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Q84XU2 (PPP5_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 89. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Serine/threonine-protein phosphatase 5

EC=3.1.3.16
Gene names
Name:PAPP5
Synonyms:PP5
Ordered Locus Names:At2g42810
ORF Names:F7D19.19
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length538 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.7

Catalytic activity

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

Cofactor

Binds 1 iron ion per subunit By similarity.

Binds 1 manganese ion per subunit By similarity.

Enzyme regulation

Activated by arachidonic acid (AA).

Subunit structure

Interacts with PHYA and PHYB, mostly when they are phosphorylated and in Pfr forms. Ref.7

Subcellular location

Isoform 1: Endoplasmic reticulum membrane; Multi-pass membrane protein. Nucleus membrane; Multi-pass membrane protein By similarity Ref.7.

Isoform 2: Cytoplasm. Nucleusnucleoplasm. Nucleus speckle. Note: Cytoplasmic in darkness, but translocated to the nucleus upon illumination, when associated with phytochromes into speckles. Ref.7

Domain

TPR repeats are required for the binding with phytochromes.

Sequence similarities

Belongs to the PPP phosphatase family. PP-5 (PP-T) subfamily.

Contains 3 TPR repeats.

Biophysicochemical properties

Kinetic parameters:

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

KM=160 mM for pNPP (at pH 7.5 and 30 degrees Celsius) Ref.7

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

Ontologies

Keywords
   Cellular componentCytoplasm
Endoplasmic reticulum
Membrane
Nucleus
   Coding sequence diversityAlternative splicing
   DomainRepeat
TPR repeat
Transmembrane
Transmembrane helix
   LigandIron
Manganese
Metal-binding
   Molecular functionHydrolase
Protein phosphatase
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processchloroplast-nucleus signaling pathway

Inferred from genetic interaction PubMed 23555952. Source: TAIR

negative regulation of chlorophyll biosynthetic process

Inferred from mutant phenotype PubMed 23555952. Source: TAIR

nucleocytoplasmic transport

Inferred from sequence or structural similarity PubMed 11716463. Source: TAIR

protein dephosphorylation

Inferred from electronic annotation. Source: InterPro

red or far-red light signaling pathway

Inferred from mutant phenotype Ref.7. Source: TAIR

response to cadmium ion

Inferred from expression pattern PubMed 16502469. Source: TAIR

   Cellular_componentcytoplasm

Inferred from direct assay Ref.1Ref.7. Source: TAIR

cytosol

Inferred from direct assay PubMed 21166475. Source: TAIR

integral component of endoplasmic reticulum membrane

Inferred from direct assay Ref.1. Source: TAIR

nuclear envelope

Inferred from direct assay Ref.1. Source: TAIR

nuclear membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

nuclear speck

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from direct assay Ref.1Ref.7. Source: TAIR

plasmodesma

Inferred from direct assay PubMed 21533090. Source: TAIR

   Molecular_functionmetal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

phosphoprotein phosphatase activity

Inferred from direct assay Ref.7. Source: TAIR

protein serine/threonine phosphatase activity

Inferred from sequence or structural similarity PubMed 12068129. Source: TAIR

tetrapyrrole binding

Inferred from direct assay PubMed 23555952. Source: TAIR

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

AGO1D6RUV92EBI-4445012,EBI-7498167From a different organism.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q84XU2-1)

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.
Isoform 2 (identifier: Q84XU2-2)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 538538Serine/threonine-protein phosphatase 5
PRO_0000308988

Regions

Transmembrane163 – 18321Helical; Potential
Transmembrane185 – 20521Helical; Potential
Repeat13 – 4634TPR 1
Repeat48 – 8033TPR 2
Repeat81 – 11434TPR 3

Sites

Active site3441Proton donor By similarity
Metal binding2821Iron By similarity
Metal binding2841Iron By similarity
Metal binding3111Iron By similarity
Metal binding3111Manganese By similarity
Metal binding3431Manganese By similarity
Metal binding3921Manganese By similarity
Metal binding4671Manganese By similarity

Natural variations

Alternative sequence157 – 21155GNKPR…SFSGK → E in isoform 2.
VSP_029087

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified June 1, 2003. Version 1.
Checksum: 93ECC937F02D3541

FASTA53860,283
        10         20         30         40         50         60 
METKNENSDV SRAEEFKSQA NEAFKGHKYS SAIDLYTKAI ELNSNNAVYW ANRAFAHTKL 

        70         80         90        100        110        120 
EEYGSAIQDA SKAIEVDSRY SKGYYRRGAA YLAMGKFKDA LKDFQQVKRL SPNDPDATRK 

       130        140        150        160        170        180 
LKECEKAVMK LKFEEAISVP VSERRSVAES IDFHTIGNKP RSSSMPTKTA LAAVVAAVMV 

       190        200        210        220        230        240 
VAVRGFATTE ILMVLVSVVL GTFWWGSFSG KVEPQYSGAR IEGEEVTLDF VKTMMEDFKN 

       250        260        270        280        290        300 
QKTLHKRYAY QIVLQTRQIL LALPSLVDIS VPHGKHITVC GDVHGQFYDL LNIFELNGLP 

       310        320        330        340        350        360 
SEENPYLFNG DFVDRGSFSV EIILTLFAFK CMCPSSIYLA RGNHESKSMN KIYGFEGEVR 

       370        380        390        400        410        420 
SKLSEKFVDL FAEVFCYLPL AHVINGKVFV VHGGLFSVDG VKLSDIRAID RFCEPPEEGL 

       430        440        450        460        470        480 
MCELLWSDPQ PLPGRGPSKR GVGLSFGGDV TKRFLQDNNL DLLVRSHEVK DEGYEVEHDG 

       490        500        510        520        530 
KLITVFSAPN YCDQMGNKGA FIRFEAPDMK PNIVTFSAVP HPDVKPMAYA NNFLRMFN 

« Hide

Isoform 2 [UniParc].

Checksum: 04780D6007B69EF8
Show »

FASTA48454,702

References

« Hide 'large scale' references
[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]"Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana."
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. expand/collapse author list , 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.
Nature 402:761-768(1999) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRE84858.
RefSeqNP_001031534.1. NM_001036457.2.
NP_565985.1. NM_129842.3.
UniGeneAt.23737.

3D structure databases

ProteinModelPortalQ84XU2.
SMRQ84XU2. Positions 10-536.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid4218. 1 interaction.
IntActQ84XU2. 2 interactions.
MINTMINT-8375614.

Proteomic databases

PaxDbQ84XU2.
PRIDEQ84XU2.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT2G42810.2; AT2G42810.2; AT2G42810. [Q84XU2-1]
GeneID818881.
KEGGath:AT2G42810.

Organism-specific databases

TAIRAT2G42810.

Phylogenomic databases

eggNOGCOG0639.
HOGENOMHOG000172698.
InParanoidQ84XU2.
KOK04460.
OMAFKLLYPN.
PhylomeDBQ84XU2.
ProtClustDBCLSN2688898.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorQ84XU2.

Family and domain databases

Gene3D1.25.40.10. 1 hit.
InterProIPR004843. Calcineurin-like_PHP_apaH.
IPR013235. PPP_dom.
IPR006186. Ser/Thr-sp_prot-phosphatase.
IPR011236. Ser/Thr_PPase_5.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical.
IPR001440. TPR_1.
IPR019734. TPR_repeat.
[Graphical view]
PANTHERPTHR11668:SF12. PTHR11668:SF12. 1 hit.
PfamPF00149. Metallophos. 1 hit.
PF08321. PPP5. 2 hits.
PF00515. TPR_1. 1 hit.
[Graphical view]
PIRSFPIRSF033096. PPPtase_5. 1 hit.
PRINTSPR00114. STPHPHTASE.
SMARTSM00156. PP2Ac. 1 hit.
SM00028. TPR. 3 hits.
[Graphical view]
PROSITEPS50005. TPR. 3 hits.
PS50293. TPR_REGION. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROQ84XU2.

Entry information

Entry namePPP5_ARATH
AccessionPrimary (citable) accession number: Q84XU2
Secondary accession number(s): Q56X87 expand/collapse secondary AC list , Q8RXU0, Q8W581, Q9SJH5
Entry history
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: June 1, 2003
Last modified: April 16, 2014
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names