4Q0W

he catalytic core of Rad2 in complex with DNA substrate (complex II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding.

Mietus, M.Nowak, E.Jaciuk, M.Kustosz, P.Studnicka, J.Nowotny, M.

(2014) Nucleic Acids Res 42: 10762-10775

  • DOI: 10.1093/nar/gku729
  • Primary Citation of Related Structures:  
    4Q10, 4Q0R, 4Q0W, 4Q0Z

  • PubMed Abstract: 
  • Rad2/XPG belongs to the flap nuclease family and is responsible for a key step of the eukaryotic nucleotide excision DNA repair (NER) pathway. To elucidate the mechanism of DNA binding by Rad2/XPG, we solved crystal structures of the catalytic core of Rad2 in complex with a substrate ...

    Rad2/XPG belongs to the flap nuclease family and is responsible for a key step of the eukaryotic nucleotide excision DNA repair (NER) pathway. To elucidate the mechanism of DNA binding by Rad2/XPG, we solved crystal structures of the catalytic core of Rad2 in complex with a substrate. Rad2 utilizes three structural modules for recognition of the double-stranded portion of DNA substrate, particularly a Rad2-specific α-helix for binding the cleaved strand. The protein does not specifically recognize the single-stranded portion of the nucleic acid. Our data suggest that in contrast to related enzymes (FEN1 and EXO1), the Rad2 active site may be more accessible, which would create an exit route for substrates without a free 5' end.


    Organizational Affiliation

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland mnowotny@iimcb.gov.pl.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein RAD2A, B365Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAD2YGR258C
EC: 3.1
UniProt
Find proteins for P07276 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07276 
Go to UniProtKB:  P07276
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*TP*TP*GP*AP*TP*CP*CP*GP*TP*CP*CP*AP*CP*CP*TP*TP*T)-3')C18N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*TP*AP*GP*GP*TP*GP*GP*AP*CP*GP*GP*AP*TP*CP*AP*TP*T)-3')D18N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      E [auth A], G [auth B]CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      K
      Query on K

      Download Ideal Coordinates CCD File 
      F [auth A], H [auth B]POTASSIUM ION
      K
      NPYPAHLBTDXSSS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.10 Å
      • R-Value Free: 0.230 
      • R-Value Work: 0.183 
      • R-Value Observed: 0.186 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 126.641α = 90
      b = 76.813β = 90
      c = 108.192γ = 90
      Software Package:
      Software NamePurpose
      MAR345data collection
      PHASERphasing
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2014-08-27
        Type: Initial release
      • Version 1.1: 2014-09-17
        Changes: Structure summary
      • Version 1.2: 2014-10-01
        Changes: Database references
      • Version 1.3: 2014-10-29
        Changes: Structure summary
      • Version 1.4: 2017-08-09
        Changes: Refinement description, Source and taxonomy
      • Version 1.5: 2017-11-22
        Changes: Refinement description