Computational approach and functional analysis of Pectobacterium carotovorum subsp. carotovorum low-molecular weight bacteriocin Carocin S2

Abstract

Pectobacterium carotovorum subsp. Carotovorum 3F3 is a gram-negative phyto-parasitic enterobacterium. This strain is a producer of Carocin S2 bacteriocin, which comprises of two proteins of different sizes. Carocin S2K (killer protein) which is responsible for antibiotic resistance and Carocin S2I (immunity protein) which inhibits the antibiotic activity. The present study aimed to predict the structure and functional properties of Carocin S2. Computational approaches utilizing various bioinformatic tools predicted that Carocin S2 is a putative membrane protein having the N-terminal at the extracellular side and the central domain at the coiled-coil region. Carocin S2 was predicted to have three domains, the translocation domains, receptor binding domain and the killer domain. Moreover, the killer domain was calculated to have the catalytic cleft. The in-vivo assays confirmed that for Carocin S2K, bound immunity protein was not a pre-requisite for cell attachment or translocation. The site-directed mutagenesis experiment led us to hypothesized the hydrolysis mechanism of Carocin S2. The predicted structure of Carocin S2K provided a system of understanding on the biochemical and structural function which led to the mechanism of Carocin S2. It revealed that the role of immunity protein to Carocin S2 is not a pre-requisite for translocation pathway. Furthermore, this research led to hypothesized a hydrolytic mechanism of Carocin S2 to target the tRNA.