6UG1

Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex

Summary for 6UG1

• Entry DOI: 10.2210/pdb6ug1/pdb
• Descriptor: DNA repair protein RAD4, UV excision repair protein RAD23, DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3'), ... (4 entities in total)
• Functional Keywords: dna damage recognition, dna repair, beta-hairpin motif, xeroderma pigmentosum, xpc, rad4, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 4
• Total formula weight: 78119.13

Authors

Paul, D.,Min, J.-H. (deposition date: 2019-09-25, release date: 2021-03-31, Last modification date: 2024-11-20)

Primary citation

Paul, D.,Mu, H.,Tavakoli, A.,Dai, Q.,Chakraborty, S.,He, C.,Ansari, A.,Broyde, S.,Min, J.H.
Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex.
DNA Repair (Amst), 107:103194-103194, 2021

PubMed Abstract: Rad4/XPC recognizes diverse DNA lesions to initiate nucleotide excision repair (NER). However, NER propensities among lesions vary widely and repair-resistant lesions are persistent and thus highly mutagenic. Rad4 recognizes repair-proficient lesions by unwinding ('opening') the damaged DNA site. Such 'opening' is also observed on a normal DNA sequence containing consecutive C/G's (CCC/GGG) when tethered to Rad4 to prevent protein diffusion. However, it was unknown if such tethering-facilitated DNA 'opening' could occur on any DNA or if certain structures/sequences would resist being 'opened'. Here, we report that DNA containing alternating C/G's (CGC/GCG) failed to be opened even when tethered; instead, Rad4 bound in a 180°-reversed manner, capping the DNA end. Fluorescence lifetime studies of DNA conformations in solution showed that CCC/GGG exhibits local pre-melting that is absent in CGC/GCG. In MD simulations, CGC/GCG failed to engage Rad4 to promote 'opening' contrary to CCC/GGG. Altogether, our study illustrates how local sequences can impact DNA recognition by Rad4/XPC and how certain DNA sites resist being 'opened' even with Rad4 held at that site indefinitely. The contrast between CCC/GGG and CGC/GCG sequences in Rad4-DNA recognition may help decipher a lesion's mutagenicity in various genomic sequence contexts to explain lesion-determined mutational hot and cold spots.

PubMed: 34428697
DOI: 10.1016/j.dnarep.2021.103194

Experimental method

X-RAY DIFFRACTION (2.833 Å)