Abstract
ATPases associated with diverse cellular activities (AAA+ proteins) are macromolecular machines that convert the chemical energy contained in ATP molecules into powerful mechanical forces to remodel a vast array of cellular substrates, including protein aggregates, macromolecular complexes and polymers. AAA+ proteins have key functionalities encompassing unfolding and disassembly of such substrates in different subcellular localizations and, hence, power a plethora of fundamental cellular processes, including protein quality control, cytoskeleton remodelling and membrane dynamics. Over the past 35 years, many of the key elements required for AAA+ activity have been identified through genetic, biochemical and structural analyses. However, how ATP powers substrate remodelling and whether a shared mechanism underlies the functional diversity of the AAA+ superfamily were uncertain. Advances in cryo-electron microscopy have enabled high-resolution structure determination of AAA+ proteins trapped in the act of processing substrates, revealing a conserved core mechanism of action. It has also become apparent that this common mechanistic principle is structurally adjusted to carry out a diverse array of biological functions. Here, we review how substrate-bound structures of AAA+ proteins have expanded our understanding of ATP-driven protein remodelling.
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Acknowledgements
The authors thank M. Shin for helpful discussions. Preparation of this Review was supported by an American Heart Association predoctoral fellowship to C.P. (17PRE32910005), a National Science Foundation predoctoral fellowship to C.R.S. (2016219351) and a Pew Scholarship in the Biomedical Sciences from the Pew Charitable Trusts and the National Institutes of Health (DP2EB020402 and R21AG06169701) to G.C.L.
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C.P. conceived and drafted the manuscript, C.R.S and C.P. prepared the figures. All authors edited the manuscript.
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Glossary
- ESCRT-III
-
(Endosomal sorting complex required for transport III). ESCRT-III proteins are recruited to membrane constriction sites, including nearly all subcellular membrane compartments, where they are activated and assemble into filaments, which in turn recruit VPS4, a type I AAA+ protein. ATP-dependent VPS4 activity remodels and disassembles ESCRT-III polymers, thereby powering ESCRT-dependent membrane fission reactions that are required for diverse biological processes, such as vesicle formation in the secretory system, budding of enveloped viruses from the plasma membrane and membrane repair.
- SNARE complexes
-
Protein complexes consisting of syntaxin, synaptobrevin and SNAP25 (synaptosome-associated protein), which assemble into a four-helix bundle that aids in the fusion of membranes.
- ER-associated degradation
-
A cellular pathway that targets misfolded proteins for selective ubiquitylation by endoplasmic reticulum (ER)-resident ubiquitin ligases. The type II AAA+ protein p97/Cdc48 recognizes and dislocates these polyubiquitylated substrates from the ER membrane and into the cytosol. The resulting unfolded polypeptides are subsequently degraded by the 26S proteasome.
- Mitochondria-associated degradation
-
The process by which the AAA+ protein p97/Cdc48 recognizes and retrotranslocates polyubiquitylated substrates from the outer mitochondrial membrane for subsequent degradation by the 26S proteasome.
- Retrotranslocation
-
Following translation in the cytosol, proteins are translocated into the respective cellular subcompartments. When a protein is misfolded, AAA+ proteins extract these proteins from the membrane, dislocating them into the cytosol. This process is known as retrotranslocation (from the subcompartment back into the cytosol).
- 26S proteasome
-
A large multisubunit complex located in the cytosol of eukaryotes with numerous ubiquitin receptors that selectively bind polyubiquitylated protein substrates for degradation. Targeted substrates are unfolded by a AAA+ motor within the complex, while another enzyme called a deubiquitinase cleaves the covalently linked ubiquitin chain from the substrate. The AAA+ ATPase directs the unfolded substrate into a barrel-shaped proteolytic chamber which contains six proteolytic active sites that degrade the substrate.
- NTPases
-
A generic term that encompasses enzymes capable of binding nucleotide triphosphate (NTP) molecules, such as ATP and GTP. AAA+ proteins are defined as a subclass of P-loop NTPases.
- α–β Rossman fold
-
A super-secondary structure composed of alternating β-strand–α-helix–β-strand segments. The β-strands form a β-sheet and the α–helices surround both faces of the sheet, producing a three-layered sandwich.
- Walker A
-
A G-XXXX-GK-[T/S] sequence motif, where X can be any amino acid. This motif (also known as the P-loop) stabilizes the binding of the nucleotide by interacting with the β-phosphate, and is present in many nucleotide-binding proteins.
- Walker B
-
A consensus sequence (hhhhDE) where h represents any bulky, hydrophobic amino acid. The aspartic acid (D) is important for coordination of a magnesium ion, which in turn helps neutralize the negative charges of the phosphate groups present in the nucleotide. The adjacent glutamate (E) residue serves as a catalytic base, activating water for nucleophilic attack on the γ-phosphate during ATP hydrolysis.
- Nucleophilic attack
-
A fundamental reaction class in which a partially or fully positively-charged group (electrophile) is attacked by an electron-rich molecule (nucleophile) that substitutes a leaving group.
- Cation–π interactions
-
Non-covalent interactions between an electron-rich π system (for example, aromatic amino acids — phenylalanine, tryptophan and tyrosine) and an adjacent cation (for example, basic residues — arginine, lysine and histidine).
- van der Waals interactions
-
Distance-dependent interactions between atoms or molecules that are significantly weaker than other kinds of interactions, such as electrostatic ones.
- SNAPs
-
(Soluble N-ethylmaleimide-sensitive factor (NSF) attachment proteins). Adaptor proteins that bind both the N-terminal domains of type II AAA+ protein NSF and a SNARE complex, giving rise to the so-called 20S complex.
- π-stacking interactions
-
Electrostatic interactions that can occur between two π systems. In proteins, aromatic residues that are in close proximity to each other can engage in such interactions.
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Puchades, C., Sandate, C.R. & Lander, G.C. The molecular principles governing the activity and functional diversity of AAA+ proteins. Nat Rev Mol Cell Biol 21, 43–58 (2020). https://doi.org/10.1038/s41580-019-0183-6
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DOI: https://doi.org/10.1038/s41580-019-0183-6
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