Uracil-DNA glycosylase

Uracil-DNA glycosylase, also known as UNG or UDG, is a human gene though orthologs exist ubiquitously among prokaryotes and eukaryotes and even in some DNA viruses. The first uracil DNA-glycosylase was isolated from Escherichia coli.

Function

The human gene encodes one of several uracil-DNA glycosylases. Alternative promoter usage and splicing of this gene leads to two different isoforms: the mitochondrial UNG1 and the nuclear UNG2. One important function of uracil-DNA glycosylases is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosylic bond and initiating the base-excision repair (BER) pathway. Uracil bases occur from cytosine deamination or misincorporation of dUMP residues. After a mutation occurs, the mutagenic threat of uracil propagates through any subsequent DNA replication steps. Once unzipped, mismatched guanine and uracil pairs are separated, and DNA polymerase inserts complementary bases to form a guanine-cytosine (GC) pair in one daughter strand and an adenine-uracil (AU) pair in the other. Half of all progeny DNA derived from the mutated template inherit a shift from GC to AU at the mutation site. UDG excises uracil in both AU and GU pairs to prevent propagation of the base mismatch to downstream transcription and translation processes. With high efficiency and specificity, this glycosylase repairs more than 10,000 bases damaged daily in the human cell. Human cells express five to six types of DNA glycosylases, all of which share a common mechanism of base eversion and excision as a means of DNA repair.

Structure

UDG is made of a four-stranded parallel β-sheet surrounded by eight α-helices. The active site comprises five highly conserved motifs that collectively catalyze glycosidic bond cleavage:

1. Water-activating loop: 63-QDPYH-67
2. Pro-rich loop: 165-PPPPS-169
3. Uracil-binding motif: 199-GVLLLN-204
4. Gly-Ser loop: 246-GS-247
5. Minor groove intercalation loop: 268-HPSPLS-273

Mechanism

Glycosidic bond cleavage follows a “pinch-push-pull” mechanism using the five conserved motifs.

Pinch: UDG scans DNA for uracil by nonspecifically binding to the strand and creating a kink in the backbone, thereby positioning the selected base for detection. The Pro-rich and Gly-Ser loops form polar contacts with the 3’ and 5’ phosphates flanking the examined base. This compression of the DNA backbone, or “pinch,” allows for close contact between UDG and base of interest.

Push: To fully assess the nucleotide identity, the intercalation loop penetrates, or pushes into, the DNA minor groove and induces a conformational change to flip the nucleotide out of the helix. Backbone compression favors eversion of the now extrahelical nucleotide, which is positioned for recognition by the uracil-binding motif. The coupling of intercalation and eversion helps compensate for the disruption of favorable base stacking interactions within the DNA helix. Leu272 fills the void left by the flipped nucleotide to create dispersion interactions with neighboring bases and restore stacking stability.

Pull: Now accessible to the active site, the nucleotide interacts with the uracil binding motif. The active site shape complements the everted uracil structure, allowing for high substrate specificity. Purines are too large to fit in the active site, while unfavorable interactions with other pyrimidines discourage binding alternative substrates. The side chain of Tyr147 interferes sterically with the thymine C5 methyl group, while a specific hydrogen bond between the uracil O2 carbonyl and Gln144 discriminates against a cytosine substrate, which lacks the necessary carbonyl. Once uracil is recognized, cleavage of the glycosidic bond proceeds according to the mechanism below.

File:UDGStep1.JPG

Step 1: Nucleophilic water attacks the C-N glycosidic bond (intercalation by Leu272 not shown for simplicity).

File:UDGMechStep2.jpg

Step 2: Uracil intermediate leaves the DNA helix; hydrogen bonds in the active site stabilize the DNA backbone.

File:UDGMechStep3.JPG

Step 3: Proton exchange generates free uracil.

The position of the residues that activate the water nucleophile and protonate the uracil leaving group are widely debated, though the most commonly followed mechanism employs the water activating loop detailed in the enzyme structure. Regardless of position, the identities of the aspartic acid and histidine residues are consistent across catalytic studies.

Interactions

Uracil-DNA glycosylase has been shown to interact with RPA2.