Affinage · Plasmodium

UBC13

PF3D7_0527100 · ubiquitin-conjugating enzyme E2 13

Annotated
2026-09-07
6 papers in source corpus 6 papers cited in narrative 6 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PF3D7_0527100 (UBC13) is the ubiquitin-conjugating (E2) enzyme responsible for K63-linkage-specific polyubiquitination in Plasmodium falciparum, and this activity is essential for asexual blood-stage growth (PMID:34750454). Genetic deletion of ubc13 reduces cellular K63-linked ubiquitination, impairs parasite proliferation, and sensitizes parasites to the DNA mutagen methyl methanesulfonate and to dihydroartemisinin but not chloroquine, linking UBC13-dependent K63-ubiquitination to DNA repair and artemisinin response (PMID:34750454). Catalysis depends on the enzyme's catalytic cysteine, which is covalently and potently targeted by the inhibitor NSC697923; inhibition selectively lowers K63-ubiquitination, reduces nascent protein synthesis, and identifies UBC13 substrates enriched in transcription, translation, and proteasome-associated processes, extending its role to protein translation (PMID:40491475). UBC13 activity is negatively regulated by phosphorylation at the conserved residue S106, which suppresses its ubiquitin-conjugating activity in vitro (PMID:17452636); in P. falciparum this modification is mediated by the kinase PfPK9 (PMID:17452636, PMID:30595530), whereas in P. berghei S106 phosphorylation is essential for blood-stage viability but occurs independently of PbPK9, indicating redundant kinase activity (PMID:35490588). UBC13 physically associates with the P. falciparum RBR-E3 ligase (PMID:40035193).

Mechanistic history

Synthesis pass · year-by-year structured walk · 6 steps
  1. 2007 High

    Establishing how UBC13 activity is controlled, this work identified UBC13 as a phospho-substrate whose conjugating activity is switched off by modification of a conserved E2 residue.

    Evidence In vitro kinase assay with recombinant PfPK9 and UBC13, phosphopeptide mapping to S106, and ubiquitin-conjugating activity assay

    PMID:17452636

    Open questions at the time
    • In vitro only; cellular consequences of S106 phosphorylation not tested
    • Whether phosphorylation blocks E2 charging or thioester transfer not resolved
  2. 2018 Medium

    Connecting UBC13 regulation to a specific ubiquitin output, chemical inhibition of its upstream kinase reduced K63-linked ubiquitination in living parasites, tying UBC13 to K63 chain formation in cells.

    Evidence Chemical inhibition of PfPK9 (takinib, HS220) in P. falciparum with K63-Ub immunoblot readout

    PMID:30595530

    Open questions at the time
    • Effect on K63-Ub is indirect, inferred through PfPK9 inhibition rather than direct UBC13 perturbation
    • Kinase inhibitors may have off-target effects on other substrates
  3. 2021 High

    Directly testing UBC13's cellular role, inducible deletion established it as the E2 enzyme driving K63-ubiquitination and required for blood-stage growth, DNA repair, and artemisinin sensitivity.

    Evidence Inducible Di-Cre deletion of ubc13 in P. falciparum with K63-Ub immunoblot, growth and drug-sensitivity (MMS, DHA, chloroquine) assays, and chemical inhibition (NSC697923)

    PMID:34750454

    Open questions at the time
    • Substrates whose K63-ubiquitination mediates DNA repair not identified
    • Mechanism linking K63-ubiquitination to DHA response unresolved
  4. 2022 Medium

    Assessing kinase specificity in vivo, a P. berghei knockout showed S106 phosphorylation is essential for viability yet occurs independently of PbPK9, revealing kinase redundancy for this regulatory mark.

    Evidence PK9 knockout in P. berghei, site-directed mutation of UBC13 S106, phosphorylation analysis, immunofluorescence co-localization, and life-cycle viability assays

    PMID:35490588

    Open questions at the time
    • Identity of the redundant kinase(s) phosphorylating S106 unknown
    • Species divergence from P. falciparum PfPK9 dependence not mechanistically explained
  5. 2025 High

    Pinpointing the catalytic requirement and downstream biology, covalent targeting of the catalytic cysteine defined UBC13's substrate landscape and revealed a role in translation, with therapeutic synergy against DHA.

    Evidence Covalent inhibitor (NSC697923) characterization, in vitro potency, parasite K63-Ub immunoblot, chemoproteomic substrate identification (31 substrates), nascent protein synthesis assay, and DHA synergy assay in P. falciparum

    PMID:40491475

    Open questions at the time
    • Which of the 31 putative substrates are direct, physiologically K63-ubiquitinated targets not validated individually
    • Mechanism by which K63-ubiquitination promotes translation not defined
  6. 2025 Low

    Placing UBC13 in an E2-E3 pairing, co-immunoprecipitation showed physical association with the P. falciparum RBR-E3 ligase capable of multiple ubiquitin linkages.

    Evidence Co-immunoprecipitation of Pf RBR-E3 ligase with UBC13 in P. falciparum

    PMID:40035193

    Open questions at the time
    • Single co-IP without reciprocal pulldown or functional validation of the UBC13-RBR interaction
    • Whether UBC13 cooperates with this E3 to build K63 chains specifically not shown

Open questions

Synthesis pass · forward-looking unresolved questions
  • The physiological substrates whose K63-ubiquitination by UBC13 drives DNA repair, translation, and artemisinin response, and the identity of the redundant S106 kinase(s), remain undefined.
  • No validated direct substrate list for UBC13-dependent K63 chains
  • Cognate E3 ligase(s) partnering UBC13 for each cellular output not established
  • Structural basis for S106 phospho-regulation of catalysis unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification
Partners
PF RBR-E3 LIGASE (CO-IP INTERACTOR)PFPK9 (KINASE PHOSPHORYLATING UBC13 S106 IN P. FALCIPARUM)

Evidence

Reading pass · 6 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 PF3D7_0527100 (UBC13) is a substrate of the P. falciparum kinase PfPK9; PfPK9 phosphorylates UBC13 at S106, a conserved residue among eukaryotic E2 ubiquitin-conjugating enzymes, and this phosphorylation suppresses UBC13's ubiquitin-conjugating activity in vitro. In vitro kinase assay with recombinant PfPK9 and UBC13, phosphopeptide mapping identifying S106 as phosphorylation site, ubiquitin-conjugating activity assay Proceedings of the National Academy of Sciences of the United States of America High 17452636
2018 PF3D7_0527100 (UBC13) mediates K63-linkage-specific polyubiquitination in P. falciparum; inhibition of PfPK9 (which phosphorylates UBC13) with small molecules takinib or HS220 decreases K63-linked ubiquitination in parasite cells. Chemical inhibition of PfPK9 (takinib, HS220) in P. falciparum followed by quantification of K63-linked ubiquitination by immunoblot Cell chemical biology Medium 30595530
2022 In P. berghei, phosphorylation of UBC13 at regulatory S106 is essential for blood-stage parasite viability; however, PbPK9 is dispensable for this phosphorylation (phosphorylation of S106 still occurs in PK9 knockout parasites), demonstrating redundancy in the kinase(s) responsible for this modification. UBC13 and PK9 co-localize in the cytosol of erythrocytic and liver stages. Genetic knockout of PK9 in P. berghei, site-directed mutation of UBC13 S106, phosphorylation analysis, co-localization by immunofluorescence, parasite viability assays across life cycle stages Microbiological research Medium 35490588
2021 Deletion of UBC13 (PF3D7_0527100) in P. falciparum reduces K63-linked ubiquitination of protein substrates, impairs asexual blood-stage parasite growth in vitro, and increases parasite sensitivity to the DNA mutagen methyl methanesulfonate and to dihydroartemisinin (but not chloroquine), establishing UBC13 as the E2 enzyme responsible for K63-ubiquitylation and implicating this pathway in DNA repair and artemisinin response. Inducible Di-Cre genetic deletion of ubc13 in P. falciparum, K63-Ub immunoblot, in vitro growth assay, drug sensitivity assays (MMS, DHA, chloroquine), chemical inhibition with NSC697923 Scientific reports High 34750454
2025 PF3D7_0527100 (UBC13) is an E3 ligase-interacting E2 enzyme; the P. falciparum RBR-E3 ligase physically interacts with UBC13 (and UBCH5) as shown by immunoprecipitation, and the E3 catalyzes K6, K11, K48, and K63-mediated polyubiquitination. Co-immunoprecipitation of Pf RBR-E3 ligase with UBC13 in P. falciparum Proteins Low 40035193
2025 NSC697923 covalently targets the catalytic cysteine of PF3D7_0527100 (UBC13) with nanomolar inhibitory potency, specifically reduces K63-linked ubiquitination in blood-stage P. falciparum, and chemoproteomic profiling identified 31 putative UBC13 substrates enriched in transcription, translation, and proteasome processes. Inhibition of UBC13 reduces nascent protein synthesis, establishing a role for UBC13-dependent K63-ubiquitination in protein translation. NSC697923 synergizes with dihydroartemisinin. Covalent inhibitor characterization (NSC697923), in vitro inhibitory potency assay, K63-Ub immunoblot in parasites, chemoproteomic substrate identification (31 substrates), nascent protein synthesis assay (puromycin incorporation or similar), drug synergy assay iScience High 40491475

Source papers

Stage 0 corpus · 6 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2007 Characterization of a UBC13 kinase in Plasmodium falciparum. Proceedings of the National Academy of Sciences of the United States of America 25 17452636
2018 Plasmodium PK9 Inhibitors Promote Growth of Liver-Stage Parasites. Cell chemical biology 14 30595530
2022 Protein kinase 9 is not required for completion of the Plasmodium berghei life cycle. Microbiological research 13 35490588
2021 Deletion of Plasmodium falciparum ubc13 increases parasite sensitivity to the mutagen, methyl methanesulfonate and dihydroartemisinin. Scientific reports 9 34750454
2025 Understanding the Role of RING-Between-RING E3 Ligase of the Human Malaria Parasite. Proteins 2 40035193
2025 Covalent inhibition of Plasmodium falciparum Ubc13 impairs global protein synthesis. iScience 0 40491475