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bioRxiv · 10.1101/2023.05.22.541725

Is the hydrogen of the 2'-hydroxyl group of HENMT1 a Schrodinger's hydrogen?

Kaldis, P.·Zhao, L. N.
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Abstract

piRNAs 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.

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Kaldis, P., Zhao, L. N.. 2023-05-24. Is the hydrogen of the 2'-hydroxyl group of HENMT1 a Schrodinger's hydrogen?. https://doi.org/10.1101/2023.05.22.541725

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