Structural Elements Regulating AAA+ Protein Quality Control Machines

Abstract

Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins. In this mini-review, we will discuss structural elements present in AAA+ proteins involved in protein quality control, drawing similarities to their known role in substrate interaction by AAA+ proteins involved in DNA translocation. Elements to be discussed include the pore loop-1, the Inter-Subunit Signaling (ISS) motif, and the Pre-Sensor I insert (PS-I) motif. Lastly, we will summarize our current understanding on the inter-relationship of those structural elements and propose a model how ATP binding and hydrolysis might be coupled to polypeptide translocation in protein quality control machines.

Keywords: AAA+ proteins; Pre-Sensor I insert; inter-subunit signaling motif; pore loop; protein quality control.

Figure 1

(A) Conserved structural elements of the PS-I superclade mapped onto the crystal structure of the ClpB-D2 domain (PDB: 4FD2) (Biter et al., 2012). Walker A motif (WA; pink), Walker B motif (WB; red), Arg-finger (Arg; green), pore loop-1 (loop-1; blue), ISS motif (yellow), PS-I β-hairpin (PS-I; magenta), sensor-1 (S1; orange), sensor-2 (S2; brown), and the glutamate-switch (Glu; cyan) (Zhang and Wigley, 2008). The same colors are used throughout in all figures. (B) Multiple sequence alignment of PS-I members generated using PROMALS3D (Pei et al., 2008) showing the conservation of the ISS and PS-I motifs. Escherichia coli ClpA; Thermus thermophilus ClpB; Bacillus subtilis ClpC; Saccharomyces cerevisiae Hsp104; S. cerevisiae Hsp78; E. coli ClpX; E. coli HslU; E. coli LonA; Macaca mulatta polyomavirus 1 Large Tumor antigen (LTag); Deltapapillomavirus 4 E1; E. coli PspF; Aquifex aeolicus NtrC; E. coli RuvB.

Figure 2

(A) Model for inter-subunit communication in the PS-I insert superclade of AAA+ proteins involved in PQC. Composite model based on the crystal structure of a ClpC hexamer (PDB: 3PXI) (Wang et al., 2011) following the subunit arrangement proposed by Biter et al. (2012). The hexamer model is compatible with a sequential ATP binding and hydrolysis mechanism, and consists of crystal structures of the ClpB-D2 monomer in the ATP-bound (blue, PDB: 4LJ9), ADP-bound (gray, PDB: 4FD2), nucleotide-free states (pink, PDB: 4LJ4) (Biter et al., ; Zeymer et al., 2014) superposed onto the ClpC-D2 large domain of the ClpC ring-shaped hexamer (Wang et al., 2011). The pore loop-1 of the ClpB-D2 domain in the nucleotide-free state, which is disordered in the available crystal structures, is indicated by a dotted line. The blue circle indicates section shown in the enlarged view. (B) Ribbon diagram of the SV40 LTag homo-hexamer structure bound to double-stranded DNA (PDB: 5TCT) (Gai et al., 2016). Only the helicase domains are shown. For clarity, neighboring subunits are colored differently (cyan and gray). The blue circle indicates section shown in the enlarged view.