4HQB

Crystal structure of DdrB from Deinococcus radiodurans bound to ssDNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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This is version 1.3 of the entry. See complete history. 


Literature

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

Sugiman-Marangos, S.N., Peel, J.K., Weiss, Y.M., Ghirlando, R., Junop, M.S.

(2013) Nucleic Acids Res 41: 9934-9944

  • DOI: https://doi.org/10.1093/nar/gkt759
  • Primary Citation of Related Structures:  
    4HQB

  • 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 ...

    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.

    Organizational Affiliation: 

    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.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Single-stranded DNA-binding protein DdrBA, B, C, D, E148Deinococcus radioduransMutation(s): 0 
Gene Names: ddrB, ddrB (DR0070), DR_0070
UniProt
Find proteins for Q9RY80 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RY80 
Go to UniProtKB:  Q9RY80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RY80
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*TP*TP*TP*T)-3'F [auth M]4N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(P*TP*TP*TP*TP*T)-3'G [auth N]5N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.7α = 90
b = 110.7β = 90
c = 58.776γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2013-12-04
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description