7DOG

Crystal structure of a nuclease and capping domain of SbcD from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the nuclease and capping domain of SbcD from Staphylococcus aureus.

Lee, J.Jo, I.Ahn, J.Hong, S.Jeong, S.Kwon, A.Ha, N.C.

(2021) J Microbiol 59: 584-589

  • DOI: https://doi.org/10.1007/s12275-021-1012-0
  • Primary Citation of Related Structures:  
    7DOG

  • PubMed Abstract: 

    The SbcCD complex is an essential component of the DNA double-strand break (DSB) repair system in bacteria. The bacterial SbcCD complex recognizes and cleaves the DNA ends in DSBs by ATP-dependent endo- and exonuclease activities as an early step of the DNA repair process. SbcD consists of nuclease, capping, and helix-loop-helix domains. Here, we present the crystal structure of a SbcD fragment from Staphylococcus aureus, which contained nuclease and capping domains, at a resolution of 2.9 Å. This structure shows a dimeric assembly similar to that of the corresponding domains of SbcD from Escherichia coli. The S. aureus SbcD fragment exhibited endonuclease activities on supercoiled DNA and exonuclease activity on linear and nicked DNA. This study contributes to the understanding of the molecular basis for how bacteria can resist sterilizing treatment, causing DNA damage.


  • Organizational Affiliation

    Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclease SbcCD subunit D
A, B
323Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: sbcDSAV1345
UniProt
Find proteins for Q99UD1 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore Q99UD1 
Go to UniProtKB:  Q99UD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99UD1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.906α = 90
b = 89.465β = 90
c = 116.575γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description