For the Better or for the Worse? The Effect of Manganese on the Activity of Eukaryotic DNA Polymerases

Abstract

DNA polymerases constitute a versatile group of enzymes that not only perform the essential task of genome duplication but also participate in various genome maintenance pathways, such as base and nucleotide excision repair, non-homologous end-joining, homologous recombination, and translesion synthesis. Polymerases catalyze DNA synthesis via the stepwise addition of deoxynucleoside monophosphates to the 3' primer end in a partially double-stranded DNA. They require divalent metal cations coordinated by active site residues of the polymerase. Mg²⁺ is considered the likely physiological activator because of its high cellular concentration and ability to activate DNA polymerases universally. Mn²⁺ can also activate the known DNA polymerases, but in most cases, it causes a significant decrease in fidelity and/or processivity. Hence, Mn²⁺ has been considered mutagenic and irrelevant during normal cellular function. Intriguingly, a growing body of evidence indicates that Mn²⁺ can positively influence some DNA polymerases by conferring translesion synthesis activity or altering the substrate specificity. Here, we review the relevant literature focusing on the impact of Mn²⁺ on the biochemical activity of a selected set of polymerases, namely, Polβ, Polλ, and Polµ, of the X family, as well as Polι and Polη of the Y family of polymerases, where congruous data implicate the physiological relevance of Mn²⁺ in the cellular function of these enzymes.

Keywords: DNA polymerases; catalytic activity; manganese; polymerase families; translesion synthesis.

Figure 1

Structures of the catalytic cores of the eukaryotic DNA polymerases. (A) The proteins are shown in surface representation and the DNA helices are shown in cartoon representation (colored grey) [6]. The view in all the structures is down the DNA helix axis, except for Polβ, which introduces a 90° bend into the DNA. A family Pols, represented by human Polθ (4X0P) [7], possess palm (blue), fingers (yellow), thumb (orange), and exonuclease (red) domains. Exonuclease domain is positioned behind the palm and thumb domains in the figure. B family Pols, represented by yeast Polδ (3IAY) [8], have N-terminal (purple), exonuclease (magenta), palm (blue), fingers (yellow), and thumb (orange) domains. X family pols, such as human Polβ (4KLE) [9], employ palm, fingers, and thumb domains, as well as a 5′-dRP lyase domain (violet). Y family pols, represented by human Polη (3MR2) [10], have palm, fingers, and thumb domains, and possess a unique polymerase-associated domain (PAD) (green). (B) Schematic of the conformational change of high-fidelity polymerases. The pol binds the DNA in an “open” conformation; then, upon binding the incoming nucleotide, the finger domain (yellow) moves to a “closed” conformation that ensures correct base pairing.