Structural determinants for specific recognition by T4 endonuclease V

Amanda McCullough, Orlando Schärer, Gregory L. Verdine, Robert (Stephen) Lloyd

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

DNA glycosylases catalyze the scission of the N-glycosyl bond linking either a damaged or mismatched base to the DNA sugar phosphate backbone. T4 endonuclease V is a glycosylase/apurinic (AP) lyase that is specific for UV light-induced cis-syn pyrimidine dimers. As a proposed transition state analog/inhibitor for glycosylases, a phosphoramidite derivative containing a pyrrolidine residue has been synthesized. The binding of endonuclease V to this duplex was analyzed by gel mobility shift assays and resulted in a single stable complex of reduced mobility and an apparent K(d) of 17 nM. To assess the importance of the positive charge for specific binding, studies using other non-cleavable substrate analogs were performed. Wild type T4 endonuclease V shows an 8-fold decreased affinity for a tetrahydrofuran as compared with the pyrrolidine residue, demonstrating the significance of the positive charge for recognition. A 2-fold increase in binding affinity for a reduced AP site was observed. Similar assays using catalytically compromised mutants (E23Q and E23D) of endonuclease V demonstrate altered affinities for the pyrrolidine as well as tetrahydrofuran and reduced AP sites. This approach has provided insight into the structural mechanism by which specific lesions are targeted by the protein as well as the structural determinants of the DNA required for specific recognition by T4 endonuclease V.

Original languageEnglish (US)
Pages (from-to)32147-32152
Number of pages6
JournalJournal of Biological Chemistry
Volume271
Issue number50
DOIs
StatePublished - 1996
Externally publishedYes

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Deoxyribonuclease (Pyrimidine Dimer)
Assays
Sugar Phosphates
DNA Glycosylases
Pyrimidine Dimers
Lyases
DNA
Electrophoretic Mobility Shift Assay
Ultraviolet Rays
Ultraviolet radiation
Gels
Derivatives
Substrates
phage T4 endonuclease V
pyrrolidine
Proteins
tetrahydrofuran

ASJC Scopus subject areas

  • Biochemistry

Cite this

Structural determinants for specific recognition by T4 endonuclease V. / McCullough, Amanda; Schärer, Orlando; Verdine, Gregory L.; Lloyd, Robert (Stephen).

In: Journal of Biological Chemistry, Vol. 271, No. 50, 1996, p. 32147-32152.

Research output: Contribution to journalArticle

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AU - Schärer, Orlando

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AB - DNA glycosylases catalyze the scission of the N-glycosyl bond linking either a damaged or mismatched base to the DNA sugar phosphate backbone. T4 endonuclease V is a glycosylase/apurinic (AP) lyase that is specific for UV light-induced cis-syn pyrimidine dimers. As a proposed transition state analog/inhibitor for glycosylases, a phosphoramidite derivative containing a pyrrolidine residue has been synthesized. The binding of endonuclease V to this duplex was analyzed by gel mobility shift assays and resulted in a single stable complex of reduced mobility and an apparent K(d) of 17 nM. To assess the importance of the positive charge for specific binding, studies using other non-cleavable substrate analogs were performed. Wild type T4 endonuclease V shows an 8-fold decreased affinity for a tetrahydrofuran as compared with the pyrrolidine residue, demonstrating the significance of the positive charge for recognition. A 2-fold increase in binding affinity for a reduced AP site was observed. Similar assays using catalytically compromised mutants (E23Q and E23D) of endonuclease V demonstrate altered affinities for the pyrrolidine as well as tetrahydrofuran and reduced AP sites. This approach has provided insight into the structural mechanism by which specific lesions are targeted by the protein as well as the structural determinants of the DNA required for specific recognition by T4 endonuclease V.

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