Contribution of Gln9 and Phe80 to substrate binding in ribonuclease MC1 from bitter gourd seeds

Ribonuclease MC1 (RNase MC1) isolated from bitter gourd (Momordica charantia) seeds specifically cleaves phosphodiester bonds on the 5′-side of uridine. The crystal structures of RNase MC1 in complex with 2′-UMP or 3′-UMP reveal that Gln9, Asn71, Leu73, and Phe80 are involved in uridine binding by hydrogen bonding and hydrophobic interactions [Suzuki et al. (2000) Biochem. Biophys. Res. Commun. 275, 572 - 576]. To evaluate the contribution of Gln9 and Phe80 to uridine binding, Gln9 was replaced with Ala, Phe, Glu, or His, and Phe80 with Ala by site-directed mutagenesis. The kinetic properties of the resulting mutant enzymes were characterized using cytidylyl-3′,5′-uridine (CpU) as a substrate. The mutant Q9A exhibited a 3.7-fold increased K_m and 27.6-fold decreased k_cat, while three other mutations, Q9F, Q9E, and Q9H, predominantly affected the k_cat value. Replacing Phe80 with Ala drastically reduced the catalytic efficiency (k_cat/K_m) with a minimum K_m value equal to 8 mM. It was further found that the hydrolytic activities of the mutants toward cytidine-2′,3′-cyclic monophosphate (cCMP) were reduced. These results demonstrate that Gln9 and Phe80 play essential roles not only in uridine binding but also in hydrolytic activity. Moreover, we produced double Ala substituted mutants at Gln9, Asn71, Leu73, and Phe80, and compared their kinetic properties with those of the corresponding single mutants. The results suggest that these four residues may contribute to uridine binding in a mutually independent manner.