4HTU

Structure of 5-chlorouracil modified A:U base pair

4HTU の概要

• エントリーDOI: 10.2210/pdb4htu/pdb
• 関連するPDBエントリー: 4HUE 4HUF 4HUG
• 分子名称: Ribonuclease H, DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UCL)P*CP*GP*CP*G)-3'), MAGNESIUM ION, ... (6 entities in total)
• 機能のキーワード: 5-chloro-2'-deoxyuridine, w-c base pair, wobble base pair, double helix, base pairing pattern, hydrolase-dna complex, hydrolase/dna
• 由来する生物種: Bacillus halodurans
• 細胞内の位置: Cytoplasm (Potential): Q9KEI9
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 45980.95

構造登録者

Patra, A.,Egli, M. (登録日: 2012-11-01, 公開日: 2012-12-19, 最終更新日: 2023-09-20)

主引用文献

Patra, A.,Harp, J.,Pallan, P.S.,Zhao, L.,Abramov, M.,Herdewijn, P.,Egli, M.
Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs.
Nucleic Acids Res., 41:2689-2697, 2013

PubMed Abstract: The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli strain relies on the four building blocks 5-chloro-2'-deoxyuridine (ClU), A, C and G instead of the standard T, A, C, G alphabet [Marlière,P., Patrouix,J., Döring,V., Herdewijn,P., Tricot,S., Cruveiller,S., Bouzon,M. and Mutzel,R. (2011) Chemical evolution of a bacterium's genome. Angew. Chem. Int. Ed., 50, 7109-7114]. The residual fraction of T in the DNA of adapted bacteria was <2% and the switch from T to ClU was accompanied by a massive number of mutations, including >1500 A to G or G to A transitions in a culture. The former is most likely due to wobble base pairing between ClU and G, which may be more common for ClU than T. To identify potential changes in the geometries of base pairs and duplexes as a result of replacement of T by ClU, we determined four crystal structures of a B-form DNA dodecamer duplex containing ClU:A or ClU:G base pairs. The structures reveal nearly identical geometries of these pairs compared with T:A or T:G, respectively, and no consequences for stability and cleavage by an endonuclease (EcoRI). The lack of significant changes in the geometry of ClU:A and ClU:G base pairs relative to the corresponding native pairs is consistent with the sustained unlimited self-reproduction of E. coli strains with virtually complete T→ClU genome substitution.

PubMed: 23275540
DOI: 10.1093/nar/gks1316

実験手法

X-RAY DIFFRACTION (1.489 Å)