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Introduction

Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix^[1].

Function

Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase^[2].

Uracil-DNA Glycosylase

The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix takes its place in the minor groove since AP sites can be mutagenic^[3]. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil.

References

1. ↑ Schormann N, Ricciardi R, Chattopadhyay D. Uracil-DNA glycosylases-structural and functional perspectives on an essential family of DNA repair enzymes. Protein Sci. 2014 Dec;23(12):1667-85. doi: 10.1002/pro.2554. Epub 2014 Oct 25. PMID:25252105 doi:http://dx.doi.org/10.1002/pro.2554
2. ↑ Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA. Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA. EMBO J. 1998 Sep 1;17(17):5214-26. PMID:9724657 doi:10.1093/emboj/17.17.5214
3. ↑ Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285 doi:http://dx.doi.org/10.1038/384087a0