Q84XU2 (PPP5_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	538 AA.
Sequence status	Complete.
Protein existence	Evidence 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 phosphoprotein + H2O = a protein + 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. Nucleus › nucleoplasm. 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 component	Cytoplasm Endoplasmic reticulum Membrane Nucleus
Coding sequence diversity	Alternative splicing
Domain	Repeat TPR repeat Transmembrane Transmembrane helix
Ligand	Iron Manganese Metal-binding
Molecular function	Hydrolase Protein phosphatase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chloroplast-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_component	cytosol Inferred from direct assay PubMed 21166475. Source: TAIR integral to 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 plasmodesma Inferred from direct assay PubMed 21533090. Source: TAIR
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW 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
AGO1	D6RUV9	2	EBI-4445012,EBI-7498167	From 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 key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 538	538	Serine/threonine-protein phosphatase 5		PRO_0000308988
Regions
	Transmembrane	163 – 183	21	Helical; Potential
	Transmembrane	185 – 205	21	Helical; Potential
	Repeat	13 – 46	34	TPR 1
	Repeat	48 – 80	33	TPR 2
	Repeat	81 – 114	34	TPR 3
Sites
	Active site	344	1	Proton donor By similarity
	Metal binding	282	1	Iron By similarity
	Metal binding	284	1	Iron By similarity
	Metal binding	311	1	Iron By similarity
	Metal binding	311	1	Manganese By similarity
	Metal binding	343	1	Manganese By similarity
	Metal binding	392	1	Manganese By similarity
	Metal binding	467	1	Manganese By similarity
Natural variations
	Alternative sequence	157 – 211	55	GNKPR…SFSGK → E in isoform 2.		VSP_029087

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: 93ECC937F02D3541	FASTA	538	60,283
	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
	Isoform 2 [UniParc]. Checksum: 04780D6007B69EF8	FASTA	484	54,702
	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 IDFHTIEVEP QYSGARIEGE EVTLDFVKTM 190 200 210 220 230 240 MEDFKNQKTL HKRYAYQIVL QTRQILLALP SLVDISVPHG KHITVCGDVH GQFYDLLNIF 250 260 270 280 290 300 ELNGLPSEEN PYLFNGDFVD RGSFSVEIIL TLFAFKCMCP SSIYLARGNH ESKSMNKIYG 310 320 330 340 350 360 FEGEVRSKLS EKFVDLFAEV FCYLPLAHVI NGKVFVVHGG LFSVDGVKLS DIRAIDRFCE 370 380 390 400 410 420 PPEEGLMCEL LWSDPQPLPG RGPSKRGVGL SFGGDVTKRF LQDNNLDLLV RSHEVKDEGY 430 440 450 460 470 480 EVEHDGKLIT VFSAPNYCDQ MGNKGAFIRF EAPDMKPNIV TFSAVPHPDV KPMAYANNFL RMFN

References

	« Hide 'large scale' referencesShow '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. , 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. , 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.
+	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.
IPI	IPI00542290. IPI00542877.
PIR	E84858.
RefSeq	NP_001031534.1. NM_001036457.2. NP_565985.1. NM_129842.3.
UniGene	At.23737.
3D structure databases
ProteinModelPortal	Q84XU2.
SMR	Q84XU2. Positions 10-162, 216-530.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q84XU2. 2 interactions.
MINT	MINT-8375614.
Proteomic databases
PaxDb	Q84XU2.
PRIDE	Q84XU2.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT2G42810.2; AT2G42810.2; AT2G42810.
GeneID	818881.
KEGG	ath:AT2G42810.
Organism-specific databases
TAIR	AT2G42810.
Phylogenomic databases
eggNOG	COG0639.
HOGENOM	HOG000172698.
InParanoid	Q84XU2.
KO	K04460.
OMA	FKLLYPN.
PhylomeDB	Q84XU2.
ProtClustDB	CLSN2688898.
Gene expression databases
ArrayExpress	Q84XU2.
Genevestigator	Q84XU2.
Family and domain databases
Gene3D	1.25.40.10. 1 hit.
InterPro	IPR004843. PEstase_dom. 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]
PANTHER	PTHR11668:SF12. PTHR11668:SF12. 1 hit.
Pfam	PF00149. Metallophos. 1 hit. PF08321. PPP5. 2 hits. PF00515. TPR_1. 1 hit. [Graphical view]
PIRSF	PIRSF033096. PPPtase_5. 1 hit.
PRINTS	PR00114. STPHPHTASE.
SMART	SM00156. PP2Ac. 1 hit. SM00028. TPR. 3 hits. [Graphical view]
PROSITE	PS00125. SER_THR_PHOSPHATASE. False negative. PS50005. TPR. 3 hits. PS50293. TPR_REGION. 1 hit. [Graphical view]
ProtoNet	Search...
Other
PRO	Q84XU2.

Entry information

Entry name

PPP5_ARATH

Accession

Primary (citable) accession number: Q84XU2
Secondary accession number(s): Q56X87 , Q8RXU0, Q8W581, Q9SJH5

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 13, 2007
Last sequence update:	June 1, 2003
Last modified:	October 16, 2013
This is version 84 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program