%0 Journal Article
%T A Model for Transition of 5กไ-Nuclease Domain of DNA Polymerase I from Inert to Active Modes
%A Ping Xie
%A Jon R. Sayers
%J PLOS ONE
%D 2012
%I Public Library of Science (PLoS)
%R 10.1371/journal.pone.0016213
%X Bacteria contain DNA polymerase I (PolI), a single polypeptide chain consisting of ~930 residues, possessing DNA-dependent DNA polymerase, 3กไ-5กไ proofreading and 5กไ-3กไ exonuclease (also known as flap endonuclease) activities. PolI is particularly important in the processing of Okazaki fragments generated during lagging strand replication and must ultimately produce a double-stranded substrate with a nick suitable for DNA ligase to seal. PolI's activities must be highly coordinated both temporally and spatially otherwise uncontrolled 5กไ-nuclease activity could attack a nick and produce extended gaps leading to potentially lethal double-strand breaks. To investigate the mechanism of how PolI efficiently produces these nicks, we present theoretical studies on the dynamics of two possible scenarios or models. In one the flap DNA substrate can transit from the polymerase active site to the 5กไ-nuclease active site, with the relative position of the two active sites being kept fixed; while the other is that the 5กไ-nuclease domain can transit from the inactive mode, with the 5กไ-nuclease active site distant from the cleavage site on the DNA substrate, to the active mode, where the active site and substrate cleavage site are juxtaposed. The theoretical results based on the former scenario are inconsistent with the available experimental data that indicated that the majority of 5กไ-nucleolytic processing events are carried out by the same PolI molecule that has just extended the upstream primer terminus. By contrast, the theoretical results on the latter model, which is constructed based on available structural studies, are consistent with the experimental data. We thus conclude that the latter model rather than the former one is reasonable to describe the cooperation of the PolI's polymerase and 5กไ-3กไ exonuclease activities. Moreover, predicted results for the latter model are presented.
%U http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016213