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Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Domain structures and inter-domain interactions defining the holoenzyme architecture of archaeal d-family DNA
Ikuo Matsui1, Eriko Matsui2, Kazuhiko Yamasaki3
1Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan. ik-matsui@aist.go.jp.
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.
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