The processive reaction mechanism of ribonuclease II

Ribonuclease II is a processive 3' exoribonuclease in Escherichia coli. It degraded substrates with 3'-OH or 2',3'-cyclicP ends slightly faster than those with 3'-P or 2'-P groups with a turnover number of approximately 70 nt/s at 37 degrees C. RNase II does not degrade DNA but the specificity for ribose was not for the cleavage bond but rather for ribo-bonds three to four nucleotides (nt) upstream, which could explain why the limit digest is a dimer. Oligonucleotides (oligos) of deoxy(C) were reversible competitive inhibitors of the enzyme and indicated a strong upstream binding site (approximately 15 to 27 nt from the 3' end). These oligos could protect RNase II from inactivation by heat or from diethylpyrocarbonate, an agent that preferentially reacts with His residues. Compared to oligo(dC), oligos of (dA) were at least 500 times less effective inhibitors of RNase II. Using mixed oligo(dAdC) inhibitors, an obligatory 3' to 5' direction of binding into the catalytic site was shown. From the reaction kinetics of RNase II under different conditions it was concluded that the enzyme recognition differs for poly(A), poly(C) and poly(U). Poly(C) was degraded more slowly than poly(A) or poly(U) with a 3.5 times slower Vmax, while rate differences between small oligos were extreme; oligo(A)7 was degraded > 100 times faster than oligo(C)7. Ethanol, which weakens hydrophobic interactions, increased the reaction velocity of poly(C) to that of poly(A) and poly(U). It had no effect on the reaction velocities of poly(A) or poly(U), but decreased the binding of poly(A) markedly. Oligo(A) was bound more strongly to a hydrophobic column than was oligo(C). Salt, which affects charge interactions, decreased the binding affinity and/or association rate of poly(C) to RNase II, had a lesser effect on poly(U), but the reactions of poly(A) were unaffected even in much higher concentrations of salt. A clue to the slower reaction velocity of poly(C) was shown when the reaction intermediates were viewed by PAGE. At lower temperatures of reaction (< 25 degrees C), there were more intense bands separated by discrete distances of approximately 12 nt during the degradation of poly(C) by RNase II. Chase experiments showed that these stops were accounted for by dissociation of poly(C) from the enzyme. They were not seen when poly(C) was degraded at 37 degrees C or degraded in the presence of 20% ethanol at any temperatures, nor were they seen when poly(A) or poly(U) was degraded even at low temperatures.(ABSTRACT TRUNCATED AT 400 WORDS)