9GXN

C. thermocellum UvrA in complex with unmodified DNA and AMPPNP (ATP-bound conformation 1)

Summary for 9GXN

• Entry DOI: 10.2210/pdb9gxn/pdb
• EMDB information: 51668
• Descriptor: UvrABC system protein A, Unmodified DNA (50-MER) - (random sequence built in model), ZINC ION, ... (4 entities in total)
• Functional Keywords: dna binding protein, dna repair pathway, nucleotide excision repair pathway, ner
• Biological source: Acetivibrio thermocellus; More
• Total number of polymer chains: 4
• Total formula weight: 247268.92

Authors

Nirwal, S.,Czarnocki-Cieciura, M.,Nowotny, M. (deposition date: 2024-09-30, release date: 2025-12-24)

Primary citation

Nirwal, S.,Czarnocki-Cieciura, M.,Zajko, W.,Skowronek, K.,Szczepanowski, R.H.,Nowotny, M.
Structural snapshots of the mechanism of ATP-dependent DNA damage recognition by UvrA.
Nat Commun, 2025

PubMed Abstract: Nucleotide excision repair is a DNA repair pathway which detects and fixes various DNA lesions that distort the structure of DNA. In bacteria, the pathway starts with the UvrA protein which has two adenosine triphosphatase modules and forms dimers. The DNA is handed over from UvrA to UvrB, which is a weak helicase that verifies the presence of damage. Despite intense studies, the role of the ATPase activity of UvrA in damage recognition is unclear. Here, we present a series of cryo-electron microscopy structures of UvrA in complex with three different DNAs and in the presence and absence of nucleotides. We also present a structure of UvrA:UvrB:DNA complex. These structures reveal a major rearrangement of the UvrA dimer upon ATP binding. We propose that these conformational changes are used to mechanically probe the integrity of DNA for damage localization. Collectively, our results present snapshots of UvrA's ATP-dependent DNA damage detection.

PubMed: 41381534
DOI: 10.1038/s41467-025-67075-y

Experimental method

ELECTRON MICROSCOPY (3.14 Å)