2OKS

X-ray Structure of a DNA Repair Substrate Containing an Alkyl Interstrand Crosslink at 1.65 Resolution

2OKS の概要

• エントリーDOI: 10.2210/pdb2oks/pdb
• 関連するPDBエントリー: 1EN8
• 分子名称: 5'-D(*CP*CP*AP*AP*(C34)P*GP*TP*TP*GP*G)-3', CALCIUM ION (3 entities in total)
• 機能のキーワード: interstrand crosslink, dna, dna damage
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 3179.26

構造登録者

Swenson, M.C.,Paranawithana, S.R.,Miller, P.S.,Kielkopf, C.L. (登録日: 2007-01-17, 公開日: 2007-02-13, 最終更新日: 2023-08-30)

主引用文献

Swenson, M.C.,Paranawithana, S.R.,Miller, P.S.,Kielkopf, C.L.
Structure of a DNA repair substrate containing an alkyl interstrand cross-link at 1.65 a resolution.
Biochemistry, 46:4545-4553, 2007

PubMed Abstract: Chemotherapeutic alkylating agents, such as bifunctional nitrogen mustards and cisplatins, generate interstrand DNA cross-links that inhibit cell proliferation by arresting DNA transcription and replication. A synthetic N4C-ethyl-N4C interstrand cross-link between opposing cytidines mimics the DNA damage produced by this class of clinically important compounds and can be synthesized in large quantities to study the repair, physical properties, and structures of these DNA adducts. The X-ray structure of a DNA duplex d(CCAAC*GTTGG)2 containing a synthetic N4C-ethyl-N4C interstrand cross-link between the cytosines of the central CpG step (*) has been determined at 1.65 A resolution. This structure reveals that the ethyl cross-link in the CpG major groove does not significantly disrupt the B-form DNA helix. Comparison of the N4C-ethyl-N4C cross-linked structure with the structure of an un-cross-linked oligonucleotide of the same sequence reveals that the cross-link selectively stabilizes a preexisting alternative conformation. The conformation preferred by the cross-linked DNA is constrained by the geometry of the ethyl group bridging the cytosine amines. Characteristics of the cross-linked CpG step include subtle differences in the roll of the base pairs, optimized Watson-Crick hydrogen bonds, and loss of a divalent cation binding site. Given that the N4C-ethyl-N4C cross-link stabilizes a preexisting conformation of the CpG step, this synthetically accessible substrate presents an ideal model system for studying the genomic effects of covalently coupling the DNA strands, independent of gross alterations in DNA structure.

PubMed: 17375936
DOI: 10.1021/bi700109r

実験手法

X-RAY DIFFRACTION (1.65 Å)