A critical role of water in the specific cleavage of the anticodon loop of some eukaryotic methionine initiator tRNAs.

We have noticed that during a long storage and handling, the plant methionine initiator tRNA is spontaneously hydrolyzed within the anticodon loop at the C34-A35 phosphodiester bond. A literature search indicated that there is also the case for human initiator tRNA(Met) but not for yeast tRNA(i)Met or E. coli tRNA(f)Met. All these tRNAs have an identical nucleotide sequence of the anticodon stems and loops with only one difference at position 33 within the loop. It means that cytosine 33 (C33) makes the anticodon loop of plant and human tRNA(i)Met susceptible to the specific cleavage reaction. Using crystallographic data of tRNA(f)Met of E. coli with U33, we modeled the anticodon loop of this tRNA with C33. We found that C33 within the anticodon loop creates a pocket that can accomodate a hydrogen bonded water molecule that acts as a general base and catalyzes a hydrolysis of C-A bond. We conclude that a single nucleotide change in the primary structure of tRNA(i)Met made changes in hydration pattern and readjustment in hydrogen bonding which lead to a cleavage of the phosphodiester bond.