Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase

Abstract

Edited by Patrick SungThe highly mutagenic A:8-oxoguanine (oxoG) base pair is generated mainly by misreplication of the C:oxoG base pair, the oxidation product of the C:G base pair.

Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process

“…The subsequent transitions starting from the S2 state involve the compression of the DNA backbone and eversion of the target nt into the active site, which are also actively promoted by TDG. The active role of other DNA repair/modify proteins in promoting the base flipping have also been demonstrated by former biochemical or crystallographic studies ( 40 , 45 , 48 , 63 , 64 , 111 ). For example, the key intercalation residues, e.g.…”

“…Whether the repair enzyme actively promotes the base-flipping or passively traps the extrahelical nt has been a subject of many structural ( 39 , 40 , 63 ), biochemical ( 48 ), NMR ( 23 ) and single-molecule studies ( 47 , 51 , 66 ). One way to answer this question is to directly compare the flipping rate of the damaged nt with and without protein binding, as evidenced by previous imino proton exchange assay for UDG ( 23 ).…”

“…For example, the key intercalation residues, e.g. the Leu125 in AlkA ( 63 ) and Tyr88 in MutY ( 40 ), are shown to be capable of recognizing the intrahelical lesion bases though the intercalation domains have not penetrated into the DNA minor groove yet, implying an active role of the glycosylase in promoting the base extrusion.…”

“…Their results are supported by several crystal structures of the MutM–DNA complex in which an oxoG or normal G base is trapped in diverse forms, from intrahelical ( 39 , 59 , 60 ), partially ( 61 ) to fully extruded states ( 60 , 62 ). Likewise, both bacterial 3-methyladenine (3mA) glycosylase (AlkA) and MutY adenine DNA glycosylase that specifically excise 3mA and A (from A·oxoG lesion), respectively, have been trapped targeting to an intrahelical base pair (bp), in complex with either undamaged (for AlkA) ( 63 ) or damaged DNA (for MutY) ( 40 ). Taken together, the above static structures of different glycosylases suggest an active role of the enzyme in promoting the base extrusion initiated from an intrahelical state.…”

Structure–Activity Relationships Reveal Key Features of 8-Oxoguanine: A Mismatch Detection by the MutY Glycosylase

“…Comparing this structure to that of full-length MutY bound to lesion-containing DNA suggested that a loop region of the C-terminal domain may be in proximity to interact with OG:A from the major groove side. 35 Due to the known role of the CTD in OG recognition, 13,20,34,36−38 and its required presence for cellular repair of OG:A mismatches, 20,39 the idea that this CTD loop region could be important for OG syn recognition via interactions with the 2-amino group is appealing. Indeed, these recognition features could involve direct hydrogen-bonding or steric interactions that aid in stalling MutY as it moves along DNA.…”