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

Cupo, Ryan R.; Rizo, Alexandrea N.; Braun, Gabriel A.; Tse, Eric; Chuang, Edward; Gupta, Kushol; Southworth, Daniel R.; Shorter, James

doi:10.1016/j.celrep.2022.111408

Cited by 16 publications

(37 citation statements)

References 88 publications

(193 reference statements)

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“…Unexpectedly, we found that apo CLPB assembles into higher-order structures, in the form of a double-heptamer through inter-molecular interactions mediated by N-terminal ANK domains (Fig 1). This high-order organization is consistent with recent structural studies of purified CLPB [20,21] and a previous native gel analysis of endogenous CLPB proteins [11]. We further demonstrate that the double-heptamers could be efficiently converted to double-hexamers upon the addition of a model substrate and ATPγS (Fig 2).…”

Section: Discussionsupporting

confidence: 91%

“…Therefore, this insertion is likely involved in the substrate recognition and may also contribute to the translocation of the substrate to the C-terminal NBD ring. In agreement with our data, Cupo and colleagues also found that the deletion of this loop (Skd3 ΔL ), as well as the deletion of the first 2 AMs or the last 2 AMs, all resulted in more than 50% of reduction in the disaggregase activity [20].…”

Section: Plos Biologysupporting

confidence: 92%

“…Both the double-heptamer and double-hexamer are highly dynamic. As also observed in another structural study of CLPB [20], several factors contribute to the conformational flexibility of the full-length complexes. The first is the hexamer/heptamer interface.…”

Section: Plos Biologysupporting

confidence: 74%

“…Interestingly, both gel filtration and nsEM showed that the purified CLPB complex is in a higher oligomeric state rather than a hexamer as expected from typical AAA+ unfoldases and disaggregases ( S2A and S2B Fig ). Very recently, 2 independent studies have also reported that purified CLPB exhibits an unusual higher-order oligomeric form [ 20 , 21 ]. And this higher-order organization is irrelevant of exogenously supplemented AMPPNP ( S2A Fig ).…”

Section: Resultsmentioning

confidence: 99%

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Comprehensive structural characterization of the human AAA+ disaggregase CLPB in the apo- and substrate-bound states reveals a unique mode of action driven by oligomerization

Liu

Dai

et al. 2023

PLoS Biol

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The human AAA+ ATPase CLPB (SKD3) is a protein disaggregase in the mitochondrial intermembrane space (IMS) and functions to promote the solubilization of various mitochondrial proteins. Loss-of-function CLPB mutations are associated with a few human diseases with neutropenia and neurological disorders. Unlike canonical AAA+ proteins, CLPB contains a unique ankyrin repeat domain (ANK) at its N-terminus. How CLPB functions as a disaggregase and the role of its ANK domain are currently unclear. Herein, we report a comprehensive structural characterization of human CLPB in both the apo- and substrate-bound states. CLPB assembles into homo-tetradecamers in apo-state and is remodeled into homo-dodecamers upon substrate binding. Conserved pore-loops (PLs) on the ATPase domains form a spiral staircase to grip and translocate the substrate in a step-size of 2 amino acid residues. The ANK domain is not only responsible for maintaining the higher-order assembly but also essential for the disaggregase activity. Interactome analysis suggests that the ANK domain may directly interact with a variety of mitochondrial substrates. These results reveal unique properties of CLPB as a general disaggregase in mitochondria and highlight its potential as a target for the treatment of various mitochondria-related diseases.

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Section: Discussionsupporting

confidence: 91%

Section: Plos Biologysupporting

confidence: 92%

Section: Plos Biologysupporting

confidence: 74%

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Comprehensive structural characterization of the human AAA+ disaggregase CLPB in the apo- and substrate-bound states reveals a unique mode of action driven by oligomerization

Liu

Dai

et al. 2023

PLoS Biol

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“…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].…”

Section: Protein Quality Controlmentioning

confidence: 99%

Mitochondrial biology and dysfunction in secondary mitochondrial disease

et al. 2022

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Mitochondrial diseases are a broad, genetically heterogeneous class of metabolic disorders characterized by deficits in oxidative phosphorylation (OXPHOS). Primary mitochondrial disease (PMD) defines pathologies resulting from mutation of mitochondrial DNA (mtDNA) or nuclear genes affecting either mtDNA expression or the biogenesis and function of the respiratory chain. Secondary mitochondrial disease (SMD) arises due to mutation of nuclear-encoded genes independent of, or indirectly influencing OXPHOS assembly and operation. Despite instances of novel SMD increasing year-on-year, PMD is much more widely discussed in the literature. Indeed, since the implementation of next generation sequencing (NGS) techniques in 2010, many novel mitochondrial disease genes have been identified, approximately half of which are linked to SMD. This review will consolidate existing knowledge of SMDs and outline discrete categories within which to better understand the diversity of SMD phenotypes. By providing context to the biochemical and molecular pathways perturbed in SMD, we hope to further demonstrate the intricacies of SMD pathologies outside of their indirect contribution to mitochondrial energy generation.

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Decoding Skd3 (Human CLPB): a Mitochondrial Protein Disaggregase Critical for Human Health

Cupo,

Shorter

2024

Israel Journal of Chemistry

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Protein folding is important for all life. Indeed, protein misfolding can result in catastrophic protein aggregation and toxicity. The pathways involved in reversing protein aggregation within human mitochondria had long been unknown. We recently discovered that Skd3 (human CLPB) is a potent mitochondrial protein disaggregase, which is regulated by the rhomboid protease PARL, and maintains the solubility of many important mitochondrial proteins. Skd3 variants underlie several debilitating human diseases, including 3‐methylglutaconic aciduria, severe congenital neutropenia, and premature ovarian insufficiency. Here, we describe advances in understanding Skd3 function, mechanism, and structure and place these discoveries in the context of physiology and disease.

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

Cited by 16 publications

References 88 publications

Comprehensive structural characterization of the human AAA+ disaggregase CLPB in the apo- and substrate-bound states reveals a unique mode of action driven by oligomerization

Comprehensive structural characterization of the human AAA+ disaggregase CLPB in the apo- and substrate-bound states reveals a unique mode of action driven by oligomerization

Mitochondrial biology and dysfunction in secondary mitochondrial disease

Decoding Skd3 (Human CLPB): a Mitochondrial Protein Disaggregase Critical for Human Health

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