Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile,Thermus thermophilusHB8

Abstract

The MutM [formamidopyrimidine DNA glycosylase (Fpg)] protein is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidatively damaged bases (N‐glycosylase activity) and cleaves both the 3′‐ and 5′‐phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity). The crystal structure of MutM from an extreme thermophile, Thermus thermophilus HB8, was determined at 1.9 Å resolution with multiwavelength anomalous diffraction phasing using the intrinsic Zn²⁺ ion of the zinc finger. MutM is composed of two distinct and novel domains connected by a flexible hinge. There is a large, electrostatically positive cleft lined by highly conserved residues between the domains. On the basis of the three‐dimensional structure and taking account of previous biochemical experiments, we propose a DNA‐binding mode and reaction mechanism for MutM. The locations of the putative catalytic residues and the two DNA‐binding motifs (the zinc finger and the helix–two‐turns–helix motifs) suggest that the oxidized base is flipped out from double‐stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes.