Presteady-state analysis of a single catalytic turnover by Escherichia coli uracil-DNA glycosylase reveals a "pinch-pull-push" mechanism

J Biol Chem. 2002 May 31;277(22):19424-32. doi: 10.1074/jbc.M201198200. Epub 2002 Mar 20.

Abstract

Uracil-DNA glycosylase catalyzes the excision of uracils from DNA via a mechanism where the uracil is extrahelically flipped out of the DNA helix into the enzyme active site. A conserved leucine is inserted into the DNA duplex space vacated by the uracil leading to the paradigmatic "push-pull" mechanism of nucleotide flipping. However, the order of these two steps during catalysis has not been conclusively established. We report a complete kinetic analysis of a single catalytic turnover using a hydrolyzable duplex oligodeoxyribonucleotide substrate containing a uracil:2-aminopurine base pair. Rapid chemical-quenched-flow methods defined the kinetics of excision at the active site during catalysis. Stopped-flow fluorometry monitoring the 2-aminopurine fluorescence defined the kinetics of uracil flipping. Parallel experiments detecting the protein fluorescence showed a slower Leu(191) insertion step occurring after nucleotide flipping but before excision. The inserted Leu(191) acts as a doorstop to prevent the return of the flipped-out uracil residue, thereby facilitating the capture of the uracil in the active site and does not play a direct role in "pushing" the uracil out of the DNA helix. The results define for the first time the proper sequence of events during a catalytic cycle and establish a "pull-push", as opposed to a "push-pull", mechanism for nucleotide flipping.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Catalysis
  • Catalytic Domain
  • DNA Glycosylases*
  • Dose-Response Relationship, Drug
  • Escherichia coli / enzymology*
  • Kinetics
  • Leucine / chemistry
  • N-Glycosyl Hydrolases / chemistry*
  • N-Glycosyl Hydrolases / metabolism
  • Oligodeoxyribonucleotides / chemistry
  • Protein Conformation
  • Spectrometry, Fluorescence
  • Time Factors
  • Uracil / chemistry
  • Uracil-DNA Glycosidase

Substances

  • Oligodeoxyribonucleotides
  • Uracil
  • DNA Glycosylases
  • N-Glycosyl Hydrolases
  • Uracil-DNA Glycosidase
  • Leucine