a model for transition of 5′-nuclease domain of dna polymerase i from inert to active modes模型过渡5u2032核酸酶dna聚合酶领域我从惰性主动模式.pdfVIP

A Model for Transition of 59-Nuclease Domain of DNA Polymerase I from Inert to Active Modes 1 2 Ping Xie , Jon R. Sayers * 1 Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China, 2 Department of Infection and Immunity, Krebs Institute, University of Sheffield Medical School, Sheffield, United Kingdom Abstract Bacteria contain DNA polymerase I (PolI), a single polypeptide chain consisting of ,930 residues, possessing DNA- dependent DNA polymerase, 39-59 proofreading and 59-39 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 59-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 59-nuclease active site, with the relative position of the two active sites being kept fixed; while the other is that the 59-nuclease domain can transit from the inactive mode, with the 59- 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