PPP5_ARATH
ID PPP5_ARATH Reviewed; 538 AA.
AC Q84XU2; Q56X87; Q8RXU0; Q8W581; Q9SJH5;
DT 13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Serine/threonine-protein phosphatase 5;
DE EC=3.1.3.16;
GN Name=PAPP5; Synonyms=PP5; OrderedLocusNames=At2g42810; ORFNames=F7D19.19;
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] (ISOFORM 1), AND ALTERNATIVE PRODUCTS.
RX PubMed=12972652; DOI=10.1104/pp.103.026617;
RA de la Fuente van Bentem S., Vossen J.H., Vermeer J.E.M., de Vroomen M.J.,
RA Gadella T.W.J. Jr., Haring M.A., Cornelissen B.J.C.;
RT "The subcellular localization of plant protein phosphatase 5 isoforms is
RT determined by alternative splicing.";
RL Plant Physiol. 133:702-712(2003).
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] (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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 424-538 (ISOFORMS 1 AND 2).
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 REVIEW.
RX PubMed=15707886; DOI=10.1016/j.cell.2005.01.023;
RA Rubio V., Deng X.W.;
RT "Phy tunes: phosphorylation status and phytochrome-mediated signaling.";
RL Cell 120:290-292(2005).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVATION
RP BY ARACHIDONIC ACID, AND INTERACTION WITH PHYA AND PHYB.
RX PubMed=15707897; DOI=10.1016/j.cell.2004.12.019;
RA Ryu J.S., Kim J.-I., Kunkel T., Kim B.C., Cho D.S., Hong S.H., Kim S.-H.,
RA Fernandez A.P., Kim Y., Alonso J.M., Ecker J.R., Nagy F., Lim P.O.,
RA Song P.-S., Schaefer E., Nam H.G.;
RT "Phytochrome-specific type 5 phosphatase controls light signal flux by
RT enhancing phytochrome stability and affinity for a signal transducer.";
RL Cell 120:395-406(2005).
RN [8]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=17368080; DOI=10.1016/j.tplants.2007.03.003;
RA Farkas I., Dombradi V., Miskei M., Szabados L., Koncz C.;
RT "Arabidopsis PPP family of serine/threonine phosphatases.";
RL Trends Plant Sci. 12:169-176(2007).
CC -!- FUNCTION: Isoform 2 dephosphorylates phosphorylated phytochromes, with
CC a preference toward Pfr forms, and enhances phytochrome-mediated
CC photoresponses, probably by enhancing their stability and their binding
CC affinity for light signal transducers such as NDPK2. Can use para-
CC nitrophenylphosphate (pNPP) as substrate.
CC {ECO:0000269|PubMed:15707897}.
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 -!- 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 -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000250};
CC -!- ACTIVITY REGULATION: Activated by arachidonic acid (AA).
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=160 mM for pNPP (at pH 7.5 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:15707897};
CC Vmax=22 umol/min/mg enzyme with pNPP as substrate (at pH 7.5 and 30
CC degrees Celsius) {ECO:0000269|PubMed:15707897};
CC Note=Experiments have been done in the presence of 100 uM arachidonic
CC acid (AA).;
CC -!- SUBUNIT: Interacts with PHYA and PHYB, mostly when they are
CC phosphorylated and in Pfr forms. {ECO:0000269|PubMed:15707897}.
CC -!- INTERACTION:
CC Q84XU2; D6RUV9: AGO1; Xeno; NbExp=2; IntAct=EBI-4445012, EBI-7498167;
CC -!- SUBCELLULAR LOCATION: [Isoform 1]: Endoplasmic reticulum membrane;
CC Multi-pass membrane protein. Nucleus membrane {ECO:0000250}; Multi-pass
CC membrane protein {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: [Isoform 2]: Cytoplasm. Nucleus, nucleoplasm.
CC Nucleus speckle. Note=Cytoplasmic in darkness, but translocated to the
CC nucleus upon illumination, when associated with phytochromes into
CC speckles.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q84XU2-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q84XU2-2; Sequence=VSP_029087;
CC -!- DOMAIN: TPR repeats are required for the binding with phytochromes.
CC -!- MISCELLANEOUS: [Isoform 2]: Partial isoform 2 lacking TPR repeats
CC exhibits enhanced activity at pH 7.5 with pNPP as substrate. This
CC partial protein is in addition inhibited by okadaic acid.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the PPP phosphatase family. PP-5 (PP-T)
CC subfamily. {ECO:0000305}.
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DR EMBL; AY182779; AAO26216.1; -; mRNA.
DR EMBL; AC006931; AAD21727.2; -; Genomic_DNA.
DR EMBL; CP002685; AEC10171.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC10172.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM61627.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM61628.1; -; Genomic_DNA.
DR EMBL; AF419574; AAL31906.1; -; mRNA.
DR EMBL; AY080674; AAL86350.1; -; mRNA.
DR EMBL; BT010180; AAQ22649.1; -; mRNA.
DR EMBL; AK221789; BAD93924.1; -; mRNA.
DR PIR; E84858; E84858.
DR RefSeq; NP_001031534.1; NM_001036457.3. [Q84XU2-1]
DR RefSeq; NP_001323832.1; NM_001336995.1. [Q84XU2-2]
DR RefSeq; NP_001323833.1; NM_001336996.1. [Q84XU2-2]
DR RefSeq; NP_565985.1; NM_129842.4. [Q84XU2-2]
DR PDB; 5JJT; X-ray; 2.10 A; A/B=5-537.
DR PDB; 7OBE; X-ray; 3.00 A; A/B=1-484.
DR PDBsum; 5JJT; -.
DR PDBsum; 7OBE; -.
DR AlphaFoldDB; Q84XU2; -.
DR SMR; Q84XU2; -.
DR BioGRID; 4218; 7.
DR IntAct; Q84XU2; 3.
DR MINT; Q84XU2; -.
DR STRING; 3702.AT2G42810.2; -.
DR iPTMnet; Q84XU2; -.
DR PaxDb; Q84XU2; -.
DR PRIDE; Q84XU2; -.
DR ProteomicsDB; 234699; -. [Q84XU2-1]
DR EnsemblPlants; AT2G42810.1; AT2G42810.1; AT2G42810. [Q84XU2-2]
DR EnsemblPlants; AT2G42810.2; AT2G42810.2; AT2G42810. [Q84XU2-1]
DR EnsemblPlants; AT2G42810.4; AT2G42810.4; AT2G42810. [Q84XU2-2]
DR EnsemblPlants; AT2G42810.5; AT2G42810.5; AT2G42810. [Q84XU2-2]
DR GeneID; 818881; -.
DR Gramene; AT2G42810.1; AT2G42810.1; AT2G42810. [Q84XU2-2]
DR Gramene; AT2G42810.2; AT2G42810.2; AT2G42810. [Q84XU2-1]
DR Gramene; AT2G42810.4; AT2G42810.4; AT2G42810. [Q84XU2-2]
DR Gramene; AT2G42810.5; AT2G42810.5; AT2G42810. [Q84XU2-2]
DR KEGG; ath:AT2G42810; -.
DR Araport; AT2G42810; -.
DR TAIR; locus:2052345; AT2G42810.
DR eggNOG; KOG0376; Eukaryota.
DR InParanoid; Q84XU2; -.
DR OMA; NHFFMSR; -.
DR OrthoDB; 671536at2759; -.
DR PhylomeDB; Q84XU2; -.
DR PRO; PR:Q84XU2; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q84XU2; baseline and differential.
DR Genevisible; Q84XU2; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0030176; C:integral component of endoplasmic reticulum membrane; IDA:TAIR.
DR GO; GO:0005635; C:nuclear envelope; IDA:TAIR.
DR GO; GO:0031965; C:nuclear membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0017018; F:myosin phosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0004721; F:phosphoprotein phosphatase activity; IDA:TAIR.
DR GO; GO:0004722; F:protein serine/threonine phosphatase activity; ISS:TAIR.
DR GO; GO:0046906; F:tetrapyrrole binding; IDA:TAIR.
DR GO; GO:0010019; P:chloroplast-nucleus signaling pathway; IGI:TAIR.
DR GO; GO:1902325; P:negative regulation of chlorophyll biosynthetic process; IMP:TAIR.
DR GO; GO:0006913; P:nucleocytoplasmic transport; ISS:TAIR.
DR GO; GO:0010017; P:red or far-red light signaling pathway; IMP:TAIR.
DR CDD; cd07417; MPP_PP5_C; 1.
DR Gene3D; 1.25.40.10; -; 1.
DR Gene3D; 3.60.21.10; -; 1.
DR InterPro; IPR004843; Calcineurin-like_PHP_ApaH.
DR InterPro; IPR029052; Metallo-depent_PP-like.
DR InterPro; IPR041753; PP5_C.
DR InterPro; IPR013235; PPP_dom.
DR InterPro; IPR006186; Ser/Thr-sp_prot-phosphatase.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR InterPro; IPR001440; TPR_1.
DR InterPro; IPR019734; TPR_repeat.
DR Pfam; PF00149; Metallophos; 1.
DR Pfam; PF08321; PPP5; 1.
DR Pfam; PF00515; TPR_1; 1.
DR PRINTS; PR00114; STPHPHTASE.
DR SMART; SM00156; PP2Ac; 1.
DR SMART; SM00028; TPR; 3.
DR SUPFAM; SSF48452; SSF48452; 1.
DR SUPFAM; SSF56300; SSF56300; 1.
DR PROSITE; PS50005; TPR; 3.
DR PROSITE; PS50293; TPR_REGION; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Cytoplasm; Endoplasmic reticulum;
KW Hydrolase; Manganese; Membrane; Metal-binding; Nucleus;
KW Protein phosphatase; Reference proteome; Repeat; TPR repeat; Transmembrane;
KW Transmembrane helix.
FT CHAIN 1..538
FT /note="Serine/threonine-protein phosphatase 5"
FT /id="PRO_0000308988"
FT TRANSMEM 163..183
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 185..205
FT /note="Helical"
FT /evidence="ECO:0000255"
FT REPEAT 13..46
FT /note="TPR 1"
FT REPEAT 48..80
FT /note="TPR 2"
FT REPEAT 81..114
FT /note="TPR 3"
FT ACT_SITE 344
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 282
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 284
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 311
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 311
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 343
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 392
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 467
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT VAR_SEQ 157..211
FT /note="GNKPRSSSMPTKTALAAVVAAVMVVAVRGFATTEILMVLVSVVLGTFWWGSF
FT SGK -> E (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172, ECO:0000303|Ref.5"
FT /id="VSP_029087"
FT HELIX 12..25
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 29..42
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 47..59
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 63..76
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 81..93
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 97..110
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 118..136
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 141..143
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 147..149
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 153..155
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 223..225
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 228..239
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 246..261
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 265..269
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 276..280
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 287..297
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 302..304
FT /evidence="ECO:0007829|PDB:7OBE"
FT STRAND 306..310
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 313..317
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 319..332
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 334..336
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 337..340
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 347..353
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 355..362
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 365..375
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 380..384
FT /evidence="ECO:0007829|PDB:5JJT"
FT TURN 385..387
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 388..393
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 397..399
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 403..407
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 417..419
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 420..426
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 431..437
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 441..446
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 448..457
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 461..465
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 473..477
FT /evidence="ECO:0007829|PDB:5JJT"
FT TURN 478..481
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 482..485
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 491..493
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 499..505
FT /evidence="ECO:0007829|PDB:5JJT"
FT TURN 506..508
FT /evidence="ECO:0007829|PDB:5JJT"
FT STRAND 511..516
FT /evidence="ECO:0007829|PDB:5JJT"
FT TURN 526..529
FT /evidence="ECO:0007829|PDB:5JJT"
FT HELIX 532..535
FT /evidence="ECO:0007829|PDB:5JJT"
SQ SEQUENCE 538 AA; 60283 MW; 93ECC937F02D3541 CRC64;
METKNENSDV SRAEEFKSQA NEAFKGHKYS SAIDLYTKAI ELNSNNAVYW ANRAFAHTKL
EEYGSAIQDA SKAIEVDSRY SKGYYRRGAA YLAMGKFKDA LKDFQQVKRL SPNDPDATRK
LKECEKAVMK LKFEEAISVP VSERRSVAES IDFHTIGNKP RSSSMPTKTA LAAVVAAVMV
VAVRGFATTE ILMVLVSVVL GTFWWGSFSG KVEPQYSGAR IEGEEVTLDF VKTMMEDFKN
QKTLHKRYAY QIVLQTRQIL LALPSLVDIS VPHGKHITVC GDVHGQFYDL LNIFELNGLP
SEENPYLFNG DFVDRGSFSV EIILTLFAFK CMCPSSIYLA RGNHESKSMN KIYGFEGEVR
SKLSEKFVDL FAEVFCYLPL AHVINGKVFV VHGGLFSVDG VKLSDIRAID RFCEPPEEGL
MCELLWSDPQ PLPGRGPSKR GVGLSFGGDV TKRFLQDNNL DLLVRSHEVK DEGYEVEHDG
KLITVFSAPN YCDQMGNKGA FIRFEAPDMK PNIVTFSAVP HPDVKPMAYA NNFLRMFN
