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Structure paper

TitleUnique structural features govern the activity of a human mitochondrial AAA+ disaggregase, Skd3.
Journal, issue, pagesCell Rep, Vol. 40, Issue 13, Page 111408, Year 2022
Publish dateSep 27, 2022
AuthorsRyan R Cupo / Alexandrea N Rizo / Gabriel A Braun / Eric Tse / Edward Chuang / Kushol Gupta / Daniel R Southworth / James Shorter /
PubMed AbstractThe AAA+ protein, Skd3 (human CLPB), solubilizes proteins in the mitochondrial intermembrane space, which is critical for human health. Skd3 variants with defective protein-disaggregase activity ...The AAA+ protein, Skd3 (human CLPB), solubilizes proteins in the mitochondrial intermembrane space, which is critical for human health. Skd3 variants with defective protein-disaggregase activity cause severe congenital neutropenia (SCN) and 3-methylglutaconic aciduria type 7 (MGCA7). 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). 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. These advances illuminate Skd3 structure and mechanism, explain SCN and MGCA7 inheritance patterns, and suggest therapeutic strategies.
External linksCell Rep / PubMed:36170828 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 2.96 Å
Structure data

26121

7ttr

EMDB-26121, PDB-7ttr:
Skd3_ATPyS_FITC-casein Hexamer, AAA+ only
Method: EM (single particle) / Resolution: 2.96 Å

26122

7tts

EMDB-26122, PDB-7tts:
Skd3, hexamer, filtered
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

Source
  • homo sapiens (human)
  • bos taurus (cattle)
KeywordsCHAPERONE / cryoEM / AAA+

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