PPH3 phosphoprotein phosphatase PP4 catalytic subunit PPH3 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: PPH3
Official Full Name: phosphoprotein phosphatase PP4 catalytic subunit PPH3
Primary source: SGD:S000002482
Locus tag: YDR075W
See related: AllianceGenome:SGD:S000002482; FungiDB:YDR075W; VEuPathDB:YDR075W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables protein serine/threonine phosphatase activity. Involved in several processes, including negative regulation of glucose mediated signaling pathway; positive regulation of double-strand break repair via nonhomologous end joining; and regulation of cell cycle phase transition. Acts upstream of or within regulation of TORC1 signaling. Located in nuclear periphery. Part of protein phosphatase 4 complex. Orthologous to human PPP4C (protein phosphatase 4 catalytic subunit). [provided by Alliance of Genome Resources, Jan 2025]
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Genomic context

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See PPH3 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 1

Sequence:: Chromosome: IV; NC_001136.10 (597156..598082)

Chromosome IV - NC_001136.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001136.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Deletion of PPH3, encoding a 2A-like protein phosphatase, accelerated telomere-shortening-mediated senescence without affecting normal telomere length or the telomere erosion rate in Saccharomyces cerevisiae.
Title: Phosphatase-dependent fluctuations in DNA-damage checkpoint activation at partially defective telomeres.
Physical interaction between Pph3 and Mec1, mediated by cofactors Psy2 and Ddc2, is important for regulating the checkpoint response in yeast.
Title: Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling.
Data indicate that the phosphatase complex Pph3/Psy2 connects homologous end-joining (NHEJ) repair to cell cycle progression.
Title: Phosphatase complex Pph3/Psy2 is involved in regulation of efficient non-homologous end-joining pathway in the yeast Saccharomyces cerevisiae.
Data show that Pph3-Psy2 targets the glucose signal transducer protein Mth1, which is required for the dephosphorylation of Rgt1 upon glucose withdrawal, a critical event in the repression of HXT genes, which encode glucose transporters.
Title: Psy2 targets the PP4 family phosphatase Pph3 to dephosphorylate Mth1 and repress glucose transporter gene expression.
Results suggest that the trimeric Pph3p-Psy4p-Psy2p complex may dephosphorylate both gammaH2AX and Rad53p.
Title: Characterization of the role of a trimeric protein phosphatase complex in recovery from cisplatin-induced versus noncrosslinking DNA damage.
Mutational analyses of conserved regions of Tap42/alpha4 identified a region critical for its interactions with PP2Ac. We propose a scaffolding function for Tap42/alpha4 whereby the interaction of PP2Ac promotes the dephosphorylation of substrates.
Title: The structure of Tap42/alpha4 reveals a tetratricopeptide repeat-like fold and provides insights into PP2A regulation.
a three-protein complex (HTP-C, for histone H2A phosphatase complex) containing the phosphatase Pph3 that regulates the phosphorylation status of gammaH2AX in vivo and efficiently dephosphorylates gammaH2AX in vitro
Title: A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery.
Mutants lacking either the phosphatase activator Rrd1 or the phosphatase Pph3 are resistant to rapamycin, double mutants exhibit a synergistic response.
Title: The Saccharomyces cerevisiae phosphatase activator RRD1 is required to modulate gene expression in response to rapamycin exposure.
Rad53 regulates replication fork restart and initiation of late firing origins independently
Title: Pph3-Psy2 is a phosphatase complex required for Rad53 dephosphorylation and replication fork restart during recovery from DNA damage.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables MAP kinase serine/threonine phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables calmodulin-dependent protein phosphatase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AXS140 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables myosin phosphatase activity	IEA Inferred from Electronic Annotation more info
enables phosphoprotein phosphatase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein serine/threonine phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein serine/threonine phosphatase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine phosphatase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair via homologous recombination	IBA Inferred from Biological aspect of Ancestor more info
involved_in double-strand break repair via homologous recombination	IGI Inferred from Genetic Interaction more info	PubMed
involved_in meiotic recombination checkpoint signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA damage checkpoint	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of glucose mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of double-strand break repair via nonhomologous end joining	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of TORC1 signaling	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	HDA more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nuclear periphery	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of protein phosphatase 4 complex	IDA Inferred from Direct Assay more info	PubMed
part_of protein phosphatase 4 complex	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: phosphoprotein phosphatase PP4 catalytic subunit PPH3

NP_010360.1

EC 3.1.3.16

Catalytic subunit of protein phosphatase PP4 complex; Pph3p and Psy2p form active complex, Psy4p may provide substrate specificity; regulates recovery from the DNA damage checkpoint, the gene conversion- and single-strand annealing-mediated pathways of meiotic double-strand break repair and efficient Non-Homologous End-Joining (NHEJ) pathway; involved in activation of Gln3p to alleviate nitrogen catabolite repression; Pph3p and Psy2p localize to foci on meiotic chromosomes

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001136.10 Reference assembly

Range

597156..598082

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001180383.1 → NP_010360.1 TPA: phosphoprotein phosphatase PP4 catalytic subunit PPH3 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010360.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VS61, P32345

UniProtKB/TrEMBL

A6ZY40, B3LGJ5, B5VFX1, C7GVR2, C8Z4Z3, G2WAH9, N1P842

Conserved Domains (1) summary

cd07415
Location:3 → 286

MPP_PP2A_PP4_PP6; PP2A, PP4, and PP6 phosphoprotein phosphatases, metallophosphatase domain