1LV5

Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP

1LV5 の概要

• エントリーDOI: 10.2210/pdb1lv5/pdb
• 関連するPDBエントリー: 1L3S 1L3T 1L3U 1L3V 1L5U
• 分子名称: 5'-D(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3', 5'-D(*AP*CP*GP*TP*CP*GP*CP*TP*GP*AP*TP*CP*CP*G)-3', DNA POLYMERASE I, ... (8 entities in total)
• 機能のキーワード: dna polymerase i, dna replication, klenow fragment, protein-dna-dntp complex, closed conformation, transferase-dna complex, transferase/dna
• 由来する生物種: Geobacillus stearothermophilus
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 148219.91

構造登録者

Johnson, S.J.,Taylor, J.S.,Beese, L.S. (登録日: 2002-05-24, 公開日: 2003-03-25, 最終更新日: 2024-02-14)

主引用文献

Johnson, S.J.,Taylor, J.S.,Beese, L.S.
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
Proc.Natl.Acad.Sci.USA, 100:3895-3900, 2003

PubMed Abstract: DNA polymerases replicate DNA by adding nucleotides to a growing primer strand while avoiding frameshift and point mutations. Here we present a series of up to six successive replication events that were obtained by extension of a primed template directly in a crystal of the thermostable Bacillus DNA polymerase I. The 6-bp extension involves a 20-A translocation of the DNA duplex, representing the largest molecular movement observed in a protein crystal. In addition, we obtained the structure of a "closed" conformation of the enzyme with a bound triphosphate juxtaposed to a template and a dideoxy-terminated primer by constructing a point mutant that destroys a crystal lattice contact stabilizing the wild-type polymerase in an "open" conformation. Together, these observations allow many of the steps involved in DNA replication to be observed in the same enzyme at near atomic detail. The successive replication events observed directly by catalysis in the crystal confirm the general reaction sequence deduced from observations obtained by using several other polymerases and further refine critical aspects of the known reaction mechanism, and also allow us to propose new features that concern the regulated transfer of the template strand between a preinsertion site and an insertion site. We propose that such regulated transfer is an important element in the prevention of frameshift mutations in high-fidelity DNA polymerases. The ability to observe processive, high-fidelity replication directly in a crystal establishes this polymerase as a powerful model system for mechanistic studies in which the structural consequences of mismatches and DNA adducts are observed.

PubMed: 12649320
DOI: 10.1073/pnas.0630532100

実験手法

X-RAY DIFFRACTION (1.95 Å)