P32345 (PP4C_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Serine/threonine-protein phosphatase 4 catalytic subunit
Short name=PP4C
EC=3.1.3.16

Alternative name(s):
Phosphatase PP2A-like catalytic subunit PPH3

Gene names

Name:	PPH3
Ordered Locus Names:	YDR075W
ORF Names:	D4421

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	308 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Forms the histone H2A phosphatase complex in association with the regulatory subunits PSY2 and PSY4, which dephosphorylates H2AS128ph (gamma-H2A) that has been displaced from sites of DNA lesions in the double-stranded DNA break repair process. Dephosphorylation is necessary for efficient recovery from the DNA damage checkpoint. PPH3 is directly involved in the dephosphorylation and activation of the transcription factor GLN3 in response to nutrient availability. Ref.6 Ref.12
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.
Subunit structure	Catalytic subunit of the histone H2A phosphatase complex (HTP-C) containing PPH3, PSY2 and PSY4. Inactivated in a complex with phosphatase methylesterase PPE1 (PP2Ai). Interacts with phosphatase 2A activator RRD1, which can reactivate PP2Ai by dissociating the catalytic subunit from the complex. Interacts with SPT5 and TAP42. Ref.7 Ref.10 Ref.11 Ref.12
Subcellular location	Cytoplasm. Nucleus Ref.8.
Miscellaneous	Present with 2840 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the PPP phosphatase family. PP-4 (PP-X) subfamily.

Ontologies

Keywords
Cellular component	Cytoplasm Nucleus
Ligand	Iron Manganese Metal-binding
Molecular function	Hydrolase Protein phosphatase
PTM	Methylation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	double-strand break repair via homologous recombination Inferred from genetic interaction PubMed 21135129. Source: SGD negative regulation of DNA damage checkpoint Inferred from mutant phenotype Ref.12PubMed 17517611. Source: SGD positive regulation of nitrogen compound metabolic process Inferred from mutant phenotype Ref.6. Source: SGD protein dephosphorylation Inferred from direct assay Ref.2. Source: SGD signal transduction involved in meiotic recombination checkpoint Inferred from mutant phenotype PubMed 20951350. Source: SGD
Cellular_component	cytoplasm Inferred from direct assay Ref.8. Source: SGD nucleus Inferred from direct assay Ref.8. Source: SGD
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein serine/threonine phosphatase activity Inferred from direct assay Ref.2. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PSY4	P38193	9	EBI-12759,EBI-21239

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 308	308	Serine/threonine-protein phosphatase 4 catalytic subunit		PRO_0000058875
Sites
	Active site	112	1	Proton donor By similarity
	Metal binding	51	1	Iron By similarity
	Metal binding	53	1	Iron By similarity
	Metal binding	79	1	Iron By similarity
	Metal binding	79	1	Manganese By similarity
	Metal binding	111	1	Manganese By similarity
	Metal binding	161	1	Manganese By similarity
	Metal binding	235	1	Manganese By similarity
Amino acid modifications
	Modified residue	308	1	Leucine methyl ester By similarity
Experimental info
	Sequence conflict	245	1	M → I in CAA41662. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P32345 [UniParc]. Last modified February 1, 1995. Version 2. Checksum: AFE99582C7F44052	FASTA	308	35,264
	10 20 30 40 50 60 MMDLDKIIAS LRDGKHIPEE TVFRLCLNSQ ELLMNEGNVT QVDTPVTICG DIHGQLHDLL 70 80 90 100 110 120 TLFEKSGGVE KTRYIFLGDF VDRGFYSLES FLLLLCYKLR YPDRITLIRG NHETRQITKV 130 140 150 160 170 180 YGFYDEVVRK YGNSNVWRYC CEVFDYLSLG AIINNSIFCV HGGLSPDMTT VDEIRTIDRK 190 200 210 220 230 240 QEVPHEGAMC DLLWSDPEDV DTWSLSPRGA GFLFGKREVD QFLEKNNVEL IARAHQLVME 250 260 270 280 290 300 GYKEMFDGGL VTVWSAPNYC YRCGNVAAVL KIDDDLNREY TIFEAVQAQN EVGNAIIPTK KSQMDYFL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Protein phosphatase 2A in Saccharomyces cerevisiae: effects on cell growth and bud morphogenesis." Ronne H., Carlberg M., Hu G.-Z., Nehlin J.O. Mol. Cell. Biol. 11:4876-4884(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 208353 / W303-1A.
[2]	"The Saccharomyces cerevisiae gene PPH3 encodes a protein phosphatase with properties different from PPX, PP1 and PP2A." Hoffmann R., Jung S., Ehrmann M., Hofer H.W. Yeast 10:567-578(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	"Tripartite regulation of Gln3p by TOR, Ure2p, and phosphatases." Bertram P.G., Choi J.H., Carvalho J., Ai W., Zeng C., Chan T.-F., Zheng X.F.S. J. Biol. Chem. 275:35727-35733(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN GLN3 DEPHOSPHORYLATION.
[7]	"Interaction with Tap42 is required for the essential function of Sit4 and type 2A phosphatases." Wang H., Wang X., Jiang Y. Mol. Biol. Cell 14:4342-4351(2003) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH TAP42.
[8]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[9]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[10]	"Specific interactions of PP2A and PP2A-like phosphatases with the yeast PTPA homologues, Ypa1 and Ypa2." Van Hoof C., Martens E., Longin S., Jordens J., Stevens I., Janssens V., Goris J. Biochem. J. 386:93-102(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PPE1 AND RRD1.
[11]	"A novel, evolutionarily conserved protein phosphatase complex involved in cisplatin sensitivity." Gingras A.-C., Caballero M., Zarske M., Sanchez A., Hazbun T.R., Fields S., Sonenberg N., Hafen E., Raught B., Aebersold R. Mol. Cell. Proteomics 4:1725-1740(2005) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN HTP-C COMPLEX, MASS SPECTROMETRY, INTERACTION WITH SPT5.
[12]	"A phosphatase complex that dephosphorylates gamma-H2AX regulates DNA damage checkpoint recovery." Keogh M.-C., Kim J.-A., Downey M., Fillingham J., Chowdhury D., Harrison J.C., Onishi M., Datta N., Galicia S., Emili A., Lieberman J., Shen X., Buratowski S., Haber J.E., Durocher D., Greenblatt J.F., Krogan N.J. Nature 439:497-501(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN HTP-C COMPLEX, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Z46796 Genomic DNA. Translation: CAA86797.1. X58858 Genomic DNA. Translation: CAA41662.1. X82086 Genomic DNA. Translation: CAA57602.1. Z74371 Genomic DNA. Translation: CAA98894.1. AY557686 Genomic DNA. Translation: AAS56012.1. BK006938 Genomic DNA. Translation: DAA11921.1.
PIR	PABY3. S44331.
RefSeq	NP_010360.1. NM_001180383.1.
3D structure databases
ProteinModelPortal	P32345.
SMR	P32345. Positions 3-284.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-3905N.
IntAct	P32345. 14 interactions.
MINT	MINT-509529.
STRING	4932.YDR075W.
Proteomic databases
PaxDb	P32345.
PeptideAtlas	P32345.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YDR075W; YDR075W; YDR075W.
GeneID	851647.
KEGG	sce:YDR075W.
Organism-specific databases
CYGD	YDR075w.
SGD	S000002482. PPH3.
Phylogenomic databases
eggNOG	COG0639.
GeneTree	ENSGT00700000105882.
HOGENOM	HOG000172696.
KO	K01090.
OMA	LCYKLRY.
OrthoDB	EOG4HX88W.
Enzyme and pathway databases
BioCyc	YEAST:G3O-29680-MONOMER.
Gene expression databases
Genevestigator	P32345.
GermOnline	YDR075W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR004843. Metallo_PEstase_dom. IPR006186. Ser/Thr-sp_prot-phosphatase. [Graphical view]
Pfam	PF00149. Metallophos. 1 hit. [Graphical view]
PRINTS	PR00114. STPHPHTASE.
SMART	SM00156. PP2Ac. 1 hit. [Graphical view]
PROSITE	PS00125. SER_THR_PHOSPHATASE. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	969227.

Entry information

Entry name

PP4C_YEAST

Accession

Primary (citable) accession number: P32345
Secondary accession number(s): D6VS61

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	February 1, 1995
Last modified:	May 29, 2013
This is version 130 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program