8ZEF

Crystal structure of Staphylococcus aureus DinG protein in complex with ssDNA and Ca2+

Summary for 8ZEF

• Entry DOI: 10.2210/pdb8zef/pdb
• Descriptor: 3'-5' exonuclease DinG, DNA (5'-D(P*TP*TP*TP*T)-3'), DNA (5'-D(*TP*TP*TP*TP*TP*TP*T)-3'), ... (4 entities in total)
• Functional Keywords: exonuclease, hydrolase/dna, dna repair, hydrolase-dna complex
• Biological source: Staphylococcus aureus (strain NCTC 8325 / PS 47); More
• Total number of polymer chains: 3
• Total formula weight: 107811.86

Authors

Cheng, K.,Gao, T.,Hao, W. (deposition date: 2024-05-06, release date: 2025-05-21, Last modification date: 2026-08-12)

Primary citation

Gao, T.,Hao, W.,Gao, J.,Sun, Y.,Sun, Y.,Yang, J.,Cheng, K.
Structural and functional investigation of DinG containing a 3'-5' exonuclease domain.
Mbio, 16:e0088425-e0088425, 2025

PubMed Abstract: Damage-inducible gene G (DinG), a bacterial homolog of SF2 helicase, has been extensively studied in . However, the structural and functional characteristics of DinG homologs fused with an N-terminal 3'-5' exonuclease domain, such as DinG (SaDinG), remain unexplored. In this study, we demonstrate that SaDinG possesses 3'-5' exonuclease activity and exhibits 5'-3' helicase activity on diverse DNA substrates, including splayed duplexes, 5'-overhangs, double flaps, bubbles, and gapped duplexes, resolving prior ambiguities about its biochemical functions. Intriguingly, both enzymatic activities were inhibited by elevated ATP concentrations, suggesting a potential ATP-dependent regulatory mechanism . We determined the crystal structures of SaDinG bound to ssDNA at ~3.2 Å resolution and identified key residues essential for its helicase and exonuclease activities through mutational analysis. Phenotypic studies revealed that a SaDinG deletion mutant exhibited heightened sensitivity to DNA crosslinking agents (mitomycin C and formaldehyde) but retained wild-type susceptibility to other DNA-damaging compounds. Complementation with either nuclease-dead or helicase-dead variants failed to restore crosslink resistance, indicating that both activities are indispensable for DNA crosslink repair. These results support a model in which SaDinG functions as a coordinated nuclease-helicase machine specifically adapted for DNA crosslink repair, with its dual enzymatic activities being tightly regulated by physiological ATP concentrations.

PubMed: 40586552
DOI: 10.1128/mbio.00884-25

Experimental method

X-RAY DIFFRACTION (3.21 Å)