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 

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This is version 1.3 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: https://doi.org/10.1016/j.str.2012.11.004
  • Primary Citation of Related Structures:  
    4B21, 4B22, 4B23, 4B24

  • 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 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2232Schizosaccharomyces pombeMutation(s): 0 
EC: 3.2.2.21
UniProt
Find proteins for O94468 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O94468 
Go to UniProtKB:  O94468
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94468
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3'B [auth X]11synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP)-3'C [auth Y]10synthetic construct
Sequence Annotations
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  • Reference Sequence
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Structure summary