4DQI

Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and dCTP (paired with dG of template)

4DQI の概要

• エントリーDOI: 10.2210/pdb4dqi/pdb
• 関連するPDBエントリー: 4DQP 4DQQ 4DQR 4DQS 4DS4 4DS5 4DSE 4DSF
• 分子名称: DNA polymerase I, DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3'), DNA (5'-D(*C*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3'), ... (7 entities in total)
• 機能のキーワード: dna polymerase i, protein-dna complex, cytosine-guanine, closed form, transferase-dna complex, transferase/dna
• 由来する生物種: Geobacillus kaustophilus; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 149975.58

構造登録者

Wang, W.,Beese, L.S. (登録日: 2012-02-15, 公開日: 2012-06-06, 最終更新日: 2023-09-13)

主引用文献

Wang, W.,Wu, E.Y.,Hellinga, H.W.,Beese, L.S.
Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.
J.Biol.Chem., 287:28215-28226, 2012

PubMed Abstract: In addition to discriminating against base pair mismatches, DNA polymerases exhibit a high degree of selectivity for deoxyribonucleotides over ribo- or dideoxynucleotides. It has been proposed that a single active site residue (steric gate) blocks productive binding of nucleotides containing 2'-hydroxyls. Although this steric gate plays a role in sugar moiety discrimination, its interactions do not account fully for the observed behavior of mutants. Here we present 10 high resolution crystal structures and enzyme kinetic analyses of Bacillus DNA polymerase I large fragment variants complexed with deoxy-, ribo-, and dideoxynucleotides and a DNA substrate. Taken together, these data present a more nuanced and general mechanism for nucleotide discrimination in which ensembles of intermediate conformations in the active site trap non-cognate substrates. It is known that the active site O-helix transitions from an open state in the absence of nucleotide substrates to a ternary complex closed state in which the reactive groups are aligned for catalysis. Substrate misalignment in the closed state plays a fundamental part in preventing non-cognate nucleotide misincorpation. The structures presented here show that additional O-helix conformations intermediate between the open and closed state extremes create an ensemble of binding sites that trap and misalign non-cognate nucleotides. Water-mediated interactions, absent in the fully closed state, play an important role in formation of these binding sites and can be remodeled to accommodate different non-cognate substrates. This mechanism may extend also to base pair discrimination.

PubMed: 22648417
DOI: 10.1074/jbc.M112.366609

実験手法

X-RAY DIFFRACTION (1.69 Å)