Study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) protein in Rosaceae by bioinformatics tools

Abstract

The enzyme 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR, EC 1.1.1.34) catalyzes the conversion of 3-hydroxy-3-methylglutaryl-CoA to mevalonate, which is the first committed step in the pathway for isoprenoid biosynthesis in plants. In this study we performed bioinformatics analyses on Rosaceae; 23 HMGR protein sequences in plants and three animal samples including human, mouse and fruit fly were aligned and analyzed by computational tools to predict the protein properties, such as molecular mass, pI, signal peptide, transmembrane and conserved domains, and secondary and spatial structures. Sequence comparison analysis revealed there is a high identity between plants and animals. The structural modeling showed that HMGR has a typical spatial structure with catalytic regions including L, N and S domains. The tertiary structure model of Malus domestica HMGR (accession number: ABQ52378) was further checked by the PROCHECK algorithm, which showed that 90.3% of the amino acid residues were located in the most favored regions in a Ramachandran plot, indicating that the simulated three-dimensional structure was reliable. Phylogenetic analysis showed that there is a close relationship among HMGR proteins in Rosaceae species; they are also similar to HMGRs of other organisms. According to these results, HMGRs are probably derived from a common ancestor.

Keywords:

• bioinformatics
• HMGR
• mevalonate pathway
• Rosaceae