Substrate-dependent millisecond domain motions in dna polymerase β

Rebecca B. Berlow, Monalisa Swain, Shibani Dalal, Joann B. Sweasy, J. Patrick Loria

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

Abstract

DNA polymerase β (Pol β) is a 39-kDa enzyme that performs the vital cellular function of repairing damaged DNA. Mutations in Pol β have been linked to various cancers, and these mutations are further correlated with altered Pol β enzymatic activity. The fidelity of correct nucleotide incorporation into damaged DNA is essential for Pol β repair function, and several studies have implicated conformational changes in Pol β as a determinant of this repair fidelity. In this work, the rate constants for domain motions in Pol β have been determined by solution NMR relaxation dispersion for the apo and substrate-bound, binary forms of Pol β. In apo Pol β, molecular motions, primarily isolated to the DNA lyase domain, are observed to occur at 1400 s- 1. Additional analysis suggests that these motions allow apo Pol β to sample a conformation similar to the gapped DNA-substrate-bound form. Upon binding DNA, these lyase domain motions are significantly quenched, whereas evidence for conformational motions in the polymerase domain becomes apparent. These NMR studies suggest an alteration in the dynamic landscape of Pol β due to substrate binding. Moreover, a number of the flexible residues identified in this work are also the location of residues, which upon mutation lead to cancer phenotypes in vivo, which may be due to the intimate role of protein motions in Pol β fidelity.

Original languageEnglish (US)
Pages (from-to)171-182
Number of pages12
JournalJournal of Molecular Biology
Volume419
Issue number3-4
DOIs
StatePublished - Jun 8 2012
Externally publishedYes

Keywords

  • conformational change
  • DNA polymerase β
  • enzyme motions
  • relaxation dispersion
  • solution NMR

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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