T4 DNA Ligase Structure Reveals a Prototypical ATP-dependent Ligase With a Unique Mode of Sliding Clamp Interaction

Nucleic Acids Res. 2018 Nov 2;46(19):10474-10488. doi: 10.1093/nar/gky776.

Abstract

DNA ligases play essential roles in DNA replication and repair. Bacteriophage T4 DNA ligase is the first ATP-dependent ligase enzyme to be discovered and is widely used in molecular biology, but its structure remained unknown. Our crystal structure of T4 DNA ligase bound to DNA shows a compact α-helical DNA-binding domain (DBD), nucleotidyl-transferase (NTase) domain, and OB-fold domain, which together fully encircle DNA. The DBD of T4 DNA ligase exhibits remarkable structural homology to the core DNA-binding helices of the larger DBDs from eukaryotic and archaeal DNA ligases, but it lacks additional structural components required for protein interactions. T4 DNA ligase instead has a flexible loop insertion within the NTase domain, which binds tightly to the T4 sliding clamp gp45 in a novel α-helical PIP-box conformation. Thus, T4 DNA ligase represents a prototype of the larger eukaryotic and archaeal DNA ligases, with a uniquely evolved mode of protein interaction that may be important for efficient DNA replication.

Publication types

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

MeSH terms

  • Archaea / enzymology
  • Archaea / genetics
  • Crystallography, X-Ray
  • DNA / chemistry*
  • DNA / genetics
  • DNA / metabolism
  • DNA Ligase ATP / chemistry*
  • DNA Ligase ATP / genetics
  • DNA Ligase ATP / metabolism
  • DNA Ligases / chemistry*
  • DNA Ligases / genetics
  • DNA Ligases / metabolism
  • DNA, Archaeal / chemistry
  • DNA, Archaeal / genetics
  • DNA, Archaeal / metabolism
  • Eukaryota / enzymology
  • Eukaryota / genetics
  • Models, Molecular
  • Nucleic Acid Conformation*
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Domains*

Substances

  • DNA, Archaeal
  • DNA
  • DNA Ligases
  • DNA Ligase ATP