4HQB

Crystal structure of DdrB from Deinococcus radiodurans bound to ssDNA

Summary for 4HQB

• Entry DOI: 10.2210/pdb4hqb/pdb
• Descriptor: Single-stranded DNA-binding protein DdrB, 5'-D(*TP*TP*TP*T)-3', 5'-D(P*TP*TP*TP*TP*T)-3', ... (4 entities in total)
• Functional Keywords: dna annealing, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Deinococcus radiodurans
• Total number of polymer chains: 7
• Total formula weight: 87247.99

Authors

Sugiman-Marangos, S.N.,Junop, M.S. (deposition date: 2012-10-25, release date: 2013-09-04, Last modification date: 2023-09-20)

Primary citation

Sugiman-Marangos, S.N.,Peel, J.K.,Weiss, Y.M.,Ghirlando, R.,Junop, M.S.
Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states.
Nucleic Acids Res., 41:9934-9944, 2013

PubMed 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.

PubMed: 23975200
DOI: 10.1093/nar/gkt759

Experimental method

X-RAY DIFFRACTION (2.301 Å)