3WDG

Staphylococcus aureus UDG / UGI complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


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Literature

Staphylococcus aureus protein SAUGI acts as a uracil-DNA glycosylase inhibitor.

Wang, H.C.Hsu, K.C.Yang, J.M.Wu, M.L.Ko, T.P.Lin, S.R.Wang, A.H.J.

(2013) Nucleic Acids Res 42: 1354-1364

  • DOI: 10.1093/nar/gkt964
  • Primary Citation of Related Structures:  
    3WDF, 3WDG

  • PubMed Abstract: 
  • DNA mimic proteins are unique factors that control the DNA binding activity of target proteins by directly occupying their DNA binding sites. The extremely divergent amino acid sequences of the DNA mimics make these proteins hard to predict, and although they are likely to be ubiquitous, to date, only a few have been reported and functionally analyzed ...

    DNA mimic proteins are unique factors that control the DNA binding activity of target proteins by directly occupying their DNA binding sites. The extremely divergent amino acid sequences of the DNA mimics make these proteins hard to predict, and although they are likely to be ubiquitous, to date, only a few have been reported and functionally analyzed. Here we used a bioinformatic approach to look for potential DNA mimic proteins among previously reported protein structures. From ∼14 candidates, we selected the Staphylococcus conserved hypothetical protein SSP0047, and used proteomic and structural approaches to show that it is a novel DNA mimic protein. In Staphylococcus aureus, we found that this protein acts as a uracil-DNA glycosylase inhibitor, and therefore named it S. aureus uracil-DNA glycosylase inhibitor (SAUGI). We also determined and analyzed the complex structure of SAUGI and S. aureus uracil-DNA glycosylase (SAUDG). Subsequent BIAcore studies further showed that SAUGI has a high binding affinity to both S. aureus and human UDG. The two uracil-DNA glycosylase inhibitors (UGI and p56) previously known to science were both found in Bacillus phages, and this is the first report of a bacterial DNA mimic that may regulate SAUDG's functional roles in DNA repair and host defense.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30050, Taiwan, Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30050, Taiwan, Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 30050, Taiwan and Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 115, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uracil-DNA glycosylaseA226Staphylococcus aureus subsp. aureus MRSA252Mutation(s): 0 
Gene Names: ungSAR0586
EC: 3.2.2.27
Find proteins for Q6GJ88 (Staphylococcus aureus (strain MRSA252))
Explore Q6GJ88 
Go to UniProtKB:  Q6GJ88
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinB112Staphylococcus aureusMutation(s): 0 
Find proteins for Q936H5 (Staphylococcus aureus)
Explore Q936H5 
Go to UniProtKB:  Q936H5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.602α = 90
b = 86.367β = 90
c = 88.518γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-05
    Type: Initial release