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Catalytic Site Atlas

CSA LITERATURE entry for 1eug

E.C. nameuracil-DNA glycosylase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 3.2.2.27
CSA Homologues of 1eugThere are 37 Homologs
CSA Entries With UniProtID P12295
CSA Entries With EC Number 3.2.2.27
PDBe Entry 1eug
PDBSum Entry 1eug
MACiE Entry M0071

Literature Report

IntroductionUracil-DNA glycosylase (UDG) initiates the base excision repair (BER) pathway for uracil by hydrolysing the N-C'1 glycosylic bond between a target uracil and an abasic site. The human BER cycle is important for restoring the chemical integrity of DNA.
MechansimThe enzyme mechanism has been hotly debated. Classically, an acid/base mechanism has been employed, but new evidence suggests a steric distortion of the DNA substrate catalyses the reaction in a mechanism similar to SN1 dissociation.
The tetrahedral distortion is imposed by the structurally rigid walls of the active site, formed by Tyr and Phe residues. The enzyme centre flattens the pucker ring of the uridine deoxyribose, raising the glycosylic bond to a semi-axial position, allowing pi-sigma* overlap. This stereoelectronic effect increases in strength as the substrate is further distorted towards the transition state.
As the transition state move towards a tetrahedral geometry, and glycosylic bond rotation occurs, an anomeric effect is coupled to the pi systems of the uracil ring, resulting in orbital overlap of the glycosylic bond and the carbonyl C2 and C4 pi systems. The developing negative charge of the transition state is stabilised by hydrogen bonding to His 268. The enzyme funnels binding energy for use is catalysis by employing substrate distortions to couple two stereoelectronic effects to promote efficient catalysis.
The abasic nucleotide relaxes into a more puckered conformation and withdraws from the enzyme while uracil tilts deeper into the active site, improving its stacking interactions with the Phen residue present. These rearrangements lower the product's energies relative to the reactant's, reducing the strain within the active site and allowing the enzyme to bind preferentially to the products.
Reaction

Catalytic Sites for 1eug

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
PheA7777macie:sideChainThe residue acts to distort the DNA substrate towards the transition state conformation by steric and pi stacking interactions with the pucker ring of the uridine deoxyribose.
HisA187187macie:sideChainThe residue hydrogen bonds to the developing anion within the transition state, lowering its energy.
TyrA6666macie:sideChainThe residue acts to distort the DNA substrate towards the transition state conformation through steric interactions with the pucker ring of the uridine deoxyribose. The residue is also implicated in preventing the binding of thymine within the active site.

Literature References

Notes:
Parikh SS
Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects.
Proc Natl Acad Sci U S A 2000 97 5083-5088
PubMed: 10805771
Parikh SS
Lessons learned from structural results on uracil-DNA glycosylase.
Mutat Res 2000 460 183-199
PubMed: 10946228
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