ccLon Bound to LarA
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Introduction
Allosteric interaction of Caulobacter crescentus Lon N-terminus domain and regulatory protein (LarA). Lon functions as an ATP depended (ATPase) AAA+ protease to degrade misfolded and denatured proteins to prevent proteoxic stress (1). Proteoxic stress caused by the accumulation of misfolded proteins can lead to cell death. AAA+ Proteases are found in all domains of life essential to maintaining the homeostasis of proteins within cells (2). For bacteria Lon is the protease that is responsible for the majority of protein homeostasis maintenance (2).
Structure
Lon is known to perform its catalytic function as a homohexamer meaning six identical subunits that form a complex for functionality. Each individual Lon polypeptide chain is made up of multiple domains. The N-terminal domain (NTD), long helix region, AAA+ ATPase domain, and a protease domain (1). This assembly represents two regulatory proteins each bound to a NTD of Lon.
Binding site/Ligands
The AAA+ ATPase and protease domains of each polypeptide interacts with the substrate proteins in an open/close spiral staircase conformation (3). There are six active sites for proteolytic function inside the chamber made by the conformation. The six long helix regions protrude from the ring overlapping with three long helix regions to make a triangular shaped region. This region positions the six N-terminus domains to surround a central tri-tyrosine pore where substrate entry can occur. These N-terminus domains are flexible and are often thought to be involved with mediating substrate recognition (1). In this assembly the LarA C-terminal His89 residue acts a binding site to C-terminal region of Lon NTDs (aa 197-205)(1)
Current Research
While the N-terminus domain of Lon has been suggested to be involved with substrate recognition there aren’t many substrates bound structures available to illustrate its role. Current research is being done to structurally illustrate through bound substrate-protein complexes the N-terminal domains regulatory function (1,4). Proteases recognize their substrates by short sequence tags called degrons that are located on the termini of proteins (4.) However, for efficient substrate recognition for protease activity requires adapters and allosteric regulators are needed (4). One of these is LarA a heat shock protein that accumulates at the onset of proteoxic stress (4). Crystallographic evidence has shown that LarA binds to a conserved groove in the N-terminal domain through an aromatic residue on its C-terminal degron (1). Evidence also shows that this binding exposes the hydrophobic core of LarA. This core can bind a leucine residue and promote local protein unfolding (1). Research on LarA indicates its regulatory function withing the Lon protease complex (1,4).
Additional features
While ccLon is active playing its role in bacteria. Other Lon proteins across the kingdoms of life perform their proteolytic functions in context to their own environments. Lon1 is a common Lon protein shown to be involved in mitochondrial biogenesis, carbon metabolism, energy supple etc. (5) These functions are all essential to the seed growth in plants showing how important maintaining protein homeostasis is in plant growth. Many protease functions are distinct to the subcellular localization (5).
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References
1. Wang, HJ., Kuan, YE., Ho, MR. et al. Structural basis for the allosteric activation of Lon by the heat shock protein LarA. Nat Commun 16, 2212 (2025). https://doi.org/10.1038/s41467-025-57482-6
2. Robert T. Sauer, Eyal Gur, Recognition of misfolded proteins by Lon, a AAA+ protease, doi:10.1101/gad.1670908 Genes & Dev. 2008. 22: 2267-2277
3. Mia Shin et al.,Structural basis for distinct operational modes and protease activation in AAA+ protease Lon.Sci. Adv.6,eaba8404(2020). DOI:10.1126/sciadv.aba8404
4. Omnus, D.J., Fink, M.J., Kallazhi, A. et al. The heat shock protein LarA activates the Lon protease in response to proteotoxic stress. Nat Commun 14, 7636 (2023). https://doi.org/10.1038/s41467-023-43385-x
5. Rigas S, Daras G, Tsitsekian D, Alatzas A and Hatzopoulos P (2014) Evolution and significance of the Lon gene family in Arabidopsis organelle biogenesis and energy metabolism. Front. Plant Sci. 5:145. doi: 10.3389/fpls.2014.00145
6. Structural and mechanistic studies on human LONP1 redefine the hand-over-hand translocation mechanism
Mindrebo, J.T., Lander, G.C.
