Low fidelity DNA synthesis by a y family DNA polymerase due to misalignment in the active site.

Abstract:

Sulfolobus solfataricus DNA polymerase IV (Dpo4) is a member of the Y family of DNA polymerases whose crystal structure has recently been solved. As a model for other evolutionarily conserved Y family members that perform translesion DNA synthesis and have low fidelity, we describe here the base substitution and frameshift fidelity of DNA synthesis by Dpo4. Dpo4 generates all 12 base-base mismatches at high rates, 11 of which are similar to those of its human homolog, DNA polymerase kappa. This result is consistent with the Dpo4 structure, implying lower geometric selection for correct base pairs. Surprisingly, Dpo4 generates C.dCMP mismatches at an unusually high average rate and preferentially at cytosine flanked by 5'-template guanine. Dpo4 also has very low frameshift fidelity and frequently generates deletions of even noniterated nucleotides, especially cytosine flanked by a 5'-template guanine. Both unusual features of error specificity suggest that Dpo4 can incorporate dNTP precursors when two template nucleotides are present in the active site binding pocket. These results have implications for mutagenesis resulting from DNA synthesis by Y family polymerases.

Polymerases:

Topics:

Historical Protein Properties (MW, pI, ...), Other Enzymatic Activities, Structure and Structure/Function, Fidelity, Exonuclease Activity

Status:

new topics/pols set partial results complete validated

Results:

Polymerase Reference Property Result Context
Dpo4 Kokoska RJ2002 3-5' Exonuclease (proofreading) No
Dpo4 Kokoska RJ2002 5-3' Exonuclease No
Dpo4 Kokoska RJ2002 Frameshift Error Rate 0.0023 errors/bp Technique: M13mp2 forward mutation assay
Dpo4 Kokoska RJ2002 Nucleotide Substitution Rate 0.0065 errors/bp Technique: M13mp2 forward mutation assay

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