Abstract
The removal of chemically damaged DNA bases such as 3-methyladenine (3-MeA) is an essential process in all living organisms and is catalyzed by the enzyme 3-MeA DNA glycosylase I. A key question is how the enzyme selectively recognizes the alkylated 3-MeA over the much more abundant adenine. The crystal structures of native and Y16F-mutant 3-MeA DNA glycosylase I from Staphylococcus aureus in complex with 3-MeA are reported to 1.8 and 2.2 Å resolution, respectively. Isothermal titration calorimetry shows that protonation of 3-MeA decreases its binding affinity, confirming previous fluorescence studies that show that charge-charge recognition is not critical for the selection of 3-MeA over adenine. It is hypothesized that the hydrogen-bonding pattern of Glu38 and Tyr16 of 3-MeA DNA glycosylase I with a particular tautomer unique to 3-MeA contributes to recognition and selection.
Highlights
Bacterial 3-methyladenine DNA glycosylase I (TAG; Forsyth et al, 2002; Ji et al, 2001) is ubiquitous in eubacteria (Supplementary Fig. S11; Drohat et al, 2002) but shows no sequence or structural similarity to mammalian 3-methyladenine DNA glycosylase (AAG; Lau et al, 2000)
TAG belongs to the alkylpurine DNA glycosylase superfamily and hydrolyzes the N9–C10 glycosylic bond between a 3-methyladenosine (3-MeA) nucleobase lesion and the deoxyribose ring (Riazuddin & Lindahl, 1978; Bjelland et al, 1993; Fig. 1a). 3-Methylation of adenine does not influence base pairing (Sedgwick et al, 2007); rather, the methyl group blocks replication by interfering with the interactions of DNA polymerase (Sedgwick et al, 2007; Engelward et al, 1996)
The crystal structure of the S. typhi enzyme complexed with 3-MeA and abasic DNA (Metz et al, 2007) and an NMR structure of the E. coli enzyme complexed with 3-MeA (Cao et al, 2003) have been reported
Summary
Bacterial 3-methyladenine DNA glycosylase I (TAG; Forsyth et al, 2002; Ji et al, 2001) is ubiquitous in eubacteria (Supplementary Fig. S11; Drohat et al, 2002) but shows no sequence or structural similarity to mammalian 3-methyladenine DNA glycosylase (AAG; Lau et al, 2000). TAG belongs to the alkylpurine DNA glycosylase superfamily and hydrolyzes the N9–C10 glycosylic bond between a 3-methyladenosine (3-MeA) nucleobase lesion and the deoxyribose ring (Riazuddin & Lindahl, 1978; Bjelland et al, 1993; Fig. 1a). TAG from Staphylococcus aureus shares around 40% amino-acid sequence identity with the structurally characterized TAG enzymes from Salmonella typhi (Metz et al, 2007) and Escherichia coli (Drohat et al, 2002). The crystal structure of the S. typhi enzyme complexed with 3-MeA and abasic DNA (Metz et al, 2007) and an NMR structure of the E. coli enzyme complexed with 3-MeA (Cao et al, 2003) have been reported. 1 Supplementary material has been deposited in the IUCr electronic archive (Reference: GX5204)
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