5A39

Structure of Rad14 in complex with cisplatin containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesion by Rad14 (Xpa).

Koch, S.C.Kuper, J.Gasteiger, K.L.Simon, N.Strasser, R.Eisen, D.Geiger, S.Schneider, S.Kisker, C.Carell, T.

(2015) Proc Natl Acad Sci U S A 112: 8272

  • DOI: 10.1073/pnas.1508509112
  • Primary Citation of Related Structures:  
    5A3D, 5A39

  • PubMed Abstract: 
  • Nucleotide excision repair (NER) is responsible for the removal of a large variety of structurally diverse DNA lesions. Mutations of the involved proteins cause the xeroderma pigmentosum (XP) cancer predisposition syndrome. Although the general mechanism of the NER process is well studied, the function of the XPA protein, which is of central importance for successful NER, has remained enigmatic ...

    Nucleotide excision repair (NER) is responsible for the removal of a large variety of structurally diverse DNA lesions. Mutations of the involved proteins cause the xeroderma pigmentosum (XP) cancer predisposition syndrome. Although the general mechanism of the NER process is well studied, the function of the XPA protein, which is of central importance for successful NER, has remained enigmatic. It is known, that XPA binds kinked DNA structures and that it interacts also with DNA duplexes containing certain lesions, but the mechanism of interactions is unknown. Here we present two crystal structures of the DNA binding domain (DBD) of the yeast XPA homolog Rad14 bound to DNA with either a cisplatin lesion (1,2-GG) or an acetylaminofluorene adduct (AAF-dG). In the structures, we see that two Rad14 molecules bind to the duplex, which induces DNA melting of the duplex remote from the lesion. Each monomer interrogates the duplex with a β-hairpin, which creates a 13mer duplex recognition motif additionally characterized by a sharp 70° DNA kink at the position of the lesion. Although the 1,2-GG lesion stabilizes the kink due to the covalent fixation of the crosslinked dG bases at a 90° angle, the AAF-dG fully intercalates into the duplex to stabilize the kinked structure.


    Organizational Affiliation

    Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians Universität München, 81377 Munich, Germany; thomas.carell@cup.uni-muenchen.de caroline.kisker@virchow.uni-wuerzburg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA REPAIR PROTEIN RAD14A, B115Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P28519 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28519 
Go to UniProtKB:  P28519
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNAC, D15Saccharomyces cerevisiae
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*DTP*GP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP)-3'E, F13Saccharomyces cerevisiae
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      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        5'-D(*DGP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP*GP)-3'G, H13Saccharomyces cerevisiae
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        • Reference Sequence
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.80 Å
        • R-Value Free: 0.256 
        • R-Value Work: 0.213 
        • R-Value Observed: 0.215 
        • Space Group: P 41
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 54.421α = 90
        b = 54.421β = 90
        c = 130.773γ = 90
        Software Package:
        Software NamePurpose
        REFMACrefinement
        XDSdata reduction
        XSCALEdata scaling
        PHASERphasing

        Structure Validation

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        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2015-06-24
          Type: Initial release
        • Version 1.1: 2015-07-01
          Changes: Database references
        • Version 1.2: 2015-07-22
          Changes: Database references