3AJL

Crystal structure of d(CGCGGATf5UCGCG): 5-Formyluridine:guanosine Base-pair in B-DNA with DAPI

Summary for 3AJL

• Entry DOI: 10.2210/pdb3ajl/pdb
• Related: 3AJJ 3AJK
• Descriptor: 5'-D(*CP*GP*CP*GP*GP*AP*TP*(UFR)P*CP*GP*CP*G)-3', 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: double helix, dna
• Total number of polymer chains: 2
• Total formula weight: 7688.38

Authors

Tsunoda, M.,Sakaue, T.,Ueno, Y.,Matsuda, A.,Takenaka, A. (deposition date: 2010-06-07, release date: 2011-04-27, Last modification date: 2023-11-01)

Primary citation

Tsunoda, M.,Sakaue, T.,Naito, S.,Sunami, T.,Abe, N.,Ueno, Y.,Matsuda, A.,Takenaka, A.
Insights into the structures of DNA damaged by hydroxyl radical: crystal structures of DNA duplexes containing 5-formyluracil
J Nucleic Acids, 2010:107289-107289, 2010

PubMed Abstract: Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU), which induces pyrimidine transition during replication. In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG) with R = A/G have been determined by X-ray crystallography. The fU residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble) with G, the latter being a new type of base pair between ionized thymine base and guanine base. In silico structural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.

PubMed: 20976303
DOI: 10.4061/2010/107289

Experimental method

X-RAY DIFFRACTION (2.7 Å)