The structure and function of ribonuclease T1. VII. Further investigations on amino acid composition and some other properties of ribonuclease T1

Hexacyanochromate ion as a paramagnetic anion probe for active sites of enzymes

Hexacyanochromate ion, (Cr(CN)6)3-, was applied to ribonuclease T1 (RNase T1), which specifically cleaves RNA chains at guanylic acid residues. From kinetic studies, this anion was shown to bind to the active site of RNase T1 as a competitive inhibitor. Therefore, the line broadening effect of NMR resonances due to binding of (Cr(CN)6)3- was analyzed for the mapping of the active site of RNase T1. His-40 C2 proton resonance was significantly broadened, following His-92 C2 proton resonance upon binding of (Cr(CN)6)3-, while His-27 C2 proton resonance did not show any appreciable line broadening. Moreover, from the pH dependence of the line broadening effect, the binding of (Cr(CN)6)3- was shown to be controlled by the ionic state of Glu-58. Based on the present NMR results and x-ray crystal structure, the active site structure of RNase T1 is discussed.

Binding modes of inhibitors to ribonuclease T1 as studied by nuclear magnetic resonance

The binding modes of inhibitors to ribonuclease T1 (RNase T1) were studied by the analyses of 270-MHz proton NMR spectra. The chemical shift changes upon binding of phosphate, guanosine, 2'-GMP, 3'-GMP, 5'-GMP, and guanosine 3',5'-bis(phosphate) were observed as high field shifted methyl proton resonances of RNase T1. One methyl resonance was shifted upon binding of phosphate and guanosine nucleotides but not upon binding of guanosine. Four other methyl resonances were shifted upon binding of guanosine and guanosine nucleotides but not upon binding of phosphate. From the analyses of nuclear Overhauser effects for the pair of H8 and H1' protons, together with the vicinal coupling constants for the pair of H1' and H2' protons, the conformation of the guanosine moiety as bound to RNase T1 is found to be C3'-endo-syn for 2'-GMP and 3'-GMP and C3'-endo-anti for 5'-GMP and guanosine 3',5'-bis(phosphate). These observations suggest that RNase T1 probably has specific binding sites for the guanine base and 3'-phosphate group (P1 site) but not for the 5'-phosphate group (PO site) or the ribose ring. The weak binding of guanosine 3',5'-bis(phosphate) and 5'-GMP to RNase T1 is achieved by taking the anti form about the glycosyl bond. The productive binding to RNase T1 probably requires the syn form of the guanosine moiety of RNA substrates.

Crystallization of a complex between ribonuclease T1 and 2'-guanylic acid

Ribonuclease T1 was crystallized under various conditions. Form I crystals were produced by microdialysis against 53% (v/v) 2-methyl-2,4-pentanediol in 0.01 M sodium acetate, 0.05% 2'-guanylic acid (2'GMP) and 0.02% NaN3 (pH 6.2-7.2). These crystals are tetragonal, space group P41212 and contain two molecules per asymmetric unit; cell dimensions are a = b = 5.86 nm, c = 13.28 nm. Form IIa and form IIb crystals were obtained by microdialysis from a buffer of 0.01-0.05 M sodium acetate, 0.25-0.5% 2'GMP, 0.02% NaN3 and 2-5 mM calcium acetate (pH 4.0-4.4) in the presence of 50-75% (v/v) 2-methyl-2,4-pentanediol. These crystals are orthorhombic, space group P212121, and contain one molecule per asymmetric unit; cell dimensions are a = 4.66 nm, b = 5.02 nm, c = 4.04 nm (form I) and alpha = 4.44 nm, b = 5.00 nm, c = 4.03 nm (form II). Using high-performance liquid chromatography, it could be shown for all crystal forms that 2'-GMP is bound in the crystals. The molecular ratio between RNase T1 and 2'GMP was 0.9 for form II crystals and thus agreed with a 1:1 enzyme-nucleotide complex. Heavy-atom derivatives were produced with lead acetate for form IIa crystals and with uranyl acetate for from IIb crystals. Three-dimensional X-ray analysis of the RNase-T1 x 2'GMP complex is under way.