Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states.

Seiji N Sugiman-Marangos,Rodolfo Ghirlando,Yoni M Weiss,John K Peel,Murray S Junop

doi:10.1093/nar/gkt759

Abstract

The ability of Deinococcus radiodurans to recover from extensive DNA damage is due in part to its ability to efficiently repair its genome, even following severe fragmentation by hundreds of double-strand breaks. The single-strand annealing pathway plays an important role early during the recovery process, making use of a protein, DdrB, shown to greatly stimulate ssDNA annealing. Here, we report the structure of DdrB bound to ssDNA to 2.3 Å. Pentameric DdrB was found to assemble into higher-order structures that coat ssDNA. To gain further mechanistic insight into the protein's function, a number of point mutants were generated altering both DNA binding and higher order oligomerization. This work not only identifies higher-order DdrB associations but also suggests the presence of an extended DNA binding surface running along the ‘top’ surface of a DdrB pentamer and continuing down between two individual subunits of the ring structure. Together this work sheds new insight into possible mechanisms for DdrB function in which higher-order assemblies of DdrB pentamers assist in the pairing of complementary ssDNA using an extended DNA binding surface.

Highlights

Deinococcus radiodurans is renowned for its ability to recover from exposure to extreme ionizing radiation (IR), desiccation, ultraviolet radiation and a variety of DNA damage-inducing agents
This has recently been corroborated by mass spectrometry-based proteomic analysis of D. radiodurans post-IR, which showed that DdrB is the second most abundant DNA repair protein during recovery [8]
DdrB1–144 was expressed and purified as described previously with the following amendments: (i) protein used in crystallography had the 6His tag removed by cleavage with TEV protease and was exchanged into 20 mM Tris pH 6.0, 100 mM KCl; (ii) protein used in DNA binding and analytical ultracentrifugation (AUC) experiments was not treated with TEV to remove the N-terminal 6His tag

Summary

Introduction

Deinococcus radiodurans is renowned for its ability to recover from exposure to extreme ionizing radiation (IR), desiccation, ultraviolet radiation and a variety of DNA damage-inducing agents. The b60–b70 hairpin is involved in direct interactions with ssDNA in the DNA-bound structure, as well as playing a key role in mediating the oligomeric assembly observed within the crystal lattice.

Results

Conclusion