Structural heterogeneity and substrate engagement mechanism of the bacterial proteasome activator Bpa

Bacterial proteasomal activator (Bpa) is a regulatory particle of the Mycobacterium tuberculosis proteasome that facilitates the recruitment of substrates and their subsequent degradation by the 20S core particle. Substrate-bound structures of Bpa are unavailable, leaving its recruitment mechanism incompletely understood. Here, we use mass spectrometry and NMR to show that Bpa reversibly assembles into dodecamers from dimers/tetramers in a temperature-dependent manner in vitro, and map the oligomerization interfaces during assembly. To overcome the limitations posed by the poor solubility of natural Bpa substrates, we establish the DNA-binding domain of hTRF1 as a model substrate. We quantify the affinity and stoichiometry of the Bpa-hTRF1 interaction using methyl-TROSY NMR, identifying a 12 Bpa subunit: 3 hTRF1 binding ratio with micromolar affinity that is modulated by salt concentration. Our work maps the Bpa-hTRF1 interface at atomic resolution, identifies determinants of substrate engagement, and introduces a tractable substrate for dissecting proteasomal recognition in mycobacteria.