National Center for
4PGQ: Structure Of Human Dna Polymerase Beta Complexed With G In The Template Base Paired With Incoming Non-hydrolyzable Ttp
The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta
Nucleic Acids Res. (2014) 42 p.11233-11245
To provide molecular-level insights into the spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta (polbeta), we report four crystal structures of polbeta complexed with dG*dTTP and dA*dCTP mismatches in the presence of Mg2+ or Mn2+. The Mg(2+)-bound ground-state structures show that the dA*dCTP-Mg2+ complex adopts an 'intermediate' protein conformation while the dG*dTTP-Mg2+ complex adopts an open protein conformation. The Mn(2+)-bound 'pre-chemistry-state' structures show that the dA*dCTP-Mn2+ complex is structurally very similar to the dA*dCTP-Mg2+ complex, whereas the dG*dTTP-Mn2+ complex undergoes a large-scale conformational change to adopt a Watson-Crick-like dG*dTTP base pair and a closed protein conformation. These structural differences, together with our molecular dynamics simulation studies, suggest that polbeta increases replication fidelity via a two-stage mismatch discrimination mechanism, where one is in the ground state and the other in the closed conformation state. In the closed conformation state, polbeta appears to allow only a Watson-Crick-like conformation for purine*pyrimidine base pairs, thereby discriminating the mismatched base pairs based on their ability to form the Watson-Crick-like conformation. Overall, the present studies provide new insights into the spontaneous replication error and the replication fidelity mechanisms of polbeta.