Abstract
Archaea-specific D-family DNA polymerase (PolD) forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain topology of the PolD holoenzyme is proposed. The experimental evidence supports various aspects of the model. The conserved amphipathic nature of the N-terminal putative α-helix of the large subunit plays a key role in the homodimeric assembly and the self-cyclization of the large subunit and is deeply involved in the archaeal PolD stability and activity. We also discuss the evolutional transformation from archaeal D-family to eukaryotic B-family polymerase on the basis of the structural information.
Highlights
Replicative DNA polymerases (DNA Pols) are divided into archaeal-eukaryotic and bacterial types that appear not to be homologous to each other [1,2]
The second subunits of eukaryotic B-family DNA polymerases (Pols α, β, ε, and ξ) show similarities to the Mre11-like exonuclease region, the catalytic residues of the second subunits are replaced by non-catalytic residues [18,19,20]
Archaea-specific D-family DNA polymerase (PolD) forms a tetramer consisting of two large polymerase subunits (DP2) and two small exonuclease subunits (DP1)
Summary
Replicative DNA polymerases (DNA Pols) are divided into archaeal-eukaryotic and bacterial types that appear not to be homologous to each other [1,2]. All eukaryotes possess four paralogous B-family polymerases, Pols α, δ, ε, and ξ, involved in DNA replication and repair [5,6]. P. horikoshii (PhoPolD) uses RNA primer for DNA synthesis even to a lesser extent than that of the DNA primer, whereas PolB uses only the DNA primer. This strongly suggested that PolD is a key enzyme responsible for lagging strand synthesis. We point out that the amphipathic nature of the N-terminal ~50 residues of the large subunit is conserved completely in Euryarchaeota and Korarchaeota, and that it possesses a possible function to modify the efficiency of the large-subunit folding and the assembly of the PolD holoenzyme
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