Is the hydrogen of the 2’-hydroxyl group of HENMT1 aSchrödinger’shydrogen?

Abstract

AbstractpiRNAs are important in protecting germline integrity. 3’-terminal 2’-O-methylation is essential for piRNA maturation and to protect it from degradation. HENMT1 carries out the 2’-O-methylation, which is of key importance for piRNA stability and functionality. However, neither the structure nor the catalytic mechanism of HENMT1 have been studied. We have constructed a catalytic-competent HENMT1 complex using computational approaches, in which Mg2+is primarily coordinated by four evolutionary conserved residues, and is further auxiliary coordinated by the 3’-O and 2’-O on the 3’-terminal nucleotide of the piRNA. Our study suggests that metal has limited effects on substrate and cofactor binding but is essential for catalysis. The reaction consists of deprotonation of the 2’-OH to 2’-O and methyl transfer from SAM to the 2’-O. The methyl transfer is spontaneous and fast. Our in-depth analysis suggests that the 2’-OH may be deprotonated before entering the active site or it may be partially deprotonated at the active site by His800 and Asp859, which are in a special alignment that facilitates the proton transfer out of the active site. Furthermore, we have developed a detailed potential reaction scenario and our study indicates that HEN1 is Mg2+utilizing but is not a Mg2+dependent enzyme.