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Serine/threonine-protein phosphatase 5 (EC 3.1.3.16)

 PPP5_ARATH              Reviewed;         538 AA.
Q84XU2; Q56X87; Q8RXU0; Q8W581; Q9SJH5;
13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
01-JUN-2003, sequence version 1.
05-DEC-2018, entry version 128.
RecName: Full=Serine/threonine-protein phosphatase 5;
EC=3.1.3.16;
Name=PAPP5; Synonyms=PP5; OrderedLocusNames=At2g42810;
ORFNames=F7D19.19;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), AND ALTERNATIVE PRODUCTS.
PubMed=12972652; DOI=10.1104/pp.103.026617;
de la Fuente van Bentem S., Vossen J.H., Vermeer J.E.M.,
de Vroomen M.J., Gadella T.W.J. Jr., Haring M.A., Cornelissen B.J.C.;
"The subcellular localization of plant protein phosphatase 5 isoforms
is determined by alternative splicing.";
Plant Physiol. 133:702-712(2003).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617197; DOI=10.1038/45471;
Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L.,
Moffat K.S., Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L.,
Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H.,
Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D.,
Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M.,
Venter J.C.;
"Sequence and analysis of chromosome 2 of the plant Arabidopsis
thaliana.";
Nature 402:761-768(1999).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 424-538 (ISOFORMS 1 AND 2).
STRAIN=cv. Columbia;
Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J.,
Hayashizaki Y., Shinozaki K.;
"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
[6]
REVIEW.
PubMed=15707886; DOI=10.1016/j.cell.2005.01.023;
Rubio V., Deng X.W.;
"Phy tunes: phosphorylation status and phytochrome-mediated
signaling.";
Cell 120:290-292(2005).
[7]
FUNCTION, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES,
ACTIVATION BY ARACHIDONIC ACID, AND INTERACTION WITH PHYA AND PHYB.
PubMed=15707897; DOI=10.1016/j.cell.2004.12.019;
Ryu J.S., Kim J.-I., Kunkel T., Kim B.C., Cho D.S., Hong S.H.,
Kim S.-H., Fernandez A.P., Kim Y., Alonso J.M., Ecker J.R., Nagy F.,
Lim P.O., Song P.-S., Schaefer E., Nam H.G.;
"Phytochrome-specific type 5 phosphatase controls light signal flux by
enhancing phytochrome stability and affinity for a signal
transducer.";
Cell 120:395-406(2005).
[8]
GENE FAMILY, AND NOMENCLATURE.
PubMed=17368080; DOI=10.1016/j.tplants.2007.03.003;
Farkas I., Dombradi V., Miskei M., Szabados L., Koncz C.;
"Arabidopsis PPP family of serine/threonine phosphatases.";
Trends Plant Sci. 12:169-176(2007).
-!- FUNCTION: Isoform 2 dephosphorylates phosphorylated phytochromes,
with a preference toward Pfr forms, and enhances phytochrome-
mediated photoresponses, probably by enhancing their stability and
their binding affinity for light signal transducers such as NDPK2.
Can use para-nitrophenylphosphate (pNPP) as substrate.
{ECO:0000269|PubMed:15707897}.
-!- CATALYTIC ACTIVITY:
Reaction=H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] +
phosphate; Xref=Rhea:RHEA:20629, Rhea:RHEA-COMP:9863, Rhea:RHEA-
COMP:11604, ChEBI:CHEBI:15377, ChEBI:CHEBI:29999,
ChEBI:CHEBI:43474, ChEBI:CHEBI:83421; EC=3.1.3.16;
-!- CATALYTIC ACTIVITY:
Reaction=H2O + O-phospho-L-threonyl-[protein] = L-threonyl-
[protein] + phosphate; Xref=Rhea:RHEA:47004, Rhea:RHEA-
COMP:11060, Rhea:RHEA-COMP:11605, ChEBI:CHEBI:15377,
ChEBI:CHEBI:30013, ChEBI:CHEBI:43474, ChEBI:CHEBI:61977;
EC=3.1.3.16;
-!- COFACTOR:
Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
Note=Binds 2 manganese ions per subunit. {ECO:0000250};
-!- ACTIVITY REGULATION: Activated by arachidonic acid (AA).
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=160 mM for pNPP (at pH 7.5 and 30 degrees Celsius)
{ECO:0000269|PubMed:15707897};
Vmax=22 umol/min/mg enzyme with pNPP as substrate (at pH 7.5 and
30 degrees Celsius) {ECO:0000269|PubMed:15707897};
Note=Experiments have been done in the presence of 100 uM
arachidonic acid (AA).;
-!- SUBUNIT: Interacts with PHYA and PHYB, mostly when they are
phosphorylated and in Pfr forms. {ECO:0000269|PubMed:15707897}.
-!- INTERACTION:
D6RUV9:AGO1 (xeno); NbExp=2; IntAct=EBI-4445012, EBI-7498167;
-!- SUBCELLULAR LOCATION: Isoform 1: Endoplasmic reticulum membrane;
Multi-pass membrane protein. Nucleus membrane {ECO:0000250};
Multi-pass membrane protein {ECO:0000250}.
-!- SUBCELLULAR LOCATION: Isoform 2: Cytoplasm. Nucleus, nucleoplasm.
Nucleus speckle. Note=Cytoplasmic in darkness, but translocated to
the nucleus upon illumination, when associated with phytochromes
into speckles.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q84XU2-1; Sequence=Displayed;
Name=2;
IsoId=Q84XU2-2; Sequence=VSP_029087;
Note=Partial isoform 2 lacking TPR repeats exhibits enhanced
activity at pH 7.5 with pNPP as substrate. This partial protein
is in addition inhibited by okadaic acid.;
-!- DOMAIN: TPR repeats are required for the binding with
phytochromes.
-!- SIMILARITY: Belongs to the PPP phosphatase family. PP-5 (PP-T)
subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AY182779; AAO26216.1; -; mRNA.
EMBL; AC006931; AAD21727.2; -; Genomic_DNA.
EMBL; CP002685; AEC10171.1; -; Genomic_DNA.
EMBL; CP002685; AEC10172.1; -; Genomic_DNA.
EMBL; CP002685; ANM61627.1; -; Genomic_DNA.
EMBL; CP002685; ANM61628.1; -; Genomic_DNA.
EMBL; AF419574; AAL31906.1; -; mRNA.
EMBL; AY080674; AAL86350.1; -; mRNA.
EMBL; BT010180; AAQ22649.1; -; mRNA.
EMBL; AK221789; BAD93924.1; -; mRNA.
PIR; E84858; E84858.
RefSeq; NP_001031534.1; NM_001036457.3. [Q84XU2-1]
RefSeq; NP_001323832.1; NM_001336995.1. [Q84XU2-2]
RefSeq; NP_001323833.1; NM_001336996.1. [Q84XU2-2]
RefSeq; NP_565985.1; NM_129842.4. [Q84XU2-2]
UniGene; At.23737; -.
PDB; 5JJT; X-ray; 2.10 A; A/B=5-537.
PDB; 5OBL; X-ray; 3.00 A; A/B=1-538.
PDBsum; 5JJT; -.
PDBsum; 5OBL; -.
ProteinModelPortal; Q84XU2; -.
SMR; Q84XU2; -.
BioGrid; 4218; 3.
IntAct; Q84XU2; 2.
MINT; Q84XU2; -.
STRING; 3702.AT2G42810.2; -.
iPTMnet; Q84XU2; -.
PaxDb; Q84XU2; -.
PRIDE; Q84XU2; -.
EnsemblPlants; AT2G42810.1; AT2G42810.1; AT2G42810. [Q84XU2-2]
EnsemblPlants; AT2G42810.2; AT2G42810.2; AT2G42810. [Q84XU2-1]
EnsemblPlants; AT2G42810.4; AT2G42810.4; AT2G42810. [Q84XU2-2]
EnsemblPlants; AT2G42810.5; AT2G42810.5; AT2G42810. [Q84XU2-2]
GeneID; 818881; -.
Gramene; AT2G42810.1; AT2G42810.1; AT2G42810. [Q84XU2-2]
Gramene; AT2G42810.2; AT2G42810.2; AT2G42810. [Q84XU2-1]
Gramene; AT2G42810.4; AT2G42810.4; AT2G42810. [Q84XU2-2]
Gramene; AT2G42810.5; AT2G42810.5; AT2G42810. [Q84XU2-2]
KEGG; ath:AT2G42810; -.
Araport; AT2G42810; -.
TAIR; locus:2052345; AT2G42810.
eggNOG; KOG0376; Eukaryota.
eggNOG; COG0639; LUCA.
HOGENOM; HOG000172698; -.
InParanoid; Q84XU2; -.
KO; K04460; -.
OMA; LYPNHFF; -.
OrthoDB; EOG0936077E; -.
PhylomeDB; Q84XU2; -.
PRO; PR:Q84XU2; -.
Proteomes; UP000006548; Chromosome 2.
ExpressionAtlas; Q84XU2; baseline and differential.
Genevisible; Q84XU2; AT.
GO; GO:0005737; C:cytoplasm; IDA:TAIR.
GO; GO:0005829; C:cytosol; IDA:TAIR.
GO; GO:0030176; C:integral component of endoplasmic reticulum membrane; IDA:TAIR.
GO; GO:0005635; C:nuclear envelope; IDA:TAIR.
GO; GO:0031965; C:nuclear membrane; IEA:UniProtKB-SubCell.
GO; GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IDA:TAIR.
GO; GO:0009506; C:plasmodesma; IDA:TAIR.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004721; F:phosphoprotein phosphatase activity; IDA:TAIR.
GO; GO:0004722; F:protein serine/threonine phosphatase activity; ISS:TAIR.
GO; GO:0046906; F:tetrapyrrole binding; IDA:TAIR.
GO; GO:0010019; P:chloroplast-nucleus signaling pathway; IGI:TAIR.
GO; GO:1902325; P:negative regulation of chlorophyll biosynthetic process; IMP:TAIR.
GO; GO:0006913; P:nucleocytoplasmic transport; ISS:TAIR.
GO; GO:0010017; P:red or far-red light signaling pathway; IMP:TAIR.
GO; GO:0046686; P:response to cadmium ion; IEP:TAIR.
Gene3D; 1.25.40.10; -; 1.
Gene3D; 3.60.21.10; -; 1.
InterPro; IPR004843; Calcineurin-like_PHP_ApaH.
InterPro; IPR029052; Metallo-depent_PP-like.
InterPro; IPR013235; PPP_dom.
InterPro; IPR006186; Ser/Thr-sp_prot-phosphatase.
InterPro; IPR011236; Ser/Thr_PPase_5.
InterPro; IPR013026; TPR-contain_dom.
InterPro; IPR011990; TPR-like_helical_dom_sf.
InterPro; IPR001440; TPR_1.
InterPro; IPR019734; TPR_repeat.
PANTHER; PTHR11668:SF391; PTHR11668:SF391; 2.
Pfam; PF00149; Metallophos; 1.
Pfam; PF08321; PPP5; 1.
Pfam; PF00515; TPR_1; 1.
PRINTS; PR00114; STPHPHTASE.
SMART; SM00156; PP2Ac; 1.
SMART; SM00028; TPR; 3.
SUPFAM; SSF48452; SSF48452; 1.
PROSITE; PS50005; TPR; 3.
PROSITE; PS50293; TPR_REGION; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Complete proteome; Cytoplasm;
Endoplasmic reticulum; Hydrolase; Manganese; Membrane; Metal-binding;
Nucleus; Protein phosphatase; Reference proteome; Repeat; TPR repeat;
Transmembrane; Transmembrane helix.
CHAIN 1 538 Serine/threonine-protein phosphatase 5.
/FTId=PRO_0000308988.
TRANSMEM 163 183 Helical. {ECO:0000255}.
TRANSMEM 185 205 Helical. {ECO:0000255}.
REPEAT 13 46 TPR 1.
REPEAT 48 80 TPR 2.
REPEAT 81 114 TPR 3.
ACT_SITE 344 344 Proton donor. {ECO:0000250}.
METAL 282 282 Manganese 1. {ECO:0000250}.
METAL 284 284 Manganese 1. {ECO:0000250}.
METAL 311 311 Manganese 1. {ECO:0000250}.
METAL 311 311 Manganese 2. {ECO:0000250}.
METAL 343 343 Manganese 2. {ECO:0000250}.
METAL 392 392 Manganese 2. {ECO:0000250}.
METAL 467 467 Manganese 2. {ECO:0000250}.
VAR_SEQ 157 211 GNKPRSSSMPTKTALAAVVAAVMVVAVRGFATTEILMVLVS
VVLGTFWWGSFSGK -> E (in isoform 2).
{ECO:0000303|PubMed:14593172,
ECO:0000303|Ref.5}.
/FTId=VSP_029087.
HELIX 12 25 {ECO:0000244|PDB:5JJT}.
HELIX 29 42 {ECO:0000244|PDB:5JJT}.
HELIX 47 59 {ECO:0000244|PDB:5JJT}.
HELIX 63 76 {ECO:0000244|PDB:5JJT}.
HELIX 81 93 {ECO:0000244|PDB:5JJT}.
HELIX 97 110 {ECO:0000244|PDB:5JJT}.
HELIX 118 136 {ECO:0000244|PDB:5JJT}.
HELIX 141 143 {ECO:0000244|PDB:5JJT}.
HELIX 147 149 {ECO:0000244|PDB:5JJT}.
HELIX 153 155 {ECO:0000244|PDB:5JJT}.
STRAND 223 225 {ECO:0000244|PDB:5JJT}.
HELIX 228 239 {ECO:0000244|PDB:5JJT}.
HELIX 246 261 {ECO:0000244|PDB:5JJT}.
STRAND 265 269 {ECO:0000244|PDB:5JJT}.
STRAND 276 280 {ECO:0000244|PDB:5JJT}.
HELIX 287 297 {ECO:0000244|PDB:5JJT}.
STRAND 302 304 {ECO:0000244|PDB:5OBL}.
STRAND 306 310 {ECO:0000244|PDB:5JJT}.
STRAND 313 317 {ECO:0000244|PDB:5JJT}.
HELIX 319 332 {ECO:0000244|PDB:5JJT}.
HELIX 334 336 {ECO:0000244|PDB:5JJT}.
STRAND 337 340 {ECO:0000244|PDB:5JJT}.
HELIX 347 353 {ECO:0000244|PDB:5JJT}.
HELIX 355 362 {ECO:0000244|PDB:5JJT}.
HELIX 365 375 {ECO:0000244|PDB:5JJT}.
STRAND 380 384 {ECO:0000244|PDB:5JJT}.
TURN 385 387 {ECO:0000244|PDB:5JJT}.
STRAND 388 393 {ECO:0000244|PDB:5JJT}.
STRAND 397 399 {ECO:0000244|PDB:5JJT}.
HELIX 403 407 {ECO:0000244|PDB:5JJT}.
STRAND 417 419 {ECO:0000244|PDB:5JJT}.
HELIX 420 426 {ECO:0000244|PDB:5JJT}.
STRAND 431 437 {ECO:0000244|PDB:5JJT}.
STRAND 441 446 {ECO:0000244|PDB:5JJT}.
HELIX 448 457 {ECO:0000244|PDB:5JJT}.
STRAND 461 465 {ECO:0000244|PDB:5JJT}.
STRAND 473 477 {ECO:0000244|PDB:5JJT}.
TURN 478 481 {ECO:0000244|PDB:5JJT}.
STRAND 482 485 {ECO:0000244|PDB:5JJT}.
HELIX 491 493 {ECO:0000244|PDB:5JJT}.
STRAND 499 505 {ECO:0000244|PDB:5JJT}.
TURN 506 508 {ECO:0000244|PDB:5JJT}.
STRAND 511 516 {ECO:0000244|PDB:5JJT}.
TURN 526 529 {ECO:0000244|PDB:5JJT}.
HELIX 532 535 {ECO:0000244|PDB:5JJT}.
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


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