4PHA: Structure Of Human Dna Polymerase Beta Complexed With A In The Template Base Paired With Incoming Non-hydrolyzable Ctp

Citation:
Abstract
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.
PDB ID: 4PHADownload
MMDB ID: 123426
PDB Deposition Date: 2014/5/5
Updated in MMDB: 2017/10
Experimental Method:
x-ray diffraction
Resolution: 2.52  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4PHA: tetrameric; determined by author and by software (PISA)
Molecular Components in 4PHA
Label Count Molecule
Protein (1 molecule)
1
DNA Polymerase Beta(Gene symbol: POLB)
Molecule annotation
Nucleotides(3 molecules)
1
DNA (5'-d(*cp*cp*gp*ap*cp*ap*tp*cp*gp*cp*ap*tp*cp*ap*gp*c)- 3')
Molecule annotation
1
DNA (5'-d(*gp*cp*tp*gp*ap*tp*gp*cp*gp*a)-3')
Molecule annotation
1
DNA (5'-d(p*gp*tp*cp*gp*g)-3')
Molecule annotation
Chemicals (5 molecules)
1
2
2
2
3
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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