Proteasome in action: substrate degradation by the 26S proteasome

Abstract

Ubiquitination is the major criteria for the recognition of a substrate-protein by the 26S proteasome. Additionally, a disordered segment on the substrate — either intrinsic or induced — is critical for proteasome engagement. The proteasome is geared to interact with both of these substrate features and prepare it for degradation. To facilitate substrate accessibility, resting proteasomes are characterised by a peripheral distribution of ubiquitin receptors on the 19S regulatory particle (RP) and a wide-open lateral surface on the ATPase ring. In this substrate accepting state, the internal channel through the ATPase ring is discontinuous, thereby obstructing translocation of potential substrates. The binding of the conjugated ubiquitin to the ubiquitin receptors leads to contraction of the 19S RP. Next, the ATPases engage the substrate at a disordered segment, energetically unravel the polypeptide and translocate it towards the 20S catalytic core (CP). In this substrate engaged state, Rpn11 is repositioned at the pore of the ATPase channel to remove remaining ubiquitin modifications and accelerate translocation. C-termini of five of the six ATPases insert into corresponding lysine-pockets on the 20S α-ring to complete 20S CP gate opening. In the resulting substrate processing state, the ATPase channel is fully contiguous with the translocation channel into the 20S CP, where the substrate is proteolyzed. Complete degradation of a typical ubiquitin-conjugate takes place over a few tens of seconds while hydrolysing tens of ATP molecules in the process (50 kDa/∼50 s/∼80ATP). This article reviews recent insight into biochemical and structural features that underlie substrate recognition and processing by the 26S proteasome.

Ubiquitination and receptor-mediated mitophagy converge to eliminate oxidation-damaged mitochondria during hypoxia

“…Mitochondria ubiquitination is an early event in hypoxia-induced mitophagy and is predominantly K48-linked. K48-linkages have been classically implicated as a signal for proteasome-mediated degradation of target proteins [ 19 , 50 ], whereas K63-linked polyubiquitin chains are important in the endosomal-lysosomal pathway [ 51 ]. Recruitment of proteasome and other components of the UPS pathway to the stressed mitochondria in this study (including UBA1, UBE2S, HUWE1, MARCH5, UBR4, TRIM25, USP33, VCP/p97, UBXN4/UBXD2, and FKBP8) provides some insight into what drives mitochondria ubiquitination, fragmentation, and clearance.…”

Fragment-Sized and Bidentate (Immuno)Proteasome Inhibitors Derived from Cysteine and Threonine Targeting Warheads

“…Protein degradation was considered a neglected field before the 1980s, but the discovery of ubiquitin pathways has put the topic in a different perspective [ 1 ]. The ubiquitin–proteasome system (UPS) [ 2 ] and, in particular, the multicatalytic activity of the 26S proteasome [ 3 , 4 , 5 , 6 , 7 ] play a fundamental role in important cellular processes such as apoptosis [ 8 ], immune response [ 9 ], cell cycle progression [ 10 ], and regulation of transcription.…”

ANTH domains within CALM, HIP1R, and Sla2 recognize ubiquitin internalization signals

“…One of the issues that arises from this study is why there are many Ub-binding domains. Other cellular machines that process ubiquitinated proteins also possess multiple Ubbinding sites, including the proteasome, which degrades ubiquitinated cytosolic proteins (Sahu and Glickman, 2021), and the ESCRT machinery, that sorts ubiquitinated proteins into endosomal intralumenal vesicles (Piper et al, 2014). Many of the same hypotheses to explain multiple Ub-binding interfaces in these complexes are also plausible for the internalization apparatus.…”