Conformational switching in the coiled-coil domains of a proteasomal ATPase regulates substrate processing

Snoberger, Aaron; Brettrager, Evan J; Smith, David M.

doi:10.1038/s41467-018-04731-6

Cited by 29 publications

(29 citation statements)

References 59 publications

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“…Within the axial channel of the RPT ring, the substrate is in contact with the tyrosine or phenylalanine residues of pore-1 loops, where the aromatic side chains intercalate with the zigzagging mainchain of the substrate polypeptide through hydrophobic interactions. Furthermore, the N-terminal CC domains of RPT subunits, in contact with the lid subcomplex, allosterically regulate ATPase activity in a long-range fashion and contribute to the conformational switch of the holoenzyme [11,128]. The RP undergoes dramatic rotation (30 • -40 • ) and translation relative to the CP during the transition of the CP gate from its closed to its open state ( Figure 3a).…”

Section: Conformational Changes Of Aaa Atpases In the 26s Proteasomementioning

confidence: 99%

AAA+ ATPases in Protein Degradation: Structures, Functions and Mechanisms

Zhang

Mao

2020

Biomolecules

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Adenosine triphosphatases (ATPases) associated with a variety of cellular activities (AAA+), the hexameric ring-shaped motor complexes located in all ATP-driven proteolytic machines, are involved in many cellular processes. Powered by cycles of ATP binding and hydrolysis, conformational changes in AAA+ ATPases can generate mechanical work that unfolds a substrate protein inside the central axial channel of ATPase ring for degradation. Three-dimensional visualizations of several AAA+ ATPase complexes in the act of substrate processing for protein degradation have been resolved at the atomic level thanks to recent technical advances in cryogenic electron microscopy (cryo-EM). Here, we summarize the resulting advances in structural and biochemical studies of AAA+ proteases in the process of proteolysis reactions, with an emphasis on cryo-EM structural analyses of the 26S proteasome, Cdc48/p97 and FtsH-like mitochondrial proteases. These studies reveal three highly conserved patterns in the structure–function relationship of AAA+ ATPase hexamers that were observed in the human 26S proteasome, thus suggesting common dynamic models of mechanochemical coupling during force generation and substrate translocation.

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Section: Conformational Changes Of Aaa Atpases In the 26s Proteasomementioning

confidence: 99%

AAA+ ATPases in Protein Degradation: Structures, Functions and Mechanisms

Zhang

Mao

2020

Biomolecules

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“…Coiled-coil registry shifts have only been reported for a few structures (Carter et al, 2008;Croasdale et al, 2011;Gibbons et al, 2005;Macheboeuf et al, 2011;Snoberger et al, 2018;Xi et al, 2012), but may potentially be an inherent property of many coiledcoil structures. The most extensively studied example is dynein itself.…”

Section: Introductionmentioning

confidence: 99%

Role of coiled-coil registry shifts in activation of human Bicaudal D2 for dynein recruitment upon cargo-binding

Noell

Loh

Debler

et al. 2019

Preprint

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Highlights• Stable, bona fide BicD2 coiled-coils with distinct registries can be formed.• We provide evidence that a human disease mutation causes a coiled-coil registry shift.• A coiled-coil registry shift could relieve BicD2-autoinhibition upon cargo-binding.• The ability to undergo registry shifts may be an inherent property of coiled-coils. In BriefOur results support that stable coiled-coils of BicD2 with distinct registries can be formed, and suggest a molecular mechanism for such registry switches. We provide evidence that disease-causing mutations in coiled-coils may alter the equilibrium between registry-shifted conformers, which we propose as a general mechanism of pathogenesis for coiled-coils. Graphical Abstract3 SUMMARY Dynein adaptors such as Bicaudal D2 (BicD2) recognize cargo for dynein-dependent transport. BicD2-dependent transport pathways are important for brain and muscle development. Cargo-bound adaptors are required to activate dynein for processive transport, but the mechanism of action is elusive. Here, we report the structure of the cargo-binding domain of human BicD2 that forms a dimeric coiled-coil with homotypic registry, in which both helices are aligned. To investigate if BicD2 can switch to an asymmetric registry, where a portion of one helix is vertically shifted, we performed molecular dynamics simulations. Both registry types are stabilized by distinct conformations of F743. For the F743I variant, which increases dynein recruitment in the Drosophila homolog, and for the human R747C variant, which causes spinal muscular atrophy, spontaneous coiled-coil registry shifts are observed, which may cause the BicD2-hyperactivation phenotype and disease. We propose that a registry shift upon cargo-binding activates auto-inhibited BicD2 for dynein recruitment.

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“…Hence, depending on the assay used, an underestimation or overestimation of the nucleotide:protein stoichiometry is feasible. On the other hand, the recent crosslinking experiments performed using PAN M87C mutant provided a surprising outcome of an asymmetric configuration of three identical coil-coil (CC) domains of PAN, with each CC adopting a different conformation(35).While these results support a notion of a pairwise model of PAN carrying a total of 4 nucleotides(14), they are contradicted by the X-Ray analyses that were performed on truncated forms of PAN from A. fulgidus(11) and from M. jannaschii (AA 74-150)(10), which pointed to an inregister arrangement of 3 CC domains. Clearly, despite the progress in proteasome-related studies, some aspects of AAA+ ATPase structure and function remain unresolved.Generation of over-charged multimers and partial hexamer dissociation in the native nanoESIMS spectra of PAN hexamer by guest on October 29, 2020…”

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Stoichiometry of Nucleotide Binding to Proteasome AAA+ ATPase Hexamer Established by Native Mass Spectrometry

Liu

et al. 2020

Molecular & Cellular Proteomics

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AAA+ ATPases constitute a large family of proteins that are involved in a plethora of cellular processes including DNA disassembly, protein degradation and protein complex disassembly. They typically form a hexametric ring-shaped structure with six subunits in a (pseudo) six-fold symmetry. In a subset of AAA+ ATPases that facilitate protein unfolding and degradation, six subunits cooperate to translocate protein substrates through a central pore in the ring. The number and type of nucleotides in an AAA+ ATPase hexamer is inherently linked to the mechanism that underlies cooperation among subunits and couples ATP hydrolysis with substrate translocation. We conducted a native mass spectrometry study of a monodispersed form of PAN, an archaeal proteasome AAA+ ATPase, to determine the number of nucleotides bound to each hexamer of the wild-type protein. We utilized ADP and its analogues (TNP-ADP and mant-ADP), and a non-hydrolysable ATP analogue (AMP-PNP) to study nucleotide site occupancy within the PAN hexamer in ADP- and ATP-binding states, respectively. Throughout all experiments we used a Walker A mutant (PANK217A) that is impaired in nucleotide binding as an internal standard to mitigate the effects of residual solvation on mass measurement accuracy and to serve as a reference protein to control for non-specific nucleotide binding. This approach led to the unambiguous finding that a wild-type PAN hexamer carried – from expression host – six tightly bound ADP molecules that could be exchanged for ADP and ATP analogues. While the Walker A mutant did not bind ADP analogues, it did bind AMP-PNP, albeit at multiple stoichiometries. We observed variable levels of hexamer dissociation and an appearance of multimeric species with the over-charged molecular ion distributions across repeated experiments. We posit that these phenomena originated during ESI process at the final stages of ESI droplet evolution.

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Conformational switching in the coiled-coil domains of a proteasomal ATPase regulates substrate processing

Cited by 29 publications

References 59 publications

AAA+ ATPases in Protein Degradation: Structures, Functions and Mechanisms

AAA+ ATPases in Protein Degradation: Structures, Functions and Mechanisms

Role of coiled-coil registry shifts in activation of human Bicaudal D2 for dynein recruitment upon cargo-binding

Stoichiometry of Nucleotide Binding to Proteasome AAA+ ATPase Hexamer Established by Native Mass Spectrometry

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