Three-dimensional structure of a mutant ribonuclease T 1 (Y45W) complexed with non-cognizable ribonucleotide, 2′AMP, and its comparison with a specific complex with 2′GMP

Abstract

The crystal structure of a mutant ribonuclease T 1 (Y45W) complexed with a non-cognizable ribonucleotide, 2′AMP, has been determined and refined to an R-factor of 0.159 using X-ray diffraction data at 1.7 Å resolution. A specific complex of the enzyme with 2′GMP was also determined and refined to an R-factor of 0.173 at 1.9 Å resolution. The adenine base of 2′AMP was found at a base-binding site that is far apart from the guanine recognition site, where the guanine base of 2′GMP binds. The binding of the adenine base is mediated by a single hydrogen bond and stacking interaction of the base with the imidazole ring of His92. The mode of stacking of the adenine base with His92 is similar to the stacking of the guanine base observed in complexes of ribonuclease T 1 with guanylyl-2′,5′-guanosine, reported by Koepke et al., and two guanosine bases, reported by Lenz et al., and in the complex of barnase with d(GpC), reported by Baudet & Janin. These observations suggest that the site is non-specific for base binding. The phosphate group of 2′AMP is tightly locked at the catalytic site with seven hydrogen bonds to the enzyme in a similar manner to that of 2′GMP. In addition, two hydrogen bonds are formed between the sugar moiety of 2′AMP and the enzyme. The 2′AMP molecule adopts the anti conformation of the glycosidic bond and C-3′- exo sugar pucker, whereas 2′GMP is in the syn conformation with C-3′- endo-C-2′-exo pucker. The mutation enhances the binding of 2′GMP with conformational changes of the sugar ring and displacement of the phosphate group towards the interior of the catalytic site from the corresponding position in the wild-type enzyme complex. Comparison of two crystal structures obtained provides a solution to the problem that non-cognizable nucleotides exhibit unexpectedly strong binding to the enzyme, compared with high specificity in nucleolytic activity. The results indicate that the discrimination of the guanine base from the other nucleotide bases at the guanine recognition site is more effective than that estimated from nucleotide-binding experiments so far.