SNAP annotations: PDB entry 8gme

PDB-id

8gme; DSSR-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein-DNA

Method

X-ray (4.98 Å)

Summary

Crystal structure of the gp32-dda-dt17 complex

Reference

He X, Yun MK, Li Z, Waddell MB, Nourse A, Churion KA, Kreuzer KN, Byrd AK, White SW (2024): "Structural and functional insights into the interaction between the bacteriophage T4 DNA processing proteins gp32 and Dda." Nucleic Acids Res., 52, 12748-12762. doi: 10.1093/nar/gkae910.

Abstract

Bacteriophage T4 is a classic model system for studying the mechanisms of DNA processing. A key protein in T4 DNA processing is the gp32 single-stranded DNA-binding protein. gp32 has two key functions: it binds cooperatively to single-stranded DNA (ssDNA) to protect it from nucleases and remove regions of secondary structure, and it recruits proteins to initiate DNA processes including replication and repair. Dda is a T4 helicase recruited by gp32, and we purified and crystallized a gp32-Dda-ssDNA complex. The low-resolution structure revealed how the C-terminus of gp32 engages Dda. Analytical ultracentrifugation analyses were consistent with the crystal structure. An optimal Dda binding peptide from the gp32 C-terminus was identified using surface plasmon resonance. The crystal structure of the Dda-peptide complex was consistent with the corresponding interaction in the gp32-Dda-ssDNA structure. A Dda-dependent DNA unwinding assay supported the structural conclusions and confirmed that the bound gp32 sequesters the ssDNA generated by Dda. The structure of the gp32-Dda-ssDNA complex, together with the known structure of the gp32 body, reveals the entire ssDNA binding surface of gp32. gp32-Dda-ssDNA complexes in the crystal are connected by the N-terminal region of one gp32 binding to an adjacent gp32, and this provides key insights into this interaction.