Thermodynamics of human DNA ligase I trimerization and association with DNA polymerase beta

J Biol Chem. 1998 Aug 7;273(32):20540-50. doi: 10.1074/jbc.273.32.20540.


The interaction between human DNA polymerase beta (pol beta) and DNA ligase I, which appear to be responsible for the gap filling and nick ligation steps in short patch or simple base excision repair, has been examined by affinity chromatography and analytical ultracentrifugation. Domain mapping studies revealed that complex formation is mediated through the non-catalytic N-terminal domain of DNA ligase I and the N-terminal 8-kDa domain of pol beta that interacts with the DNA template and excises 5'-deoxyribose phosphate residue. Intact pol beta, a 39-kDa bi-domain enzyme, undergoes indefinite self-association, forming oligomers of many sizes. The binding sites for self-association reside within the C-terminal 31-kDa domain. DNA ligase I undergoes self-association to form a homotrimer. At temperatures over 18 degreesC, three pol beta monomers attached to the DNA ligase I trimer, forming a stable heterohexamer. In contrast, at lower temperatures (<18 degreesC), pol beta and DNA ligase I formed a stable 1:1 binary complex only. In agreement with the domain mapping studies, the 8-kDa domain of pol beta interacted with DNA ligase I, forming a stable 3:3 complex with DNA ligase I at all temperatures, whereas the 31-kDa domain of pol beta did not. Our results indicate that the association between pol beta and DNA ligase I involves both electrostatic binding and an entropy-driven process. Electrostatic binding dominates the interaction mediated by the 8-kDa domain of pol beta, whereas the entropy-driven aspect of interprotein binding appears to be contributed by the 31-kDa domain.

Publication types

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

MeSH terms

  • Chromatography, Affinity
  • DNA Ligase ATP
  • DNA Ligases / chemistry*
  • DNA Polymerase beta / chemistry*
  • DNA Repair / genetics
  • Humans
  • Protein Binding / physiology
  • Protein Conformation*
  • Recombinant Proteins / chemistry
  • Static Electricity
  • Thermodynamics
  • Ultracentrifugation


  • LIG1 protein, human
  • Recombinant Proteins
  • DNA Polymerase beta
  • DNA Ligases
  • DNA Ligase ATP