5KUB

Bacillus cereus DNA glycosylase AlkD bound to 7-methylguanine nucleobase and DNA containing an oxocarbenium-intermediate analog

5KUB の概要

• エントリーDOI: 10.2210/pdb5kub/pdb
• 分子名称: DNA-7-methylguanine glycosylase, DNA (5'-D(*CP*CP*CP*GP*AP*(NRI)P*AP*GP*TP*CP*CP*G)-3'), DNA (5'-D(*CP*GP*GP*AP*CP*TP*CP*TP*CP*GP*GP*G)-3'), ... (5 entities in total)
• 機能のキーワード: dna glycosylase, protein-dna complex, heat-like repeat, hydrolase-dna complex, hydrolase/dna
• 由来する生物種: Bacillus cereus; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 35920.87

構造登録者

Mullins, E.A.,Eichman, B.F. (登録日: 2016-07-13, 公開日: 2016-09-14, 最終更新日: 2023-10-04)

主引用文献

Parsons, Z.D.,Bland, J.M.,Mullins, E.A.,Eichman, B.F.
A Catalytic Role for C-H/ pi Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD.
J.Am.Chem.Soc., 138:11485-11488, 2016

PubMed Abstract: DNA glycosylases protect genomic integrity by locating and excising aberrant nucleobases. Substrate recognition and excision usually take place in an extrahelical conformation, which is often stabilized by π-stacking interactions between the lesion nucleobase and aromatic side chains in the glycosylase active site. Bacillus cereus AlkD is the only DNA glycosylase known to catalyze base excision without extruding the damaged nucleotide from the DNA helix. Instead of contacting the nucleobase itself, the AlkD active site interacts with the lesion deoxyribose through a series of C-H/π interactions. These interactions are ubiquitous in protein structures, but evidence for their catalytic significance in enzymology is lacking. Here, we show that the C-H/π interactions between AlkD and the lesion deoxyribose participate in catalysis of glycosidic bond cleavage. This is the first demonstration of a catalytic role for C-H/π interactions as intermolecular forces important to DNA repair.

PubMed: 27571247
DOI: 10.1021/jacs.6b07399

実験手法

X-RAY DIFFRACTION (1.73 Å)