Homology Modelling and Evaluation of a Conserved Domain in Oryza sativa RING Finger Protein 45, a Putative E3 Ubiquitin Ligase

The OsRFP45 identified in Oryza sativa has been identified as a negative salt-stress regulator. Its functions have been studied previously by overexpression and knock-out lines, but it has not been experimentally validated in structural form. This study provides a homology-based three-dimensional structural prediction of OsRFP45, an E3 ubiquitin ligase discovered in Oryza sativa, based on a matching template using SWISS-MODEL.Based on the existing literature, the locus Id of the OsRFP45 was identified. The locus Id was searched on NCBI to obtain the FASTA file of the identified protein. NCBI BLAST was conducted and it was analysed that the gene responsible for the production of this protein is highly conserved among various species. The homology modelling of the RING domain of OsRFP45 was performed using a template which had the highest GMQE (Global Model Quality Estimate). The accuracy of the predicted structural model was validated by running the bioinformatics tool – ProCheck and obtaining the Ramachandran Plot and related parameters. According to sequence alignment, OsRFP45’s conserved RING domain is highly comparable to proteins from the RING domain found in other plant species.The OsRFP45 RING domain’s conserved structural characteristics align with classical C3HC4-type E3 ubiquitin ligase. The three-dimensional structure shows a compact RING-domain stabilised by conserved cysteine and histidine residues, indicating a zinc-coordinated fold required for E3 ligase function. Zero percent of the disallowed region, 85.5% of the core and 14.5% of the allowed region are concluded by the Ramachandran plot. The predicted structure is hence, confirmed as correct.