DNA glycosylases

Figure 36-23. Base excision-repair of DNA. The enzyme uracil DNA glycosylase removes the uracil created by spontaneous deamination of cytosine in the DNA. An endonuclease cuts the backbone near the defect then, after an endonuclease removes a few bases, the defect is filled in by the action of a repair polymerase and the strand is rejoined by a ligase. (Courtesy of B Alberts.)...

The great potential of QM/MM calculations has attracted much attention in the past decade and the number of studies published in recent years is now so large that it is not possible to cover them all here. Among recent QM/MM applications at different levels are para-hydroxybenzoate hydrolase [56, 74], citrate synthase [4-6, 52], uracil-DNA glycosylase [88], neuraminidase [89, 90], aldose reductase [91], human thrombin [92], glutathione S-transferases [57], and HIV protease [93]. 

Mismatch Repair. Mispairs that break the normal base-pairing rules can arise spontaneously due to DNA biosynthetic errors, events associated with genetic recombination and the deamination of methylated cytosine (Modrich, 1987). With the latter, when cytosine deaminates to uracil, an endonuclease enzyme, /V-uracil-DNA glycosylase (Lindahl, 1979), excises the uracil residue before it can pair with adenine at the next replication. However, 5-methyl cytosine deaminates to form thymine and will not be excised by a glycosylase. As a result, thymine exits on one strand paired with guanine on the sister strand, that is, a mismatch. This will result in a spontaneous point mutation if left unrepaired. For this reason, methylated cytosines form spontaneous mutation hot-spots (Miller, 1985). The cell is able to repair mismatches by being able to distinguish between the DNA strand that exists before replication and a newly synthesized strand. 

L4. Longo, M. C., Beminger, M. S., and Hartley, J. L., Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene 93, 125-128 (1990). 

Bhakat KK, Hazra TK, Mitra S (2004) Acetylation of the human DNA glycosylase NE1L2 and inhibition of its activity. Nucleic Acids Research 32(10) 3033-3039... 

METHYLADENINE-DNA GLYCOSYLASE 3-METHYLADENINE-DNA GLYCOSYLASE N-Methyl-L-alanine,... 

PYRIDOXAL 4-DEHYDROGENASE PYRIMIDINE DIMER DNA GLYCOSYLASE Pyroglutamase (ATP-hydrolyzing), 5-OXOPROLINASE... 

Tl. Thornton, C. G., Hartley, J. L., et al., Utilizing uracil DNA glycosylase to control carryover contamination in PCR Characterization of residual UDG activity following thermal cycling. Biotechniques 13(2), 180-184 (1992). 

Tomicic, M. Franckic. J. (1996) Effect of overexpression of E. coli 3-methyladenine-DNA glycosylase I (Tag) on survival and mutation induction in Salmonella typhimurium. Mutat. Res., i5, 3 -31... 

Mutation frequency lower in cells transfected with E. coli tog-expressing vector (tag gene encodes 3-methyladenine DNA glycosylase I activity)... 

Base-Excision Repair Every cell has a class of enzymes called DNA glycosylases that recognize particularly common DNA lesions (such as the products of cytosine and adenine deamination see Fig. 8-33a) and remove the affected base by cleaving the Af-glycosyl bond. This cleavage creates an apurinic or apyrimidinic site in the DNA, commonly referred to as an AP site or abasic... 

Uracil DNA glycosylases, for example, found in most cells, specifically remove from DNA the uracil that results from spontaneous deamination of cytosine. Mutant cells that lack this enzyme have a high rate of G=C to A=T mutations. This glycosylase does not remove uracil residues from RNA or thymine residues from DNA. The capacity to distinguish thymine from uracil, the product of cytosine deamination—necessary for the selective repair of the latter—may be one reason why DNA evolved to contain thymine instead of uracil (p. 293). 

Bacteria generally have just one type of uracil DNA glycosylase, whereas humans have at least four types, with different specificities—an indicator of the importance of uracil removal from DNA. The most abundant human uracil glycosylase, UNG, is associated with the human replisome, where it eliminates the occasional U residue inserted in place of a T during replication. The deamination of C residues is 100-fold faster in single-stranded DNA than in double-stranded DNA, and... 

DNA glycosylases 971 AP site 971 AP endonucleases 972 DNA photolyases 974 recombinational DNA repair 976 error-prone translesion DNA synthesis 976 SOS response 976 homologous genetic recombination 978... 

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