3NAE

RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin

3NAE の概要

• エントリーDOI: 10.2210/pdb3nae/pdb
• 関連するPDBエントリー: 1IG9 2OZS 3L8B 3LZI 3LZJ
• 分子名称: DNA polymerase, DNA (5'-D(*TP*CP*AP*(G35)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3'), ... (6 entities in total)
• 機能のキーワード: rb69 dna polymerase, fidelity, guanidinohydantoin, transferase-dna complex, transferase/dna
• 由来する生物種: Enterobacteria phage RB69 (Bacteriophage RB69)
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 114713.72

構造登録者

Wang, M.,Beckman, J.,Blaha, G.,Wang, J.,Konigsberg, W.H. (登録日: 2010-06-01, 公開日: 2010-09-15, 最終更新日: 2023-09-06)

主引用文献

Beckman, J.,Wang, M.,Blaha, G.,Wang, J.,Konigsberg, W.H.
Substitution of Ala for Tyr567 in RB69 DNA Polymerase Allows dAMP and dGMP To Be Inserted opposite Guanidinohydantoin .
Biochemistry, 49:8554-8563, 2010

PubMed Abstract: Continuous oxidative damage inflicted on DNA produces 7,8-dihydro-8-oxoguanine (8-oxoG), a commonly occurring lesion that can potentially cause cancer by producing G → T transversions during DNA replication. Mild oxidation of 8-oxoG leads to the formation of hydantoins, specifically guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), which are 100% mutagenic because they encode almost exclusively the insertion of dAMP and dGMP (encoding G → T and G → C transversions, respectively). The wild-type (wt) pol α family DNA polymerase from bacteriophage RB69 (RB69pol) inserts dAMP and dGMP with low efficiency when situated opposite Gh. In contrast, the RB69pol Y567A mutant inserts both of these dNMPs opposite Gh with >100-fold higher efficiency than wt. We now report the crystal structure of the "closed" preinsertion complex for the Y567A mutant with dATP opposite a templating Gh (R-configuration) in a 13/18mer primer-template (P/T) at 2.0 Å resolution. The structure data reveal that the Y to A substitution provides the nascent base pair binding pocket (NBP) with the flexibility to accommodate Gh by allowing G568 to move in the major-to-minor groove direction of the P/T. Thus, Gh is rejected as a templating base by wt RB69pol because G568 is inflexible, preventing Gh from pairing with the incoming dATP or dGTP base.

PubMed: 20795733
DOI: 10.1021/bi100913v

実験手法

X-RAY DIFFRACTION (2.003 Å)