SNAP output for PDB entry 5vzb [SNAP web server]

PDB-id

5vzb; SNAP-derived features in text and JSON formats; DNAproDB

Class

transferase-DNA

Method

X-ray (1.5 Å)

Summary

Post-catalytic complex of human polymerase mu (g433s) mutant with incoming utp

Reference

Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017): "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527.

Abstract

While most DNA polymerases discriminate against ribonucleotide triphosphate (rNTP) incorporation very effectively, the Family X member DNA polymerase μ (Pol μ) incorporates rNTPs almost as efficiently as deoxyribonucleotides. To gain insight into how this occurs, here we have used X-ray crystallography to describe the structures of pre- and post-catalytic complexes of Pol μ with a ribonucleotide bound at the active site. These structures reveal that Pol μ binds and incorporates a rNTP with normal active site geometry and no distortion of the DNA substrate or nucleotide. Moreover, a comparison of rNTP incorporation kinetics by wildtype and mutant Pol μ indicates that rNTP accommodation involves synergistic interactions with multiple active site residues not found in polymerases with greater discrimination. Together, the results are consistent with the hypothesis that rNTP incorporation by Pol μ is advantageous in gap-filling synthesis during DNA double strand break repair by nonhomologous end joining, particularly in nonreplicating cells containing very low deoxyribonucleotide concentrations.