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5 Uracil-DNA glycosylase
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T G C T A
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AP endonuclease
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80 90%
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A C T G C T A T G A C G A T
A C T G C T A T G A C G A T
Exonuclease, lyase, or phosphodiesterase
Exonuclease
A C T G C T A T G A C G A T
A C T G C T A T G A C G A T
DNA ligase
DNA ligase
Nucleotide Excision Repair
Whereas base excision repair is initiated by glycosylases and usually involves the replacement of only one nucleotide residue, nucleotide excision repair is initiated by enzymes that sense distortions in the DNA backbone and replace a short stretch of nucleotides. For example, six enzymes in E. coli excise a short stretch of DNA containing thymine dimers if the dimerization is not reversed by photoreactivation. Two copies of the protein product of the uvrA gene (for ultraviolet light UV repair) combine with one copy of the product of the uvrB gene to form a UvrA2UvrB complex that moves along the DNA, looking for damage ( g. 12.31). (The complex has 5 to 3 helicase activity.) When the complex nds damage such as a thymine dimer, with moderate to large distortion of the DNA double helix, the UvrA2 dimer dissociates, leaving the UvrB subunit alone. This causes the DNA to bend and attracts the protein product of the uvrC gene, UvrC. The UvrB subunit rst
A C T G C T A T G A C G A T A C T G C T A T G A C G A T
Figure 12.29 Mechanism of base excision repair. In this case,
a uracil-DNA glycosylase enzyme removes a uracil (red) from DNA. An AP (apurinic-apyrimidinic) endonuclease nicks the DNA on the 5 side of the base-free site. Between 80 and 90% of the time, a DNA polymerase will replace the single nucleotide (green); an exonuclease, lyase, or phosphodiesterase will remove the base-free nucleotide. The nal nick is sealed with DNA ligase. Between 10 and 20% of the time, the DNA polymerase will extend polymerization beyond the single nucleotide. In those cases, an exonuclease and DNA ligase nish the repair. (From T. Lindahl, The Croonian Lecture, 1996:
Endogenous Damage to DNA, Philosophical Transactions of the Royal Society of London, B351, pp. 1529 1538, gure 6, 1996.)
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
12. DNA: Its Mutation, Repair, and Recombination
The McGraw Hill Companies, 2001
Twelve
DNA: Its Mutation, Repair, and Recombination
UvrA2UvrB locates lesion 5 T G C G C G A A C T=T C G G A A A C G C G C T T G A A G C C T T 3 UvrA2 dissociates UvrC attaches 5 3
UvrC
UvrB
T G C G C G A A C T=T C G G A A A C G C G C T T G A A G C C T T
UvrB then UvrC nick DNA UvrD helicase unwinds oligonucleotide with dimer
(a) T
G C G C G A A C T=T C G G A A
A C G C G C T T G A A G C C T T
DNA polymerase I + DNA ligase
T G C G C G A A C T T C G G A A A C G C G C T T G A A G C C T T Figure 12.31 Nucleotide excision repair. A lesion in DNA (a thymine dimer) is located by a protein made of two copies of UvrA and one of UvrB. Then, the UvrA subunits detach, and UvrC attaches on the 5 side of the lesion. UvrB nicks the DNA on the 3 side and UvrC on the 5 side of the lesion; UvrD helicase unwinds the oligonucleotide containing the lesion (red). DNA polymerase I and DNA ligase then repair the patch (green).
(b) Figure 12.30 Two views of the human enzyme, uracil-DNA
glycosylase, bound to DNA that has a uracil present. In (a), the uracil-containing nucleotide residue has been ipped out and the uracil cleaved; in (b), the uracil-containing residue has been ipped out, but the uracil has not yet been cleaved. In both, DNA is a green stick gure with red oxygen, yellow phosphorus, and blue nitrogen atoms. In (a), the enzyme is shown as a ribbon diagram; note the cleaved uracil bound to the ribbon. In (b), the enzyme is shown as a molecular surface; the uracil-containing nucleotide is ipped out by the purple knob just left of and below center of the structure with the ipped-out residue to the right. (From S. Parikh, C. Mol, and
J. Tainer, Base excision repair enzyme family portrait in Structure, 1997, 5:1543 1550, g 1 a&b, p. 1544. Courtesy of J.A. Tainer, The Scripps Research Institute.)
nicks (hydrolyzes) the DNA four to ve nucleotides on the 3 side of the lesion; next, the UvrC subunit nicks the DNA eight nucleotides on the 5 side of the lesion. (The three components, UvrA, UvrB, and UvrC, are together called the ABC excinuclease, for excision endonuclease.) The enzyme helicase II, the product of the uvrD gene, then removes the twelve- to thirteen-base oligonucleotide as well as UvrC. DNA polymerase I lls in the gap and, in the process, evicts the UvrB, and DNA ligase closes the remaining nick ( g. 12.31). This is another relatively simple system designed to detect helix distortions and repair them.
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