3EZ5

Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and zinc (closed form).

3EZ5 の概要

• エントリーDOI: 10.2210/pdb3ez5/pdb
• 関連するPDBエントリー: 3EYZ
• 関連するBIRD辞書のPRD_ID: PRD_900003
• 分子名称: DNA polymerase I, 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3', 5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3', ... (8 entities in total)
• 機能のキーワード: protein-dna complex, transferase-dna complex, transferase/dna
• 由来する生物種: Bacillus stearothermophilus
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 147444.49

構造登録者

Warren, J.J.,Wu, E.Y.,Golosov, A.A.,Karplus, M.,Beese, L.S. (登録日: 2008-10-22, 公開日: 2009-11-10, 最終更新日: 2023-09-06)

主引用文献

Golosov, A.A.,Warren, J.J.,Beese, L.S.,Karplus, M.
The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis.
Structure, 18:83-93, 2010

PubMed Abstract: High-fidelity DNA polymerases copy DNA rapidly and accurately by adding correct deoxynucleotide triphosphates to a growing primer strand of DNA. Following nucleotide incorporation, a series of conformational changes translocate the DNA substrate by one base pair step, readying the polymerase for the next round of incorporation. Molecular dynamics simulations indicate that the translocation consists globally of a polymerase fingers-opening transition, followed by the DNA displacement and the insertion of the template base into the preinsertion site. They also show that the pyrophosphate release facilitates the opening transition and that the universally conserved Y714 plays a key role in coupling polymerase opening to DNA translocation. The transition involves several metastable intermediates in one of which the O helix is bent in the vicinity of G711. Completion of the translocation appears to require a gating motion of the O1 helix, perhaps facilitated by the presence of G715. These roles are consistent with the high level of conservation of Y714 and the two glycine residues at these positions. It is likely that a corresponding mechanism is applicable to other polymerases.

PubMed: 20152155
DOI: 10.1016/j.str.2009.10.014

実験手法

X-RAY DIFFRACTION (1.9 Å)