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Protein

Serine/threonine-protein phosphatase 5

Gene

PAPP5

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.1 Publication

Catalytic activityi

[a protein]-serine/threonine phosphate + H2O = [a protein]-serine/threonine + phosphate.

Cofactori

Mn2+By similarityNote: Binds 2 manganese ions per subunit.By similarity

Enzyme regulationi

Activated by arachidonic acid (AA).

Kineticsi

Experiments have been done in the presence of 100 µM arachidonic acid (AA).

  1. KM=160 mM for pNPP (at pH 7.5 and 30 degrees Celsius)1 Publication

Vmax=22 µmol/min/mg enzyme with pNPP as substrate (at pH 7.5 and 30 degrees Celsius)1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi282 – 2821Manganese 1By similarity
Metal bindingi284 – 2841Manganese 1By similarity
Metal bindingi311 – 3111Manganese 1By similarity
Metal bindingi311 – 3111Manganese 2By similarity
Metal bindingi343 – 3431Manganese 2By similarity
Active sitei344 – 3441Proton donorBy similarity
Metal bindingi392 – 3921Manganese 2By similarity
Metal bindingi467 – 4671Manganese 2By similarity

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. phosphoprotein phosphatase activity Source: TAIR
  3. protein serine/threonine phosphatase activity Source: TAIR
  4. tetrapyrrole binding Source: TAIR

GO - Biological processi

  1. chloroplast-nucleus signaling pathway Source: TAIR
  2. negative regulation of chlorophyll biosynthetic process Source: TAIR
  3. nucleocytoplasmic transport Source: TAIR
  4. protein dephosphorylation Source: InterPro
  5. red or far-red light signaling pathway Source: TAIR
  6. response to cadmium ion Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protein phosphatase

Keywords - Ligandi

Manganese, Metal-binding

Enzyme and pathway databases

BioCyciARA:AT2G42810-MONOMER.
ARA:GQT-1698-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine/threonine-protein phosphatase 5 (EC:3.1.3.16)
Gene namesi
Name:PAPP5
Synonyms:PP5
Ordered Locus Names:At2g42810
ORF Names:F7D19.19
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G42810.

Subcellular locationi

Isoform 2 :
  1. Cytoplasm
  2. Nucleusnucleoplasm
  3. Nucleus speckle

  4. Note: Cytoplasmic in darkness, but translocated to the nucleus upon illumination, when associated with phytochromes into speckles.

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei163 – 18321HelicalSequence AnalysisAdd
BLAST
Transmembranei185 – 20521HelicalSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. cytoplasm Source: TAIR
  2. cytosol Source: TAIR
  3. integral component of endoplasmic reticulum membrane Source: TAIR
  4. nuclear envelope Source: TAIR
  5. nuclear membrane Source: UniProtKB-SubCell
  6. nuclear speck Source: UniProtKB-SubCell
  7. nucleus Source: TAIR
  8. plasmodesma Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endoplasmic reticulum, Membrane, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 538538Serine/threonine-protein phosphatase 5PRO_0000308988Add
BLAST

Proteomic databases

PaxDbiQ84XU2.
PRIDEiQ84XU2.

Expressioni

Gene expression databases

ExpressionAtlasiQ84XU2. baseline and differential.
GenevestigatoriQ84XU2.

Interactioni

Subunit structurei

Interacts with PHYA and PHYB, mostly when they are phosphorylated and in Pfr forms.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
AGO1D6RUV92EBI-4445012,EBI-7498167From a different organism.

Protein-protein interaction databases

BioGridi4218. 1 interaction.
IntActiQ84XU2. 2 interactions.
MINTiMINT-8375614.

Structurei

3D structure databases

ProteinModelPortaliQ84XU2.
SMRiQ84XU2. Positions 10-536.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati13 – 4634TPR 1Add
BLAST
Repeati48 – 8033TPR 2Add
BLAST
Repeati81 – 11434TPR 3Add
BLAST

Domaini

TPR repeats are required for the binding with phytochromes.

Sequence similaritiesi

Contains 3 TPR repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, TPR repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0639.
HOGENOMiHOG000172698.
InParanoidiQ84XU2.
KOiK04460.
OMAiYGYAIAD.
PhylomeDBiQ84XU2.

Family and domain databases

Gene3Di1.25.40.10. 1 hit.
3.60.21.10. 1 hit.
InterProiIPR004843. Calcineurin-like_PHP_apaH.
IPR029052. Metallo-depent_PP-like.
IPR013235. PPP_dom.
IPR006186. Ser/Thr-sp_prot-phosphatase.
IPR011236. Ser/Thr_PPase_5.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR001440. TPR_1.
IPR019734. TPR_repeat.
[Graphical view]
PANTHERiPTHR11668:SF12. PTHR11668:SF12. 1 hit.
PfamiPF00149. Metallophos. 1 hit.
PF08321. PPP5. 2 hits.
PF00515. TPR_1. 1 hit.
[Graphical view]
PRINTSiPR00114. STPHPHTASE.
SMARTiSM00156. PP2Ac. 1 hit.
SM00028. TPR. 3 hits.
[Graphical view]
SUPFAMiSSF56300. SSF56300. 1 hit.
PROSITEiPS50005. TPR. 3 hits.
PS50293. TPR_REGION. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q84XU2-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
METKNENSDV SRAEEFKSQA NEAFKGHKYS SAIDLYTKAI ELNSNNAVYW
60 70 80 90 100
ANRAFAHTKL EEYGSAIQDA SKAIEVDSRY SKGYYRRGAA YLAMGKFKDA
110 120 130 140 150
LKDFQQVKRL SPNDPDATRK LKECEKAVMK LKFEEAISVP VSERRSVAES
160 170 180 190 200
IDFHTIGNKP RSSSMPTKTA LAAVVAAVMV VAVRGFATTE ILMVLVSVVL
210 220 230 240 250
GTFWWGSFSG KVEPQYSGAR IEGEEVTLDF VKTMMEDFKN QKTLHKRYAY
260 270 280 290 300
QIVLQTRQIL LALPSLVDIS VPHGKHITVC GDVHGQFYDL LNIFELNGLP
310 320 330 340 350
SEENPYLFNG DFVDRGSFSV EIILTLFAFK CMCPSSIYLA RGNHESKSMN
360 370 380 390 400
KIYGFEGEVR SKLSEKFVDL FAEVFCYLPL AHVINGKVFV VHGGLFSVDG
410 420 430 440 450
VKLSDIRAID RFCEPPEEGL MCELLWSDPQ PLPGRGPSKR GVGLSFGGDV
460 470 480 490 500
TKRFLQDNNL DLLVRSHEVK DEGYEVEHDG KLITVFSAPN YCDQMGNKGA
510 520 530
FIRFEAPDMK PNIVTFSAVP HPDVKPMAYA NNFLRMFN
Length:538
Mass (Da):60,283
Last modified:June 1, 2003 - v1
Checksum:i93ECC937F02D3541
GO
Isoform 2 (identifier: Q84XU2-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     157-211: GNKPRSSSMPTKTALAAVVAAVMVVAVRGFATTEILMVLVSVVLGTFWWGSFSGK → E

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.

Show »
Length:484
Mass (Da):54,702
Checksum:i04780D6007B69EF8
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei157 – 21155GNKPR…SFSGK → E in isoform 2. 2 PublicationsVSP_029087Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY182779 mRNA. Translation: AAO26216.1.
AC006931 Genomic DNA. Translation: AAD21727.2.
CP002685 Genomic DNA. Translation: AEC10171.1.
CP002685 Genomic DNA. Translation: AEC10172.1.
AF419574 mRNA. Translation: AAL31906.1.
AY080674 mRNA. Translation: AAL86350.1.
BT010180 mRNA. Translation: AAQ22649.1.
AK221789 mRNA. Translation: BAD93924.1.
PIRiE84858.
RefSeqiNP_001031534.1. NM_001036457.2. [Q84XU2-1]
NP_565985.1. NM_129842.3. [Q84XU2-2]
UniGeneiAt.23737.

Genome annotation databases

EnsemblPlantsiAT2G42810.2; AT2G42810.2; AT2G42810. [Q84XU2-1]
GeneIDi818881.
KEGGiath:AT2G42810.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY182779 mRNA. Translation: AAO26216.1.
AC006931 Genomic DNA. Translation: AAD21727.2.
CP002685 Genomic DNA. Translation: AEC10171.1.
CP002685 Genomic DNA. Translation: AEC10172.1.
AF419574 mRNA. Translation: AAL31906.1.
AY080674 mRNA. Translation: AAL86350.1.
BT010180 mRNA. Translation: AAQ22649.1.
AK221789 mRNA. Translation: BAD93924.1.
PIRiE84858.
RefSeqiNP_001031534.1. NM_001036457.2. [Q84XU2-1]
NP_565985.1. NM_129842.3. [Q84XU2-2]
UniGeneiAt.23737.

3D structure databases

ProteinModelPortaliQ84XU2.
SMRiQ84XU2. Positions 10-536.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4218. 1 interaction.
IntActiQ84XU2. 2 interactions.
MINTiMINT-8375614.

Proteomic databases

PaxDbiQ84XU2.
PRIDEiQ84XU2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G42810.2; AT2G42810.2; AT2G42810. [Q84XU2-1]
GeneIDi818881.
KEGGiath:AT2G42810.

Organism-specific databases

TAIRiAT2G42810.

Phylogenomic databases

eggNOGiCOG0639.
HOGENOMiHOG000172698.
InParanoidiQ84XU2.
KOiK04460.
OMAiYGYAIAD.
PhylomeDBiQ84XU2.

Enzyme and pathway databases

BioCyciARA:AT2G42810-MONOMER.
ARA:GQT-1698-MONOMER.

Miscellaneous databases

PROiQ84XU2.

Gene expression databases

ExpressionAtlasiQ84XU2. baseline and differential.
GenevestigatoriQ84XU2.

Family and domain databases

Gene3Di1.25.40.10. 1 hit.
3.60.21.10. 1 hit.
InterProiIPR004843. Calcineurin-like_PHP_apaH.
IPR029052. Metallo-depent_PP-like.
IPR013235. PPP_dom.
IPR006186. Ser/Thr-sp_prot-phosphatase.
IPR011236. Ser/Thr_PPase_5.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR001440. TPR_1.
IPR019734. TPR_repeat.
[Graphical view]
PANTHERiPTHR11668:SF12. PTHR11668:SF12. 1 hit.
PfamiPF00149. Metallophos. 1 hit.
PF08321. PPP5. 2 hits.
PF00515. TPR_1. 1 hit.
[Graphical view]
PRINTSiPR00114. STPHPHTASE.
SMARTiSM00156. PP2Ac. 1 hit.
SM00028. TPR. 3 hits.
[Graphical view]
SUPFAMiSSF56300. SSF56300. 1 hit.
PROSITEiPS50005. TPR. 3 hits.
PS50293. TPR_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The subcellular localization of plant protein phosphatase 5 isoforms is determined by alternative splicing."
    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.
    Plant Physiol. 133:702-712(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), ALTERNATIVE PRODUCTS.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    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.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Strain: cv. Columbia.
  5. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    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.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 424-538 (ISOFORMS 1 AND 2).
    Strain: cv. Columbia.
  6. "Phy tunes: phosphorylation status and phytochrome-mediated signaling."
    Rubio V., Deng X.W.
    Cell 120:290-292(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  7. "Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer."
    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.
    Cell 120:395-406(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVATION BY ARACHIDONIC ACID, INTERACTION WITH PHYA AND PHYB.
  8. "Arabidopsis PPP family of serine/threonine phosphatases."
    Farkas I., Dombradi V., Miskei M., Szabados L., Koncz C.
    Trends Plant Sci. 12:169-176(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE.

Entry informationi

Entry nameiPPP5_ARATH
AccessioniPrimary (citable) accession number: Q84XU2
Secondary accession number(s): Q56X87
, Q8RXU0, Q8W581, Q9SJH5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: June 1, 2003
Last modified: April 1, 2015
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.