title: Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states.
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.
authors: Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada and Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Center Drive, Bethesda, MD 20892, USA.
authors: Seiji N
authors: SN
authors: Sugiman-Marangos
authors: John K
authors: JK
authors: Peel
authors: Yoni M
authors: YM
authors: Weiss
authors: Rodolfo
authors: R
authors: Ghirlando
authors: Murray S
authors: MS
authors: Junop
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D004260:DNA Repair; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D034301:Deinococcus / Q000235:genetics*; D008958:Models, Molecular; D020836:Protein Structure, Quaternary
chemical_list: D001426:Bacterial Proteins; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins
references: Anal Biochem. 2013 Jun 1;437(1):104-8
references: 23458356
references: Mol Cell Proteomics. 2012 Jan;11(1):M111.011734
references: 21989019
references: Biophys J. 2000 Mar;78(3):1606-19
references: 10692345
references: DNA Repair (Amst). 2012 Apr 1;11(4):349-56
references: 22301370
references: DNA Repair (Amst). 2011 Dec 10;10(12):1223-31
references: 21968057
references: J Comput Chem. 2009 Dec;30(16):2785-91
references: 19399780
references: Cell. 2009 Mar 20;136(6):1044-55
references: 19303848
references: Methods Enzymol. 1997;276:307-26
references: 27754618
references: Nucleic Acids Res. 1997 Dec 15;25(24):4940-5
references: 9396800
references: Mol Cell. 2002 Aug;10(2):359-71
references: 12191481
references: Genetics. 2004 Sep;168(1):21-33
references: 15454524
references: J Mol Graph Model. 2011 Apr;29(6):888-93
references: 21310640
references: Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13492-7
references: 12370410
references: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references: 15572765
references: Nature. 2006 Oct 5;443(7111):569-73
references: 17006450
references: J Biol Chem. 2009 Aug 7;284(32):21402-11
references: 19515845
references: Science. 2004 Nov 5;306(5698):1025-8
references: 15459345
references: DNA Repair (Amst). 2010 Jul 1;9(7):805-12
references: 20451472
references: J Mol Biol. 2007 Sep 21;372(3):774-97
references: 17681537
references: Nucleic Acids Res. 2010 Jun;38(10):3432-40
references: 20129942
references: Nucleic Acids Res. 2012 Jul;40(13):6070-81
references: 22492624
references: PLoS One. 2007 Sep 26;2(9):e955
references: 17895995
references: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
references: 20124702
references: Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):4191-6
references: 12651953
references: Methods Cell Biol. 2008;84:143-79
references: 17964931
references: Anal Chem. 2012 Nov 6;84(21):9513-9
references: 23020071
references: Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Dec 1;68(Pt 12):1534-7
references: 23192041
references: PLoS Biol. 2007 Apr;5(4):e92
references: 17373858
references: Biochim Biophys Acta. 2008 Jul-Aug;1784(7-8):1050-8
references: 18424274
references: Nucleic Acids Res. 2013 Jun;41(11):5927-37
references: 23605044
references: Anal Biochem. 2003 Sep 1;320(1):104-24
references: 12895474