RPN13

PF3D7_1414000 (RPN13/PfRpn13) is an intrinsic ubiquitin receptor of the P. falciparum 26S proteasome regulatory particle, identified within affinity-purified native proteasome complexes and implicated in proteasomal substrate recognition (PMID:26639022). Its DEUBAD domain directly binds the shuttle protein PfDsk2 through PfDsk2's UBL domain, with an affinity comparable to the human homolog system, positioning PfRpn13 to receive ubiquitinated substrates and cooperate with deubiquitinating enzymes during substrate proofreading (PMID:32057831). The same DEUBAD domain also engages the deubiquitinase PfUCH37 by binding its C-terminal region, and deletion of the last 20 amino acids of PfUCH37 abolishes the interaction, establishing that the Rpn13–UCH37 binding mechanism is evolutionarily conserved in the parasite (PMID:39604441). Together these findings place PfRpn13 at the interface of ubiquitinated substrate delivery and deubiquitinase recruitment at the proteasome. A complexome profiling study did not detect PfRpn13 co-migrating with 19S or 20S proteasome assemblies in asexual blood-stage or gametocyte extracts (PMID:34155201); beyond these interaction and localization findings, no functional or genetic characterization of PfRpn13 has been reported in the available corpus.

1. 2015 Medium

   Establishing which subunit of the parasite proteasome recognizes ubiquitinated substrates was needed to map how P. falciparum targets proteins for degradation; this work placed PfRpn13 as an intrinsic ubiquitin receptor of the native 26S proteasome.

   Evidence Affinity purification of native 26S proteasome complexes with in situ crosslinking and mass spectrometry subunit identification in P. falciparum

   PMID:26639022

   Open questions at the time

   • No direct binding assay demonstrating PfRpn13 engages ubiquitin or polyubiquitin chains
   • RPN13-specific role inferred from complex composition rather than isolated functional assay
   • No genetic evidence for essentiality or phenotype
2. 2020 Medium

   Whether PfRpn13 physically receives substrate-shuttling factors was unresolved; identifying a DEUBAD-domain interaction with the shuttle protein PfDsk2 UBL domain defined a route for ubiquitinated substrate delivery to the parasite proteasome.

   Evidence Crystal structure of PfDsk2 UBL domain at 1.30 Å plus dissociation-constant measurements between PfDsk2 UBL and PfRpn13

   PMID:32057831

   Open questions at the time

   • No co-crystal structure of the PfRpn13–PfDsk2 complex
   • Functional consequence of the interaction for substrate degradation not tested in parasites
   • Single lab, binding data reported only at the level described
3. 2024 Medium

   Whether the conserved Rpn13–UCH37 deubiquitinase axis operates in the parasite was unknown; mapping the DEUBAD-to-C-terminal PfUCH37 interaction and abolishing it by truncation established a conserved mechanism for deubiquitinase recruitment.

   Evidence Co-immunoprecipitation with a defined PfUCH37 C-terminal truncation mutant and proteomics in transgenic P. falciparum parasites

   PMID:39604441

   Open questions at the time

   • No demonstration that PfRpn13 binding activates PfUCH37 deubiquitinase activity
   • Structural basis of the DEUBAD–PfUCH37 interaction not resolved
   • Functional impact on proteasomal substrate processing not measured
4. 2021 Low

   The stability of PfRpn13 association with assembled proteasomes was probed by native co-migration; PfRpn13 was not detected co-migrating with 19S or 20S assemblies, raising the question of how stably it associates under these conditions.

   Evidence Complexome profiling by native co-migration mass spectrometry across asexual blood stages and gametocytes in P. falciparum

   PMID:34155201

   Open questions at the time

   • Negative result may reflect technical dissociation during native profiling rather than true non-association
   • Does not distinguish sub-stoichiometric or transient association from absence
   • Not reconciled with detection of PfRpn13 within purified proteasomes

• Whether PfRpn13 is essential for parasite viability and how its coordinated recognition of ubiquitinated substrates and recruitment of PfUCH37 alters degradation kinetics or drug susceptibility remains unaddressed.
• No genetic knockout or knockdown phenotype reported
• No demonstration of ubiquitin/polyubiquitin binding activity for PfRpn13 itself
• Functional integration of substrate delivery and deubiquitination at the parasite proteasome not established