6M3L

Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex

6M3L の概要

• エントリーDOI: 10.2210/pdb6m3l/pdb
• 関連するPDBエントリー: 6L2N 6L2O
• 分子名称: RE_R_Pab1 domain-containing protein, DNA (5'-D(*CP*GP*CP*AP*TP*CP*GP*AP*TP*TP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*GP*CP*G)-3') (2 entities in total)
• 機能のキーワード: glycosylase, hydrolase-dna complex, hydrolase/dna
• 由来する生物種: Pyrococcus abyssi (strain GE5 / Orsay); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 57713.85

構造登録者

Miyazono, K.,Wang, D.,Ito, T.,Tanokura, M. (登録日: 2020-03-04, 公開日: 2020-03-18, 最終更新日: 2023-11-29)

主引用文献

Miyazono, K.I.,Wang, D.,Ito, T.,Tanokura, M.
Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.
Nucleic Acids Res., 48:5106-5118, 2020

PubMed Abstract: R.PabI is a restriction DNA glycosylase that recognizes the sequence 5'-GTAC-3' and hydrolyses the N-glycosidic bond of adenine in the recognition sequence. R.PabI drastically bends and unwinds the recognition sequence of double-stranded DNA (dsDNA) and flips the adenine and guanine bases in the recognition sequence into the catalytic and recognition sites on the protein surface. In this study, we determined the crystal structure of the R.PabI-dsDNA complex in which the dsDNA is drastically bent by the binding of R.PabI but the base pairs are not unwound. This structure is predicted to be important for the indirect readout of the recognition sequence by R.PabI. In the complex structure, wedge loops of the R.PabI dimer are inserted into the minor groove of dsDNA to stabilize the deformed dsDNA structure. A base stacking is distorted between the two wedge-inserted regions. R.PabI is predicted to utilize the distorted base stacking for the detection of the recognition sequence.

PubMed: 32232412
DOI: 10.1093/nar/gkaa184

実験手法

X-RAY DIFFRACTION (2.75 Å)