期刊
NUCLEIC ACIDS RESEARCH
卷 47, 期 12, 页码 6015-6028出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkz359
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资金
- National Science Foundation (NSF) [MCB-1412692]
- National Institutes of Health [R21-ES028384, R01-ES025987]
- NSF [MCB-060037]
- NCI [P30 CA008748]
- NSF/NIH
Failure in repairing ultraviolet radiation-induced DNA damage can lead to mutations and cancer. Among UV-lesions, the pyrimidine-pyrimidone (6-4) photoproduct (6-4PP) is removed from the genome much faster than the cyclobutane pyrimidine dimer (CPD), owing to the more efficient recognition of 6-4PP by XPC-RAD23B, a key initiator of global-genome nucleotide excision repair(NER). Here, we report a crystal structure of a Rad4-Rad23 (yeast XPC-Rad23B ortholog) bound to 6-4PP-containing DNA and 4-mu s molecular dynamics (MD) simulations examining the initial binding of Rad4 to 6-4PP or CPD. This first structure of Rad4/XPC bound to a physiological substrate with matched DNA sequence shows that Rad4 flips out both 6-4PP-containing nucleotide pairs, forming an open' conformation. The MD trajectories detail how Rad4/XPC initiates opening' 6-4PP: Rad4 initially engages BHD2 to bend/untwist DNA from the minor groove, leading to unstacking and extrusion of the 6-4PP:AA nucleotide pairs towards the major groove. The 5 ' partner adenine first flips out and is captured by a BHD2/3 groove, while the 3 ' adenine extrudes episodically, facilitating ensuing insertion of the BHD3 beta-hairpin to open DNA as in the crystal structure. However, CPD resists such Rad4-induced structural distortions. Untwisting/bending from the minor groove may be a common way to interrogate DNA in NER.
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