Nucleophile Reaction

In the first step, 2’-OH proton of the ribonuclease sugar undergoes deprotonation by the basic imidazole ring of His12. This produces a 2’-O-, which subsequently acts as a nucleophile for attack towards the phosphorus atom of the phosphate group bonded to the 3’-C end of the same ribonuclease sugar. During this process, it causes His12 to become protonated, thus causing it to become acidic. 21-22 Conversely, His119 acts as an acid to facilitate the departure of the leaving 3’-monophosphate group. This is achieved when the acidic imidazolium ion of His119 simultaneously protonate the oxygen of the phosphate oxyanion group. 23 This leads to the formation of 2’,3’-cyclic phosphorane monoanionic intermediate, which is stabilized by the surrounding
This process is further promoted due to the presence of an electrophile (His119) such as a proton or divalent metal ion. In the presence of metal ions, it coordinates to water molecules, causing it to become easily deprotonated. Hence, hydrolysis of RNA can be achieved by subjecting it to presence of protons and hydroxide ions, which is achieved due to the presence of His12 and His119 in RNase A. The reason why imidazole is suitable in the hydrolysis due to the well suited pHb of 7.0, allowing it to act as both an acid and a base at neutral condition. Therefore, RNase A mimic requires the presence of one or two imidazole groups modified with various ligands, such as spermine or phenazine, to mimic the active site of RNase A. Previous studies have found that RNase activity with mimic containing only 1 imidazole group is demonstrated only in the presence of an imidazole buffer. However, for RNase A mimic containing 2 imidazole groups, undergoes hydrolytic cleavage