QM/MM Study of the Uracil DNA Glycosylase Reaction Mechanism: A Competition between Asp145 and His148

J Chem Theory Comput. 2019 Aug 13;15(8):4344-4350. doi: 10.1021/acs.jctc.8b01305. Epub 2019 Jul 18.

Abstract

Uracil DNA glycosylase catalyzes the N-glycosidic bond cleavage of uracil, thereby initiating the base excision repair mechanism for this DNA lesion. Here we employ hybrid quantum mechanics/molecular mechanics calculations to investigate the exact mechanism of the nucleophile attack and the role of the conserved His148 residue. Our calculations suggest that the C1'-N1 bond dissociation proceeds by a migration of the electrophilic sugar in the direction of the water nucleophile, resulting in a planar, oxocarbenium-like transition state. The subsequent nucleophile addition and proton transfer to a nearby base occur without a barrier. We assign the role of a proton acceptor to His148 and elucidate why mutations of this residue curtail the enzymatic activity but do not fully suppress it.

MeSH terms

  • Aspartic Acid / chemistry
  • Aspartic Acid / metabolism
  • Histidine / chemistry*
  • Histidine / metabolism
  • Humans
  • Models, Molecular
  • Protons
  • Quantum Theory
  • Thermodynamics
  • Uracil-DNA Glycosidase / chemistry*
  • Uracil-DNA Glycosidase / metabolism
  • Water / chemistry

Substances

  • Protons
  • Water
  • Aspartic Acid
  • Histidine
  • Uracil-DNA Glycosidase