Sandbox reserved 1753

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== Publication Abstract from PubMed ==
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Any <scene name='92/927197/Uracil/3'>Uracil</scene> bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and viral UDGs complexed with free uracil have indicated that the enzyme binds an extrahelical uracil. Such binding of undamaged extrahelical bases has been seen in the structures of two bacterial methyltransferases and bacteriophage T4 endonuclease V. Here we characterize the DNA binding and kinetics of several engineered human UDG mutants and present the crystal structure of one of these, which to our knowledge represents the first structure of any eukaryotic DNA repair enzyme in complex with its damaged, target DNA. Electrostatic orientation along the UDG active site, insertion of an amino acid (residue 272) into the DNA through the minor groove, and compression of the DNA backbone flanking the uracil all result in the flipping-out of the damaged base from the DNA major groove, allowing specific recognition of its phosphate, deoxyribose and uracil moieties. Our structure thus provides a view of a productive complex specific for cleavage of uracil from DNA and also reveals the basis for the enzyme-assisted nucleotide flipping by this critical DNA-repair enzyme.
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== Introduction ==
== Introduction ==
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Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER) it removes and repairs damaged bases usually these are single stranded DNA breaks. BER corrects DNA damage that resulted from small leisures that do not disrupt the double helix. The way Glycosylase does this is by first cleaving the glycosidic bond of the damaged nucleotide leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved as well by AP endonuclease. The gap that is left is filled in through DNA Polymerase and DNA ligase. <scene name='92/927197/Active_site/1'>Active Site</scene>
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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 removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix.
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The structure of Glycosylase has a couple different forms in terms of its general structure. It is composed of a 10bp DNA that contains U G base pair mismatch. This is what allows it to bind the DNA flipping them out of the double helix. When the uracil mismatch is flipped out of the helix an <scene name='92/927197/Arg_side_chain/1'>ARG side chain</scene> takes its place. The actual structure is composed of a protein section bound to a DNA section. This is often represented by showing the DNA section in stick form and coloring it based on the different atoms bound. The protein section is characterized using a ribbon diagram. In our biochemistry book page 897 there is a representation of this as well.
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== Function ==
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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.
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== Uracil-DNA Glycosylase ==
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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 ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows Uracil Glycosylase to bind the DNA and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic. 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.
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Revision as of 20:11, 9 October 2022

A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA

PDB ID 4skn

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