Purification and Characterization of DNA Polymerase α-Associated Replication Protein A-Dependent Yeast DNA Helicase A

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Abstract
A novel, eukaryotic, hexameric DNA helicase that was earlier identified as a component of the multiprotein polymerase α complex [Biswas et al. (1993) Biochemistry32, 13393−13398] has been purified to homogeneity and characterized. Thus far, our studies demonstrated that helicase A shares certain unique features of two other hexameric DNA helicases: the DnaB helicase of Escherichia coli and the T-antigen helicase of the SV40 virus. The helicase activity was stimulated by yeast replication protein A (RPA) and to a lower extent by E. coli single-stranded DNA binding protein (SSB). The helicase had an apparent molecular mass of 90 kDa, as determined by its mobility on sodium dodecyl sulfate−polyacrylamide gel electrophoresis. A tryptic peptide fragment of the polypeptide was sequenced followed by a BLAST search of GenBank with the tryptic peptide sequence. The search identified a 1.8 kb open reading frame previously designated as ykl017c on chromosome XI, that codes for a 78.3 kDa (683 amino acid) polypeptide. The important features of the polypeptide sequence of helicase A included a type I ATP/GTP binding motif, and a K E E R R L N V A M T R P R R sequence at the C-terminus that may be indicative of a nuclear localization signal which is required of a nuclear DNA helicase. The polypeptide sequence of helicase A appears to have homology to the DnaB helicase of E. coli (∼25%). The facts that these two helicases are vastly separated by evolution and retained similar structural and functional features, as demonstrated here, point to a possible significance of this limited homology. Although the amount of purified helicase A was limited, we have carried out necessary enzymatic characterization so that these data could be correlated with that of immunoaffinity-purifed helicase A and recombinant helicase A expressed in heterologous systems.