Catalytic Mechanism of Escherichia coli Endonuclease VIII: Roles of the Intercalation Loop and the Zinc Finger
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- 作者：Konstantin Y. Kropachev ; Dmitry O. Zharkov ; Arthur P. Grollman
- 刊名：Biochemistry
- 出版年：2006
- 出版时间：October 3, 2006
- 年：2006
- 卷：45
- 期：39
- 页码：12039 - 12049
- 全文大小：518K
- 年卷期：v.45,no.39(October 3, 2006)
- ISSN：1520-4995
文摘
Endonuclease VIII (Nei) excises oxidatively damaged pyrimidines from DNA and sharesstructural and functional homology with formamidopyrimidine-DNA glycosylase. Although the structureof Escherichia coli Nei is solved [Zharkov et al. (2002) EMBO J. 21, 789-800], the functions of manyof its amino acid residues involved in catalysis and substrate specificity are not known. We constructeda series of Nei mutants that interfere with eversion of the damaged base from the helix (QLY69-71AAA,
QLY69-71) or perturb the conserved zinc finger (R171A, Q261A). Steady-state kinetics were measuredwith these mutant enzymes using substrates containing 5,6-dihydrouracil, two enantiomers of thymineglycol, 8-oxo-7,8-dihydroguanine, and an abasic site positioned opposite each of the four canonical DNAbases. To some extent, all Nei mutants were deficient in processing damaged DNA, with mutations in thezinc finger generally having a more profound effect. Wild-type Nei showed prominent opposite-basespecificity (G > C 
T > A) when the lesion was 5,6-dihydrouracil or cis-(5S,6R)-thymine glycol butnot for other lesions tested. Mutations in the Q69-Y71 loop eliminated this effect. Only wild-type Neiand Nei-Q261A mutants could be reductively cross-linked to damaged base-containing DNA. Experimentsinvolving trapping with NaBH4 and the kinetics of DNA cleavage catalyzed by Nei-Q261A suggestedthat this mutant was deficient in regenerating free enzyme from the Nei-DNA covalent complex formedduring the reaction. We conclude that the opposite-base specificity of Nei is primarily governed by residuesin the Q69-Y71 loop and that both this loop and the zinc finger contribute significantly to the substratespecificity of Nei.
QLY69-71) or perturb the conserved zinc finger (R171A, Q261A). Steady-state kinetics were measuredwith these mutant enzymes using substrates containing 5,6-dihydrouracil, two enantiomers of thymineglycol, 8-oxo-7,8-dihydroguanine, and an abasic site positioned opposite each of the four canonical DNAbases. To some extent, all Nei mutants were deficient in processing damaged DNA, with mutations in thezinc finger generally having a more profound effect. Wild-type Nei showed prominent opposite-basespecificity (G > C T > A) when the lesion was 5,6-dihydrouracil or cis-(5S,6R)-thymine glycol butnot for other lesions tested. Mutations in the Q69-Y71 loop eliminated this effect. Only wild-type Neiand Nei-Q261A mutants could be reductively cross-linked to damaged base-containing DNA. Experimentsinvolving trapping with NaBH4 and the kinetics of DNA cleavage catalyzed by Nei-Q261A suggestedthat this mutant was deficient in regenerating free enzyme from the Nei-DNA covalent complex formedduring the reaction. We conclude that the opposite-base specificity of Nei is primarily governed by residuesin the Q69-Y71 loop and that both this loop and the zinc finger contribute significantly to the substratespecificity of Nei.