1TEZ

COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair

Mees, A.Klar, T.Gnau, P.Hennecke, U.Eker, A.P.M.Carell, T.Essen, L.-O.

(2004) Science 306: 1789-1793

  • DOI: 10.1126/science.1101598
  • Primary Citation of Related Structures:  
    1TEZ

  • PubMed Abstract: 
  • DNA photolyases use light energy to repair DNA that comprises ultraviolet-induced lesions such as the cis-syn cyclobutane pyrimidine dimers (CPDs). Here we report the crystal structure of a DNA photolyase bound to duplex DNA that is bent by 50 degrees an ...

    DNA photolyases use light energy to repair DNA that comprises ultraviolet-induced lesions such as the cis-syn cyclobutane pyrimidine dimers (CPDs). Here we report the crystal structure of a DNA photolyase bound to duplex DNA that is bent by 50 degrees and comprises a synthetic CPD lesion. This CPD lesion is flipped into the active site and split there into two thymines by synchrotron radiation at 100 K. Although photolyases catalyze blue light-driven CPD cleavage only above 200 K, this structure apparently mimics a structural substate during light-driven DNA repair in which back-flipping of the thymines into duplex DNA has not yet taken place.


    Related Citations: 
    • Crystal Structure of DNA Photolyase from Anacystis
      Tamada, T., Kitadokoro, K., Higuchi, Y., Inaka, K., Yasui, A., De Ruiter, P.E., Eker, A.P., Miki, K.
      (1997) Nat Struct Biol 4: 887

    Organizational Affiliation

    Department of Chemistry and Biochemistry, Butenandt-Strasse 5-13, Ludwig Maximilians University, D-81377 Munich, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyribodipyrimidine photolyase ABCD474Synechococcus elongatus PCC 6301Mutation(s): 0 
Gene Names: phrphrAsyc1392_c
EC: 4.1.99.3
Find proteins for P05327 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore P05327 
Go to UniProtKB:  P05327
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3'I, K11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'J, L9N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-D(*TP*CP*GP*C)-3'M, O4N/A
        • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 4
          MoleculeChainsLengthOrganismImage
          5'-D(P*GP*CP*CP*GP*A)-3'N, P5N/A
          Small Molecules
          Ligands 6 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          FAD
          Query on FAD

          Download Ideal Coordinates CCD File 
          A, B, C, D
          FLAVIN-ADENINE DINUCLEOTIDE
          C27 H33 N9 O15 P2
          VWWQXMAJTJZDQX-UYBVJOGSSA-N
           Ligand Interaction
          HDF
          Query on HDF

          Download Ideal Coordinates CCD File 
          A, B, C, D
          8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE
          C16 H17 N3 O7
          AUEILLWDYUBWCM-AGIUHOORSA-N
           Ligand Interaction
          G
          Query on G

          Download Ideal Coordinates CCD File 
          I, K
          GUANOSINE-5'-MONOPHOSPHATE
          C10 H14 N5 O8 P
          RQFCJASXJCIDSX-UUOKFMHZSA-N
           Ligand Interaction
          C
          Query on C

          Download Ideal Coordinates CCD File 
          I, K
          CYTIDINE-5'-MONOPHOSPHATE
          C9 H14 N3 O8 P
          IERHLVCPSMICTF-XVFCMESISA-N
           Ligand Interaction
          TCP
          Query on TCP

          Download Ideal Coordinates CCD File 
          I, K
          5'-METHYLTHYMIDINE
          C11 H16 N2 O5
          KTCKNHCDUKONFQ-DJLDLDEBSA-N
           Ligand Interaction
          MG
          Query on MG

          Download Ideal Coordinates CCD File 
          A, B
          MAGNESIUM ION
          Mg
          JLVVSXFLKOJNIY-UHFFFAOYSA-N
           Ligand Interaction
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 1.80 Å
          • R-Value Free: 0.226 
          • R-Value Work: 0.205 
          • R-Value Observed: 0.205 
          • Space Group: C 1 2 1
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 173.815α = 90
          b = 88.505β = 90.11
          c = 161.622γ = 90
          Software Package:
          Software NamePurpose
          MOSFLMdata reduction
          SCALAdata scaling
          MOLREPphasing
          CNSrefinement
          CCP4data scaling

          Structure Validation

          View Full Validation Report



          Entry History 

          Deposition Data

          Revision History 

          • Version 1.0: 2004-12-14
            Type: Initial release
          • Version 1.1: 2007-10-16
            Changes: Version format compliance
          • Version 1.2: 2011-07-13
            Changes: Source and taxonomy, Version format compliance
          • Version 1.3: 2018-05-30
            Changes: Advisory, Data collection, Derived calculations