Unique structural features govern the activity of a human mitochondrial AAA+ disaggregase, Skd3

Abstract

The AAA+ protein, Skd3 (human CLPB), solubilizes proteins in the mitochondrial intermembrane space, which is critical for human health. Skd3 variants with impaired protein-disaggregase activity cause severe congenital neutropenia (SCN) and 3-methylglutaconic aciduria type 7 (MGCA7). Yet how Skd3 disaggregates proteins remains poorly understood. Here, we report a high-resolution structure of a Skd3-substrate complex. Skd3 adopts a spiral hexameric arrangement that engages substrate via pore-loop interactions in the nucleotide-binding domain (NBD). Unexpectedly, substrate-bound Skd3 hexamers stack head-to-head via unique, adaptable ankyrin-repeat domain (ANK)-mediated interactions to form dodecamers. Deleting the ANK-linker region reduces dodecamerization and disaggregase activity. We elucidate apomorphic features of the Skd3 NBD and C-terminal domain that regulate disaggregase activity. We also define how Skd3 subunits collaborate to disaggregate proteins. Importantly, SCN-linked subunits sharply inhibit disaggregase activity, whereas MGCA7-linked subunits do not. Our findings illuminate Skd3 structure and mechanism, explain SCN and MGCA7 inheritance patterns, and suggest therapeutic strategies.

Mitochondrial biology and dysfunction in secondary mitochondrial disease

“…In the presence of substrate, CLPB oligomerizes into a large (approx. 800 kDa) dodecameric species, comprising two CLPB hexamers interacting via highly versatile ankyrin repeat (ANK) domains [ 91 ]. Autosomal recessive mutations within CLPB cause 3-methylglutaconic aciduria, type 7B (MGCA7B, MIM #616271) [ 92 ], though autosomal dominant, de novo missense mutations have also been described (MGCA7A, MIM #619835) [ 93 ].…”