4B21

Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2.

Dalhus, B.Nilsen, L.Korvald, H.Huffman, J.Forstrom, R.J.Mcmurray, C.T.Alseth, I.Tainer, J.A.Bjoras, M.

(2013) Structure 21: 154

  • DOI: 10.1016/j.str.2012.11.004
  • Primary Citation of Related Structures:  
    4B24, 4B21, 4B22, 4B23

  • PubMed Abstract: 
  • Modifications and loss of bases are frequent types of DNA lesions, often handled by the base excision repair (BER) pathway. BER is initiated by DNA glycosylases, generating abasic (AP) sites that are subsequently cleaved by AP endonucleases, which fu ...

    Modifications and loss of bases are frequent types of DNA lesions, often handled by the base excision repair (BER) pathway. BER is initiated by DNA glycosylases, generating abasic (AP) sites that are subsequently cleaved by AP endonucleases, which further pass on nicked DNA to downstream DNA polymerases and ligases. The coordinated handover of cytotoxic intermediates between different BER enzymes is most likely facilitated by the DNA conformation. Here, we present the atomic structure of Schizosaccharomyces pombe Mag2 in complex with DNA to reveal an unexpected structural basis for nonenzymatic AP site recognition with an unflipped AP site. Two surface-exposed loops intercalate and widen the DNA minor groove to generate a DNA conformation previously only found in the mismatch repair MutS-DNA complex. Consequently, the molecular role of Mag2 appears to be AP site recognition and protection, while possibly facilitating damage signaling by structurally sculpting the DNA substrate.


    Organizational Affiliation

    Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway; Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: magnar.bjoras@rr-research.no.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2A232Schizosaccharomyces pombeMutation(s): 0 
EC: 3.2.2.21
Find proteins for O94468 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O94468 
Go to UniProtKB:  O94468
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3'X11synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP)-3'Y10synthetic construct
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      BGC
      Query on BGC

      Download CCD File 
      A
      beta-D-glucopyranose
      C6 H12 O6
      WQZGKKKJIJFFOK-VFUOTHLCSA-N
       Ligand Interaction
      PO4
      Query on PO4

      Download CCD File 
      A, Y
      PHOSPHATE ION
      O4 P
      NBIIXXVUZAFLBC-UHFFFAOYSA-K
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.45 Å
      • R-Value Free: 0.221 
      • R-Value Work: 0.207 
      • R-Value Observed: 0.207 
      • Space Group: I 2 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 68.926α = 90
      b = 84.746β = 90
      c = 126.713γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      HKL-2000data reduction
      SCALEPACKdata scaling
      SOLVEphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2013-01-09
        Type: Initial release
      • Version 1.1: 2013-01-30
        Changes: Database references
      • Version 1.2: 2020-07-29
        Type: Remediation
        Reason: Carbohydrate remediation
        Changes: Data collection, Derived calculations, Other, Structure summary