A Molecular Analysis of the Aminopeptidase P-Related Domain of PID-5 from Caenorhabditis elegans

• Published in: Biomolecules (Basel, Switzerland) Switzerland), 2023-07, Vol.13 (7), p.1132
• Main Authors: Lloyd, Anna C, Gregory, Kyle S, Isaac, R Elwyn, Acharya, K Ravi
• Format: Article
• Language: English
• Subjects: alphafold2; Aminopeptidase; aminopeptidase P; Aminopeptidases - chemistry; Aminopeptidases - ultrastructure; Animals; bioinformatics; Caenorhabditis elegans; Caenorhabditis elegans - genetics; Caenorhabditis elegans - metabolism; Caenorhabditis elegans Proteins - genetics; Caenorhabditis elegans Proteins - metabolism; Confidence; dimerisation; E coli; Epigenetics; Genes; Genetic engineering; Genomes; Homeostasis; Homology; Interfaces; Metalloproteinase; Metals - metabolism; Nematodes; Peptides; PID-5; Protein Domains - genetics; Protein Domains - physiology; Proteins; Proteolysis; RNA - metabolism; RNA-mediated interference; Software; Zinc; zinc metalloprotease
• ISSN: 2218-273X; 2218-273X
• DOI: 10.3390/biom13071132

A novel protein, PID-5, has been shown to be a requirement for germline immortality and has recently been implicated in RNA-induced epigenetic silencing in the embryo. Importantly, it has been shown to contain both an eTudor and aminopeptidase P-related domain. However, the silencing mechanism has not yet been fully characterised. In this study, bioinformatic tools were used to compare pre-existing aminopeptidase P molecular structures to the AlphaFold2-predicted aminopeptidase P-related domain of PID-5 (PID-5 APP-RD). Structural homology, metal composition, inhibitor-bonding interactions, and the potential for dimerisation were critically assessed through computational techniques, including structural superimposition and protein-ligand docking. Results from this research suggest that the metallopeptidase-like domain shares high structural homology with known aminopeptidase P enzymes and possesses the canonical ' '. However, the absence of conserved metal-coordinating residues indicates that only a single Zn may be bound at the active site. The PID-5 APP-RD may form transient interactions with a known aminopeptidase P inhibitor and may therefore recognise substrates in a comparable way to the known structures. However, loss of key catalytic residues suggests the domain will be inactive. Further evidence suggests that heterodimerisation with aminopeptidase P is feasible and therefore PID-5 is predicted to regulate proteolytic cleavage in the silencing pathway. PID-5 may interact with PID-2 to bring aminopeptidase P activity to the Z-granule, where it could influence WAGO-4 activity to ensure the balanced production of 22G-RNA signals for transgenerational silencing. Targeted experiments into APPs implicated in malaria and cancer are required in order to build upon the biological and therapeutic significance of this research.