Inhibition of pancreatic ribonuclease by 2'-5' and 3'-5' oligonucleotides

The active site of ribonuclease A from the crystallographic studies of ribonuclease-A-inhibitor complexes

The results of X-ray analyses of three ribonuclease-A-nucleotide complexes, at 2.3 A, are reported. A modified purine mononucleotide, 8-oxo-guanosine 2'-phosphate in a syn conformation, binds at the pyrimidine-binding site of the catalytic cleft. Solvent molecules are expelled from the active site due to inhibitor binding. The positions of the side-chains of the active-site residues Gln-11, His-12 and Thr-45 are well defined and do not alter on inhibitor binding. The mobility of Lys-41 is greatly reduced in the protein-nucleotide complexes and the terminal amino group interacts directly with the 2'-phosphate group of the nucleotides. In the complex of the enzyme with a modified pyrimidine, cytidine-N(3)-oxide 2'-phosphate, His-119 is stabilised in the minor site of the native protein [Borkakoti, N., Moss, D.S. and Palmer, R.A. (1982) Acta Crystallogr. B38, 2210-2217], while in the protein-purine derivative the imidazole group is located in the major site. Inhibitor binding induces movements in the side-chains of Lys-7 and Lys-66 which also modify the conformation of the active-site cleft of ribonuclease A.

Studies of catalysis by ribonuclease U2. Steady-state kinetics for transphosphorylation of oligonucleotide and synthetic substrates

The values of the steady-state kinetic parameters for the RNase, U2 catalyzed transphosphorylation were measured for several di- and trinucleotides such as ApXp (X = A, C, G, or U), ApYpGp, and YpApGp (Y = C or U). The pH dependence of kcat/Km for ApUp indicated a dependence for catalysis upon an unprotonated group with pK = 3.8 and two proton-associated groups with pK = 4.4 and 5.0. As judged from kcat/Km values, ApUpGp and ApCpGp are better substrates than the corresponding parent dimers, ApUp and ApCp, respectively. By contrast, the kcat/Km for UpApGp was about 1/20 relative to that of the parent dimer, ApGp. The results were compared for possible thermodynamic and structural information about the chemical consequences. The inhibition of the RNase U2 catalyzed reaction of ApUp by a series of nucleosides and nucleotides was also studied. Evidence for similarities and dissimilarities in the binding and catalysis by RNase U2 and RNase T1 is presented.

The reaction of bovine pancreatic ribonuclease A with 6-chloropurineriboside 5'-monophosphate. Evidence on the existence of a phosphate-binding sub-site

The chemical modification of bovine pancreatic ribonuclease A by 6-chloropurine 9-beta-D-ribofuranosyl 5'-monophosphate was studied under several reaction conditions. The reaction, at pH 7.3, 40 degrees C and a nucleotide: enzyme molar ratio of 60, showed a high degree of specificity in comparison to those corresponding to the base or the nucleoside. The main derivative was isolated by means of CM-cellulose chromatography. Subtilisin cleavage of this derivative showed that the substitution had taken place in the S-peptide moiety. Tryptic digestion of the S-peptide indicated that a lysine residue had been modified. Enzymatic and physico-chemical considerations showed that the actual site of reaction was the alpha-amino group of Lys-1. The structural and kinetic properties of the derivative are consistent with the existence of a phosphate-binding sub-site near the N-terminal region of the enzyme.

Geometry of the dry-state oligomerization of 2',3'-cyclic phosphates

Evaporation of a solution of thymidine plus either the exo or the endo diastereomer of uridine cyclic 2',3'-O, O-phosphorothioate (U greater than p(S) in 1,2-diaminoethane hydrochloride buffer gave the 2',5' and 3',5' isomers of (P-thio) uridylylthymidine (Up(S)dT) in a ratio of 1:2 with a combined yield of about 20%. These isomers were re-converted to U greater than p(S) and dT by a reaction that is known to proceed by an in-line mechanism. Both the 2',5' and 3',5' isomers gave as product the same diasteromer of U greater than p(S) that had been used originally in their formation. These dry-state 'prebiotic' reactions (Verlander, Lohrmann, and Orgel 1973) are thus shown to be stereospecific, and both the 2',5' and 3',5' internucleotide bonds are formed by an in-line mechanism.