Human Uracil-DNA Glycosylase
Human uracil-DNA glycosylase (UDG) is a highly conserved, extremely efficient, nuclear protein. It is an archetypical DNA glycosylase that initiates the multienzymatic DNA base excision repair pathway. The pathway repairs more than 10,000 damaged bases daily in each human cell. The RNA base, uracil (U), accidently finds itself within DNA by either cytosine deamination (G*U mismatch) or misincorporation (A*U mismatch). UDG excises uracil from single and double stranded DNA. It catalyzes this removal by flipping the base out of the double helix and into the binding pocket. It is within this pocket that the N-C1' glycosylic bond between the base and deoxyribose is cleaved by hydrolysis.

UDG is composed of 223 amino acids. It has a secondary structure that consists of both alpha helices and beta sheets. This unique arrangement is called an alpha-beta-alpha sandwich. The central beta sheet consists of four strands that run parallel to each other. This sheet is surrounded by 8 alpha helices. The central beta sheet plays an important role in the catalytic mechanism.

UDG undergoes an architecturally determined conformational change upon binding DNA. It starts in the "open" unbound state and changes to a "closed" DNA-bound state. The conformational change from "open" to "closed" creates the catalytic active center. The transition is centered on a beta zipper action. This action resembles a zipper as the two sheets get closer together during the change. DNA binds to the C-terminal end of the central all parallel beta sheet. Once the DNA is bound by UDG, the enzyme flips the uracil out of the DNA helix by compressing the DNA backbone surrounding the the uracil. It flips the uracil into the active site that was created . This active site is very tight and only allows the entry of uracil and 5-fluorouracil. It is designed to prevent thymine and other modified pyrimidines from entering. The enzyme shifts the minor groove intercalation loop to insert the side chain of Leu272. This insertion prevents the neighboring bases from collapsing onto each due to the interaction loss from the removal of uracil.

The active site of uracil-DNA glycosylase is set in the crease between beta sheet 1 and beta sheet 3. The active center consists of two motifs. The first contains and asparate residue 145 that is responsible for the activation of the water molecule used in catalysis. The second motif is used to stabilize the protein-DNA complex. His268 aids in this process by stabilizing the negative charge that develops on the uracil as the glycosidic bond is pulled apart by the active center. Before cleavage of the glycosidic bond, the trigonal planar C1 position (N1 in uracil) is distorted to a tetrahedral shape by the active site. Phe158 and Tyr147 are found on the wall of the active site and impose the geometrical change. It is thought that this change is required to obtain stereoelectric effects that promote cleavage. UDG funnels DNA-substrate binding energy into catalytic power by enforcing a distortion on the uracil substrate. During the cleavage process, the uracil tilts and moves deeper into the the active site and improves its interaction with Phe158. Later, uracil relaxes even more and withdraws from the enzyme reducing steric strain.

The complete process of repairing the base excision pathway relies on more enzymes than just UDG. After UDG finishes it job, four more enzymes perform their roles. Apurinic and apyrimidinic endonuclease is responsible for cleaving the DNA backbone, deoxyribophosphodiesterase removes the 5'-phosphate group, DNA polymerase and DNA ligase replace the correct nucleotide to result in functional DNA.

The CATH classification of human uracil-DNA glycosylase is Class: alpha beta, Architecture: alpha-beta-alpha sandwich, Topology: uracil-DNA glycosylase, subunit E, Homology: uracil-DNA glycosylase subunit E

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