Crystal structure of a ribonuclease from the seeds of bitter gourd ( Momordica charantia) at 1.75 Å resolution

Abstract

The ribonuclease MC1 (RNase MC1) from seeds of bitter gourd ( Momordica charantia) consists of 190 amino acid residues with four disulfide bridges and belongs to the RNase T 2 family, including fungal RNases typified by RNase Rh from Rhizopus niveus and RNase T 2 from Aspergillus oryzae. The crystal structure of RNase MC1 has been determined at 1.75 Å resolution with an R-factor of 19.7% using the single isomorphous replacement method. RNase MC1 structurally belongs to the (α+β) class of proteins, having ten helices (six α-helices and four 3 10-helices) and eight β-strands. When the structures of RNase MC1 and RNase Rh are superposed, the close agreement between the α-carbon positions for the total structure is obvious: the root mean square deviations calculated only for structurally related 151 α-carbon atoms of RNase MC1 and RNase Rh molecules was 1.76 Å. Furthermore, the conformation of the catalytic residues His-46, Glu-105, and His-109 in RNase Rh can be easily superposed with that of the possible catalytic residues His-34, Glu-84, and His-88 in RNase MC1. This observation strongly indicates that RNase MC1 from a plant origin catalyzes RNA degradation in a similar manner as fungal RNases.