Affinage

PPP4R3B

Serine/threonine-protein phosphatase 4 regulatory subunit 3B · UniProt Q5MIZ7

Length
849 aa
Mass
97.5 kDa
Annotated
2026-06-10
15 papers in source corpus 7 papers cited in narrative 7 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 4/4 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PPP4R3B (SMEK2/Psy2) is a regulatory subunit of the PP4-type protein phosphatase complex, where it partners with the catalytic subunit Pph3 to govern the DNA damage response (PMID:17517611). The Pph3-Psy2 complex binds and dephosphorylates the activated checkpoint kinase Rad53 during and after MMS-induced damage, an activity required to restart replication forks during recovery from checkpoint arrest (PMID:17517611), and this Rad53-directed dephosphorylation role is conserved in Candida albicans, where Psy2 loss causes hypersensitivity to genotoxins and persistent filamentous growth (PMID:21890819). Beyond checkpoint recovery, the complex promotes non-homologous end-joining of double-strand breaks in a pathway parallel to Chk1 (PMID:24498054), and Psy2 itself undergoes CDK-dependent phosphorylation that is dispensable for checkpoint inactivation but essential for DSB repair, where it enforces symmetric resection across tandem retrotransposons by limiting phosphorylation of the Pif1 and Rrm3 helicases [PMID:bio_10.1101_2025.02.19.639064]. In mammalian/rat systems, Smek2 dysfunction has been linked to a distinct physiological role in hepatic glycolysis and sarcosine/homocysteine metabolism via reduced sarcosine dehydrogenase expression (PMID:36810603). The mammalian molecular mechanism connecting PPP4R3B to these metabolic phenotypes has not been characterized in the available corpus.

Mechanistic history

Synthesis pass · year-by-year structured walk · 6 steps
  1. 2004 Low

    Before its biochemical role was known, Psy2 was placed in the replication-fork stability pathway by mapping its protein and genetic interaction network.

    Evidence Yeast two-hybrid and genetic epistasis with WSS1, TOF1, RAD52, SRS2 in budding yeast

    PMID:15598824

    Open questions at the time
    • Physical interactions rest on yeast two-hybrid alone with no biochemical reconstitution
    • Does not define Psy2's catalytic partner or molecular activity
    • Fork-processing role inferred genetically, not directly demonstrated
  2. 2007 High

    Established that Psy2 is a regulatory subunit of the Pph3 phosphatase and that this complex drives checkpoint recovery by dephosphorylating Rad53.

    Evidence Biochemical co-purification, in vitro dephosphorylation assay, and replication fork analysis in yeast

    PMID:17517611

    Open questions at the time
    • Does not resolve how Psy2 confers substrate specificity onto Pph3
    • Recruitment mechanism to damage sites not defined
    • Mammalian ortholog activity not tested
  3. 2011 Medium

    Showed the Pph3-Psy2 checkpoint-recovery function is conserved beyond budding yeast and selective for Rad53 over H2AX.

    Evidence PSY2 deletion phenotyping, phospho-western blot, and flow cytometry in Candida albicans

    PMID:21890819

    Open questions at the time
    • Substrate selectivity mechanism (Rad53 vs H2AX) unexplained
    • Single lab
    • Link between dephosphorylation and filamentous-growth phenotype not mechanistically dissected
  4. 2014 Medium

    Extended the complex's role from checkpoint recovery to active DSB repair, defining an NHEJ function parallel to the Chk1 pathway.

    Evidence NHEJ repair assays, double-mutant epistasis, and Chk1 overexpression rescue in yeast

    PMID:24498054

    Open questions at the time
    • Direct phosphatase substrate in NHEJ not identified
    • Single lab
    • Molecular basis of parallelism with Chk1 unresolved
  5. 2023 Low

    Connected the mammalian/rat ortholog to a metabolic role distinct from DNA repair, implicating Smek2 in hepatic glycolysis and sarcosine/homocysteine handling.

    Evidence Congenic rat model with Smek2 deletion, microarray expression profiling, and metabolite measurement

    PMID:36810603

    Open questions at the time
    • No direct biochemical mechanism linking Smek2 to Sardh expression
    • Link between Smek2 loss and metabolic phenotype is correlative
    • Does not establish whether the PP4 phosphatase activity underlies the metabolic defect
  6. 2025 Medium

    Distinguished a CDK-regulated DSB-repair function of Psy2 from its checkpoint-inactivation role and identified replicative helicases as relevant phospho-targets controlling resection symmetry.

    Evidence Genetic epistasis, phospho-state analysis, resection assays, phosphodeficient mutant rescue, and helicase phosphorylation analysis in yeast (preprint)

    PMID:bio_10.1101_2025.02.19.639064

    Open questions at the time
    • Preprint, not peer-reviewed; single lab
    • Whether Pif1/Rrm3 are direct Pph3-Psy2 substrates not established
    • CDK site mapping and its mechanistic effect on complex function incomplete

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the mammalian PPP4R3B/SMEK2 subunit directs PP4 substrate choice and whether its DNA-repair role and its hepatic metabolic role share a common biochemical mechanism remain unresolved.
  • No mammalian substrate of the PPP4R3B-containing complex defined in the corpus
  • Mechanism bridging phosphatase activity and Sardh/metabolic regulation unknown
  • No structural model of the regulatory subunit's substrate-targeting function

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 2 GO:0140096 catalytic activity, acting on a protein 1
Pathway
R-HSA-73894 DNA Repair 3 R-HSA-8953897 Cellular responses to stimuli 2
Partners
PPH3RAD53TOF1WSS1
Complex memberships
Pph3-Psy2 (PP4) phosphatase complex

Evidence

Reading pass · 7 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 The yeast ortholog Psy2 forms a complex with the type 2A-like protein phosphatase Pph3 (Pph3-Psy2); this complex binds and dephosphorylates activated Rad53 during and after MMS-induced DNA damage, and is required for replication fork restart during recovery from DNA damage checkpoint arrest. Genetic epistasis, biochemical co-purification, in vitro dephosphorylation assay, replication fork analysis Proceedings of the National Academy of Sciences of the United States of America High 17517611
2004 Yeast Psy2 physically interacts with Wss1 and Tof1 (by yeast two-hybrid), and genetically interacts with WSS1, TOF1, RAD52, and SRS2, placing Psy2 in a pathway that stabilizes or processes stalled/collapsed replication forks. Yeast two-hybrid, genetic interaction/epistasis analysis Nucleic acids research Low 15598824
2011 In Candida albicans, Psy2 (orf19.3685) forms a functional complex with Pph3 required for dephosphorylation of the checkpoint kinase Rad53 (but not H2AX) during recovery from DNA damage; loss of PSY2 causes hypersensitivity to DNA-damaging agents and persistent filamentous growth under genotoxic stress. Deletion mutant phenotypic analysis, phosphorylation western blot, flow cytometry Eukaryotic cell Medium 21890819
2014 Yeast Pph3/Psy2 phosphatase complex promotes efficient non-homologous end-joining (NHEJ) of double-strand breaks; its activity in NHEJ is linked to the Rad53 checkpoint and operates in a pathway parallel to Chk1, as shown by Chk1 overexpression rescuing the NHEJ defect of pph3Δ and psy2Δ strains and double mutants showing additive repair defects. Plasmid and chromosomal NHEJ repair assays, genetic epistasis (double mutant analysis), overexpression rescue PloS one Medium 24498054
2023 In rats, a deletion mutation in Smek2 (PPP4R3B ortholog) impairs glycolysis in the liver and causes extremely low sarcosine dehydrogenase (Sardh) expression, leading to hypersarcosinemia and hyperhomocysteinemia, connecting Smek2 to regulation of hepatic sarcosine and homocysteine metabolism. Congenic rat model, microarray gene expression analysis, metabolite measurement Scientific reports Low 36810603
2020 The RNA binding protein Rbm38 reduces a transcription elongation defect of the SMEK2 (PPP4R3B) gene that occurs under splicing-deficient conditions; this requires the N- and C-terminal regions of Rbm38 and its RNA-recognition motif. Transcription elongation assay under splicing-deficient conditions, Rbm38 domain deletion analysis International journal of molecular sciences Medium 33233740
2025 Yeast Psy2 (PP4 regulatory subunit) undergoes CDK-dependent phosphorylation that is essential for DSB repair but not for DNA damage checkpoint inactivation; Psy2 promotes symmetric DSB resection across tandem retrotransposons by reducing phosphorylation of Pif1 and Rrm3 helicases, and its loss causes an asymmetric resection defect that is alleviated by expressing a phosphodeficient H2A variant or depleting the checkpoint adaptor Rad9. Genetic epistasis, phosphorylation state analysis, resection assays, phosphodeficient mutant rescue, helicase substrate phosphorylation analysis bioRxivpreprint Medium bio_10.1101_2025.02.19.639064

Source papers

Stage 0 corpus · 15 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2007 Pph3-Psy2 is a phosphatase complex required for Rad53 dephosphorylation and replication fork restart during recovery from DNA damage. Proceedings of the National Academy of Sciences of the United States of America 114 17517611
1993 cDNA cloning, expression during development, and genome mapping of PSY2, a second tomato gene encoding phytoene synthase. The Journal of biological chemistry 81 8245008
2004 Coordinated functions of WSS1, PSY2 and TOF1 in the DNA damage response. Nucleic acids research 29 15598824
2011 Protein phosphatase Pph3 and its regulatory subunit Psy2 regulate Rad53 dephosphorylation and cell morphogenesis during recovery from DNA damage in Candida albicans. Eukaryotic cell 26 21890819
2014 Phosphatase complex Pph3/Psy2 is involved in regulation of efficient non-homologous end-joining pathway in the yeast Saccharomyces cerevisiae. PloS one 17 24498054
2013 The sub-cellular localisation of the potato (Solanum tuberosum L.) carotenoid biosynthetic enzymes, CrtRb2 and PSY2. Protoplasma 13 23794103
2017 Molecular analysis of the expression of a crtB transgene and the endogenous psy2-y 1 and psy2-y 2 genes of cassava and their effect on root carotenoid content. Transgenic research 7 28779475
2020 Structural and functional features of phytoene synthase isoforms PSY1 and PSY2 in pepper Capsicum annuum L. cultivars. Vavilovskii zhurnal genetiki i selektsii 6 33738386
2008 Identification of SMEK2 as a candidate gene for regulation of responsiveness to dietary cholesterol in rats. Journal of lipid research 6 18753676
2020 Rbm38 Reduces the Transcription Elongation Defect of the SMEK2 Gene Caused by Splicing Deficiency. International journal of molecular sciences 3 33233740
2011 Complete sequence and organization of the Sphingobium chungbukense DJ77 pSY2 plasmid. Journal of microbiology (Seoul, Korea) 3 21887656
2020 Variability and Phylogeny of the Pepper Phytoene Synthase Paralogs PSY1 and PSY2 in Species of Various Capsicum Complexes. Doklady. Biochemistry and biophysics 2 33368035
2024 Circadian Regulation of Expression of Carotenoid Metabolism Genes (PSY2, LCYE, CrtRB1, and NCED1) in Leaves of Tomato Solanum lycopersicum L. Doklady. Biochemistry and biophysics 1 39196523
2023 Mutation in Smek2 regulating hepatic glucose metabolism causes hypersarcosinemia and hyperhomocysteinemia in rats. Scientific reports 1 36810603
2016 [Effects of Acaulospora spinosa on plant growth and lycopene related genes (psyl and psy2) expression of tomato]. Ying yong sheng tai xue bao = The journal of applied ecology 0 27396123

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