Conformational changes of DNA repair glycosylase MutM triggered by DNA binding

Abstract

Bacterial MutM is a DNA repair glycosylase removing DNA damage generated from oxidative stress and, therefore, preventing mutations and genomic instability. MutM belongs to the Fpg/Nei family of prokaryotic enzymes sharing structural and functional similarities with their eukaryotic counterparts, for example, NEIL1–NEIL3. Here, we present two crystal structures of MutM from pathogenic Neisseria meningitidis: a MutM holoenzyme and MutM bound to DNA. The free enzyme exists in an open conformation, while upon binding to DNA, both the enzyme and DNA undergo substantial structural changes and domain rearrangement. Our data show that not only NEI glycosylases but also the MutMs undergo dramatic conformational changes. Moreover, crystallographic data support the previously published observations that MutM enzymes are rather flexible and dynamic molecules.

Recognition of a Tandem Lesion by DNA Glycosylases Explored Combining Molecular Dynamics and Machine Learning

“…Noteworthy, R264 is known to play a role in 8-oxoG extrusion 22 . The structural behavior of MutM:DNA(8-oxoG) observed here corroborates the hypothesis of a highly dynamic system, whose functional flexibility is known to be central to ensure its biological role through the recognition and extrusion of 8-oxoG 28,29 .…”

“…The residues which single out in this MLP analysis match very well with the ones evidenced by previous works on MutM and Fpg 14,15,17,19,20,28 . Our machine-learning post-processing allows to disentangle a complex interaction pathway, which is already well-established for 8-oxoG-containing DNA 29 but perturbed upon the presence of tandem lesions as revealed by the present simulations. It allows to generate an exhaustive map of residues showing importance for the protein-DNA interactions, beyond the simple visual investigation based on the data from the literature.…”

“…While in the simulation of the singly-damaged system, the classical interaction patterns are observed, the presence of an additional Ap site results in the rotation of R76 that provokes a shift of the intercalation triad. Noteworthy, as R76 is poorly conserved in MutM sequences from different organisms 20,29 , one cannot rule out the possibility of a different reorganization around the intercalation triad. First observations of our MD trajectories allowed to describe the re-shaping of the MutM:DNA interaction patterns -see Figure 2 and 3.…”

“…Nuleic acids also exhibit stronger interactions with MutM in the case of tandem lesion, which overall suggests that the presence of a second damage somehow results in a more rigid complex than when an isolated 8-oxoG is present. However, the global rigidity of the tandem-damaged MutM:DNA complex can actually be counterproductive for repair since it has been evidenced that flexibility of the DNA strand is a key feature correlating with 8-oxoG removal 29 . This consideration is also further reinforced by the fact that conversely, the catalytic N-terminal residues are less involved in the MutM:DNA complex stability in the case of tandem-damaged nucleotides.…”

“…Indeed, the combination of oxidatively-generated DNA lesions embrace a combinatorial chemistry, with contrasted structural, mechanical and dynamic properties. Additionally, MutM/Fpg are very flexible proteins 29 , certainly difficult to properly sample. The efficiency of our protocols gives perspectives for its extension towards other tandem systems and the investigation of sequence effects 12,45,46 .…”