTIC ACTIVITY, TISSUE SPECIFICITY,
RP DEVELOPMENTAL STAGE, SUBCELLULAR LOCATION, AND PATHWAY.
RC STRAIN=cv. Columbia;
RX PubMed=27541283; DOI=10.1111/tpj.13311;
RA Lin Y.-C., Kobayashi K., Hung C.-H., Wada H., Nakamura Y.;
RT "Arabidopsis phosphatidylglycerophosphate phosphatase 1 involved in
RT phosphatidylglycerol biosynthesis and photosynthetic function.";
RL Plant J. 88:1022-1037(2016).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF ASP-184, SUBCELLULAR
RP LOCATION, TISSUE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND
RP PATHWAY.
RC STRAIN=cv. Columbia;
RX PubMed=27614107; DOI=10.1111/tpj.13378;
RA Zhou Y., Hoelzl G., Vom Dorp K., Peisker H., Melzer M., Frentzen M.,
RA Doermann P.;
RT "Identification and characterization of a plastidial
RT phosphatidylglycerophosphate phosphatase in Arabidopsis thaliana.";
RL Plant J. 89:221-234(2017).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, AND SUBCELLULAR LOCATION.
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: Phosphatidylglycerophosphate (PGP) phosphatase involved in
CC the biosynthesis of phosphatidylglycerol (PG), a phosphoglycerolipid
CC predominantly present in chloroplastic thylakoid membranes and which
CC has important photosynthetic function; seems to use PGP 34:3, PGP 34:2
CC and PGP 34:1 as substrates (PubMed:27541283, PubMed:27614107,
CC PubMed:29476828). Required for thylakoid membranes development and
CC chloroplast function (PubMed:27541283, PubMed:27614107). Necessary for
CC normal cell growth (PubMed:27614107). Required for root growth and
CC columella cells organization (PubMed:29476828).
CC {ECO:0000269|PubMed:27541283, ECO:0000269|PubMed:27614107,
CC ECO:0000269|PubMed:29476828}.
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:0000269|PubMed:27541283, ECO:0000269|PubMed:27614107};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:33752;
CC Evidence={ECO:0000269|PubMed:27541283, ECO:0000269|PubMed:27614107};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:27614107};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.2 uM for phosphatidylglycerophosphate
CC {ECO:0000269|PubMed:27614107};
CC Vmax=450 pmol/min/mg enzyme with phosphatidylglycerophosphate as
CC subtrate {ECO:0000269|PubMed:27614107};
CC pH dependence:
CC Optimum pH is 8. {ECO:0000269|PubMed:27614107};
CC -!- PATHWAY: Phospholipid metabolism; phosphatidylglycerol biosynthesis;
CC phosphatidylglycerol from CDP-diacylglycerol: step 2/2.
CC {ECO:0000269|PubMed:27541283, ECO:0000269|PubMed:27614107}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:27541283, ECO:0000269|PubMed:27614107,
CC ECO:0000269|PubMed:29476828}. Mitochondrion
CC {ECO:0000269|PubMed:29476828}. Note=Localized in chloroplast of leaf
CC mesophyll cells, but in mitochondrion of root cells.
CC {ECO:0000269|PubMed:29476828}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9LXR9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LXR9-2; Sequence=VSP_060572;
CC -!- TISSUE SPECIFICITY: Mainly expressed in inflorescences (especially in
CC pollen) and, to a lower extent, in leaves, stems and siliques, as well
CC as, at low levels, in roots (PubMed:27614107). Mostly expressed in
CC hypocotyl, vasculatures, trichomes, guard cells and stigmas
CC (PubMed:27541283). {ECO:0000269|PubMed:27541283,
CC ECO:0000269|PubMed:27614107}.
CC -!- DEVELOPMENTAL STAGE: In the mature embryo, prominently expressed in the
CC shoot apical meristem (SAM) (PubMed:27541283). In young seedlings,
CC present in hypocotyls and mature part of roots, but not in root tips
CC (PubMed:27541283). Later, also observed in the vasculature of
CC cotyledons, in trichomes of emerging true leaves, and in joint part of
CC the root to shoot (PubMed:27541283). In leaves, accumulates in guard
CC cells and trichomes (PubMed:27541283). In flowers, mainly confined to
CC the stigma of pistils and to the vasculature in the filament of stamens
CC (PubMed:27541283). {ECO:0000269|PubMed:27541283}.
CC -!- DISRUPTION PHENOTYPE: Pale green phenotype with reduced
CC phosphatidylglycerol (PG) and chlorophyll contents but no defect in
CC embryo development (PubMed:27541283, PubMed:27614107). Accumulation of
CC phosphatidylglycerophosphate (PGP) 34:3, PGP 34:2 and PGP 34:1 lacking
CC 16:1 (PubMed:27614107). Strongly reduced amounts of other thylakoid
CC lipids such as monogalactosyldiacylglycerol (MGDG),
CC digalactosyldiacylglycerol (DGDG) and sulfoquinovosyldiacylglycerol
CC (SQDG), especially under phosphate deprivation conditions (-P)
CC (PubMed:27614107). Reduced amounts of chlorophyll, but unchanged
CC photosynthetic quantum yield (PubMed:27614107). Altered chloroplasts
CC development (e.g. reduced number of thylakoid membranes) and impaired
CC photosynthetic activity (PubMed:27541283, PubMed:27614107). Reduced
CC mesophyll cells size (PubMed:27614107). Strongly shorter roots
CC associated with a defective order of columella cells in the root apices
CC (PubMed:29476828). Plants lacking PTPMT1, PTPMT2 and PGPP1 have
CC strongly shorter roots associated with a defective order of columella
CC cells in the root apices, with stronger effect than in the single
CC mutant pgpp1-1 (PubMed:29476828). {ECO:0000269|PubMed:27541283,
CC ECO:0000269|PubMed:27614107, ECO:0000269|PubMed:29476828}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
CC {ECO:0000305}.
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DR EMBL; AL353032; CAB88300.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79837.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM64922.1; -; Genomic_DNA.
DR EMBL; AK227892; BAE99864.1; -; mRNA.
DR EMBL; BT004819; AAO44085.1; -; mRNA.
DR PIR; T49166; T49166.
DR RefSeq; NP_001326923.1; NM_001339940.1. [Q9LXR9-1]
DR RefSeq; NP_191442.2; NM_115745.4. [Q9LXR9-2]
DR AlphaFoldDB; Q9LXR9; -.
DR SMR; Q9LXR9; -.
DR STRING; 3702.AT3G58830.1; -.
DR PRIDE; Q9LXR9; -.
DR ProteomicsDB; 187736; -.
DR EnsemblPlants; AT3G58830.1; AT3G58830.1; AT3G58830. [Q9LXR9-2]
DR EnsemblPlants; AT3G58830.2; AT3G58830.2; AT3G58830. [Q9LXR9-1]
DR GeneID; 825052; -.
DR Gramene; AT3G58830.1; AT3G58830.1; AT3G58830. [Q9LXR9-2]
DR Gramene; AT3G58830.2; AT3G58830.2; AT3G58830. [Q9LXR9-1]
DR KEGG; ath:AT3G58830; -.
DR Araport; AT3G58830; -.
DR TAIR; locus:2099104; AT3G58830.
DR eggNOG; KOG2961; Eukaryota.
DR HOGENOM; CLU_056221_0_0_1; -.
DR OrthoDB; 1209458at2759; -.
DR PhylomeDB; Q9LXR9; -.
DR BRENDA; 3.1.3.27; 399.
DR UniPathway; UPA00084; UER00504.
DR PRO; PR:Q9LXR9; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LXR9; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
DR GO; GO:0016791; F:phosphatase activity; IBA:GO_Central.
DR GO; GO:0008962; F:phosphatidylglycerophosphatase activity; IDA:UniProtKB.
DR GO; GO:0009658; P:chloroplast organization; IMP:UniProtKB.
DR GO; GO:0046486; P:glycerolipid metabolic process; IDA:UniProtKB.
DR GO; GO:0008610; P:lipid biosynthetic process; IMP:TAIR.
DR GO; GO:0006655; P:phosphatidylglycerol biosynthetic process; IMP:TAIR.
DR GO; GO:0046839; P:phospholipid dephosphorylation; IDA:UniProtKB.
DR GO; GO:0015979; P:photosynthesis; IMP:UniProtKB.
DR GO; GO:0048364; P:root development; IMP:UniProtKB.
DR GO; GO:0010027; P:thylakoid membrane organization; IMP:UniProtKB.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006549; HAD-SF_hydro_IIIA.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR027706; PGP_Pase.
DR InterPro; IPR010021; PGPP1/Gep4.
DR Pfam; PF09419; PGP_phosphatase; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01662; HAD-SF-IIIA; 1.
DR TIGRFAMs; TIGR01668; YqeG_hyp_ppase; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chloroplast; Hydrolase; Lipid biosynthesis;
KW Lipid metabolism; Mitochondrion; Phospholipid biosynthesis;
KW Phospholipid metabolism; Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..58
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 59..348
FT /note="Phosphatidylglycerophosphate phosphatase 1,
FT chloroplastic/mitochondrial"
FT /id="PRO_0000449813"
FT REGION 17..67
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 184..188
FT /note="Phosphoryl acceptor"
FT /evidence="ECO:0000250|UniProtKB:P38812"
FT COMPBIAS 52..67
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 184
FT /note="Required for phosphatidylglycerophosphate
FT phosphatase activity"
FT /evidence="ECO:0000269|PubMed:27614107"
FT VAR_SEQ 1..5
FT /note="Missing (in isoform 2)"
FT /id="VSP_060572"
FT MUTAGEN 184
FT /note="D->N: Disturbed phosphatidylglycerophosphate
FT phosphatase activity."
FT /evidence="ECO:0000269|PubMed:27614107"
SQ SEQUENCE 348 AA; 39094 MW; 466A50CAEAC98227 CRC64;
MQTPSMAAST TSYYPIPKSF LLSPPRHKRN PNLISCSTKP ICSPPPPSSS SSSPLQTTTT
HRSQKQNLRL PTFEDSFLLY QFSSPTEDPG FSNRIPEQFD GEPRELVLPR VEDNNKGLAI
SSNMWWADLK AALGQRINIE GIVSSVSVVV KDRQFVLPHV SVKDLRYIDW EVLKRKGFKG
VVFDKDNTLT APYSLAIWPP LRPSIERCKA VFGHDIAVFS NSAGLTEYDH DDSKAKALEA
EIGIRVLRHR VKKPAGTAEE VEKHFGCTSS ELIMVGDRPF TDIVYGNRNG FLTVLTEPLS
RAEEPFIVRQ VRRLELALLK RWLRKGLKPV DHSLVSDITQ FVKVPSDL
