A structural and kinetic characterization of a fragment of the HoLaMa DNA polymerase is presented here. In particular, a truncated form of HoLaMa, devoid of a consistent portion of the thumb domain, was isolated and purified. This HoLaMa fragment, denoted as ΔNter-HoLaMa, is surprisingly competent in catalyzing DNA extension, albeit featuring a kcat one order of magnitude lower than the corresponding kinetic constant of its full-length counterpart. The conformational rearrangements, if any, of enzyme tryptophanes triggered by DNA binding or extension were assayed under pre-steady-state conditions. The fluorescence of HoLaMa tryptophanes was found to significantly change upon DNA binding and extension. On the contrary, no fluorescence changes of ΔNter-HoLaMa tryptophanes were detected under the same conditions, suggesting that major conformational transitions are not required for DNA binding or extension by this truncated DNA polymerase.
Keywords: DNA polymerase; DNA replication; Fingers closure; HoLaMa; Thumb domain.