6ug1 | pdb_00006ug1

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

spinqualitylabelsall models 6ug1, resolution 2.83Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6ug1 is a 4 chain structure with sequence from Saccharomyces cerevisiae and Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.833Å Ligands: G47 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RAD4_YEAST Involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. Publication Abstract from PubMed 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 degrees -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. Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex.,Paul D, Mu H, Tavakoli A, Dai Q, Chakraborty S, He C, Ansari A, Broyde S, Min JH DNA Repair (Amst). 2021 Nov;107:103194. doi: 10.1016/j.dnarep.2021.103194. Epub , 2021 Jul 29. PMID:34428697 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also DNA repair protein Rad4 UV excision repair protein 3D structures

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