Three-dimensional structural model of rRNA (guanine-N (2)- ) - methyltransferase by homology modeling

Abstract

The biological function of a protein is largely determined by its threedimensional structure. However, to date only -16% of protein threedimensional structures, from existing protein sequences, «have been deposited in the PDB. This gap between existing structures and available protein sequences is due to the practical difficulties associated with use of conventional methods in structure determination such as X-ray crystallography and NMR spectroscopy. Homology modeling, which relates to computational chemistry plays an important role in determining protein 3-D structures. This method largely helps to fill the above gap between known sequences and known 3D structures. In this research we have used a computational method to model a three-dimensional structure of rRNA (guanine-N (2)-)-methyl transferase (rRNA-gN2Mtase) from Vibrio cholerae, which consists of 246 amino acids. This method uses software from Uppsala Software Factory (USF) such as O, SOD and MOLEMAN, and NCBI, PDB, BLAST, CLUSTALW databases. The crystal structure of UPF0341 protein yhiq from E.coli (PDB ID: 2PGX) was used as the template for modeling of the target protein sequence using above method. The obtained structural model rRNA-gN2Mtase mainly consists of two domains. The domain I, which is the catalytic domain, contains five ahelices and five parallel p-strands and two anti-parallel P-strands forming a P-sheet. The a-helices are wrapped around the both sides of the beta sheet. The domain II contains two anti-parallel p-strands and two a-helices. This structure also shows the common topology shown by other methyltransferases. We believe that Jhis is the first structural model of rRNA (guanine-N (2)-)-methyltransferase and this will be much useful for biochemical studies of this protein and in the field of drug design.