Computational Investigations of Selected Enzymes From Two Iron and {\alpha}-ketoglutarate-Dependent Families

TL;DR

This paper reviews computational studies on enzymes AlkB and TET, highlighting their structural, mechanistic, and substrate specificity insights crucial for understanding DNA/RNA repair and epigenetic regulation.

Contribution

It provides a comprehensive overview of computational investigations into AlkB and TET enzyme families, revealing their structural and mechanistic details.

Findings

Structural insights into enzyme active sites

Mutagenesis effects on enzyme activity

Reaction pathway and substrate specificity analysis

Abstract

DNA alkylation is used as the key epigenetic mark in eukaryotes, however, most alkylation in DNA can result in deleterious effects. Therefore, this process needs to be tightly regulated. AlkB and TET are families within the Fe and $\alpha$-kg-dependent superfamily of enzymes that are tasked with dealkylating DNA and RNA in cells. Members of these families span all species and are an integral part of transcriptional regulation. While both families catalyze oxidative dealkylation of various bases, each has specific preference for alkylated base type as well as distinct catalytic mechanisms. This perspective aims to provide an overview of computational work carried out to investigate several members of these enzyme families including AlkB, ALKBH2, ALKBH3 and TET2. Insights into structural details, mutagenesis studies, reaction path analysis, electronic structure features in the active site, and substrate preferences are presented and discussed