Ligand‐Induced Compaction of the PEX5 Receptor‐Binding Cavity Impacts Protein Import Efficiency into Peroxisomes

Abstract

Peroxisomes entirely rely on the import of their proteome across the peroxisomal membrane. Recognition efficiencies of peroxisomal proteins vary by more than 1000-fold, but the molecular rationale behind their subsequent differential import and sorting has remained enigmatic.Using the protein cargo alanine-glyoxylate aminotransferase as a model, an unexpected increase from 34 to 80% in peroxisomal import efficiency of a single-residue mutant has been discovered. By high-resolution structural analysis, we found that it is the recognition receptor PEX5 that adapts its conformation for high-affinity binding rather than the cargo protein signal motif as previously thought. During receptor recognition, the binding cavity of the receptor shrinks to one third of its original volume. This process is impeded in the wild-type protein cargo because of a bulky side chain within the recognition motif, which blocks contraction of the PEX5 binding cavity. Our data provide a new insight into direct protein import efficiency by removal rather than by addition of an apparent specific sequence signature that is generally applicable to peroxisomal matrix proteins and to other receptor recognition processes.

Structural Insights into Cargo Recognition by the Yeast PTS1 Receptor

“…However, for none of these yeast proteins, the receptor interface has been defined in structural terms. Crystal structures of human PEX5-cargo complexes also revealed secondary binding sites, which were shown to increase the binding affinity to PEX5 (19,59,62). Although the interacting region of the cargo SCP2 is far apart from the PTS1-binding site, the second PEX5-binding site of AGT is next to its C terminus and thereby resembles that of Pcs60p.…”

“…Thus, alternatively, the presence of the PTS1 might trigger conformational changes in Pex5p that render it competent for subsequent import. Conformational changes upon PTS1 binding have been described for human PEX5 (62). The existence of additional binding sites beside the PTS1 is not exceptional.…”

“…10). It has been suggested that additional binding regions of AGT promote the non-autonomous binding of the non-canonical targeting sequence KKL (59,62). However, Pcs60p carries the strong targeting signal SKL, which binds with high affinity to the yeast Pex5p receptor site but still requires the adjacent region for peroxisomal targeting.…”

An Unexpected Duo: Rubredoxin Binds Nine TPR Motifs to Form LapB, an Essential Regulator of Lipopolysaccharide Synthesis

“…TPR motifs are most commonly found in groups of three consecutive repeats (Andrea et al, 2003). The structures of many TPR-containing proteins have been recently solved, including complexes with small molecules, peptides, or proteins bound to the concave face (Fodor et al, 2015;Pal et al, 2014;Wang et al, 2011).…”

Molecular Mechanisms and Physiological Significance of Organelle Interactions and Cooperation

“…The structure of the TPR resembles a bent half-pipe (Gatto et al, 2000), into which the last three amino acids of the cargo proteins insert and thereby induce a conformational change (Stanley et al, 2006;Fodor et al, 2015).…”