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.
