The interaction between nuclear restorer of fertility (RF) genes and mitochondrial cytoplasmic male sterility (CMS) causing genes has important application in hybrid seed production. Most RF and their homologous Restorer-of-fertility-like (RFL) proteins belong to P-class pentatricopeptide repeat protein (PPRs) family. Although, it is documented the majority of characterised RF and RFL protein genes can bind and induce cleavage in their mitochondrial targeting transcripts, the molecular mechanism by which the cleavage is performed, remains unknown. Comparative genomics studies revealed presence of a conserved C-terminal domain (CTD) of 60-70 amino acids in the majority of those proteins. In planta truncation experiments indicated that CTD is important for Arabidopsis thaliana RFL6 to bind and induce cleavage in 5’UTR cox3 most likely by recruiting mitochondrial endonucleases. Immunoprecipitation assays followed by mass spectrometry and yeast-interactome assays were conducted to characterise the interactome of the RFL6. Lastly, three variants of synthetic PPR proteins added with natural RFL6-CTD were designed to demonstrate in deep the role of CTD. This research by bringing new insights into the molecular mode of action of RFL proteins in plants is expanding our understanding of the mechanisms underlying CMS and fertility restoration in plants.