Structural basis for the excision repair of alkylation-damaged DNA.

Base-excision DNA repair proteins that target alkylation damage act on a variety of seemingly dissimilar adducts, yet fail to recognize other closely related lesions. The 1.8 A crystal structure of the monofunctional DNA glycosylase AlkA (E. coli 3-methyladenine-DNA glycosylase II) reveals a large hydrophobic cleft unusually rich in aromatic residues. An Asp residue projecting into this cleft is essential for catalysis, and it governs binding specificity for mechanism-based inhibitors. We propose that AlkA recognizes electron-deficient methylated bases through pi-donor/acceptor interactions involving the electron-rich aromatic cleft. Remarkably, AlkA is similar in fold and active site location to the bifunctional glycosylase/lyase endonuclease III, suggesting the two may employ fundamentally related mechanisms for base excision.

The effects of N7-methylguanine on duplex DNA structure.

BACKGROUND: Non-enzymatic methylation of DNA by endogenous and exogenous agents produces a variety of adducts, of which the predominant one is N7-methyl-2'-deoxyguanosine (m7dG). Although it is known that living organisms counter the deleterious effects of m7dG by producing adduct-specific DNA repair proteins, the molecular basis for specific recognition and catalysis by these proteins is poorly understood. In addition to its role as an endogenous DNA adduct, m7dG is also widely used as an in vitro probe of protein-DNA interactions. We set out to examine whether incorporation of m7dG into DNA affects duplex DNA structure. RESULTS: We carried out a large-scale synthesis of a dodecamer containing the m7dG adduct at a single, defined position. Because the instability of m7dG precludes its incorporation into oligonucleotides by standard solid-phase methods, a novel strategy employing chemical and enzymatic synthesis was used. Characterization of the m7dG-containing dodecamer by NMR reveals no structural distortion; indeed, m7dG appears to encourage a modest shift toward a more characteristically B-form duplex. CONCLUSIONS: These results argue strongly against induced DNA distortion as a mechanism for specific recognition of m7dG by adduct-specific repair proteins. The broad substrate specificity of these repair proteins disfavors a model involving direct recognition of aberrantly placed methyl groups; hence, it may be that m7dG is recognized indirectly, perhaps by its effects on the dynamics of DNA. On the other hand, the evidence presented here suggests that m7dG interferes directly with sequence-specific recognition by DNA-binding proteins by steric blockage or by masking of required contact functionalities. The synthetic methodology used here should be generally applicable to high-resolution structural studies of oligonucleotides bearing adducts that are unstable to the conditions of solid-phase DNA synthesis.

Construction of an overproduction vector containing the novel srp (sterically repressed) promoter.

We report the design, synthesis, and evaluation of a novel Escherichia coli promoter intended for use in overproduction of proteins that are deleterious to the host. In this sterically repressed promoter (srp), the lac operator site is positioned between the -10 and -35 elements, where it can interfere sterically with RNA polymerase and thereby prevent assembly of a poised transcriptional complex. An srp-containing phagemid, pKEN1, and a tac-containing phagemid, pHN1, which has been widely used in protein overproduction but is often unstable, are compared with respect to levels of uninduced and induced protein expression. The level of uninduced protein synthesis by the srp promoter in vivo is approximately 50% of that observed with tac, whereas the levels of induced protein synthesis with the 2 vectors are approximately equal. A remarkable increase in stability of overproduction and growth was observed when the toxic Ada protein was overproduced in pKEN1, demonstrating the potential utility of this vector in overproducing toxic proteins.

Direct identification of the active-site nucleophile in a DNA (cytosine-5)-methyltransferase.

The overproduction, purification, and determination of the active-site catalytic nucleophile of the DNA (cytosine-5)-methyltransferase (DCMtase) enzyme M.HaeIII are reported. Incubation of purified M.HaeIII with an oligodeoxynucleotide specifically modified with the mechanism-based inhibitor 5-fluoro-2'-deoxycytidine [Osterman, D. G., et al. (1988) Biochemistry 27, 5204-5210], in the presence of the cofactor S-adenosyl-L-methionine (AdoMet), resulted in the formation of a covalent DNA-M.HaeIII complex, which was purified to homogeneity. Characterization of the intact complex showed it to consist of one molecule of the FdC-containing duplex oligonucleotide, one molecule of M.HaeIII, and one methyl group derived from AdoMet. Exhaustive proteolysis, reduction, and alkylation of the DNA-M.HaeIII complex led to the isolation of two DNA-bound peptides--one each from treatment with Pronase or trypsin--which were subjected to peptide sequencing in order to identify the DNA attachment site. Both peptides were derived from the region of M.HaeIII containing a Pro-Cys sequence that is conserved in all known DCMtases. At the position of this conserved Cys residue (Cys71), in the sequence of each peptide, was found an unidentified amino acid residue; all other amino acid residues were in accord with the known sequence. It is thus concluded that Cys71 of M.HaeIII forms a covalent bond to DNA during catalytic methyl transfer. This finding represents a direct experimental verification for the hypothesis that the conserved Cys residue of DCMtases is the catalytic nucleophile [Wu, J. C., & Santi, D. V. (1987) J. Biol. Chem. 262, 4778-4786].(ABSTRACT TRUNCATED AT 250 WORDS)