5ZCW

Structure of the Methanosarcina mazei class II CPD-photolyase in complex with intact, phosphodiester linked, CPD-lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA.

Maestre-Reyna, M.Yamamoto, J.Huang, W.C.Tsai, M.D.Essen, L.O.Bessho, Y.

(2018) IUCrJ 5: 608-618

  • DOI: 10.1107/S205225251800996X
  • Primary Citation of Related Structures:  
    5ZCW

  • PubMed Abstract: 
  • Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, ...

    Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, called base-flipping, induces a kink in the DNA, as well as an unpaired bubble, which are stabilized by a network of protein-nucleic acid interactions. Previously, several co-crystal structures have been reported in which the binding mode of CPD photolyases has been studied in detail. However, in all cases the internucleoside linkage of the photodamage site was a chemically synthesized formacetal analogue and not the natural phosphodiester. Here, the first crystal structure and conformational analysis via molecular-dynamics simulations of a class II CPD photolyase in complex with photodamaged DNA that contains a natural cyclobutane pyrimidine dimer with an intra-lesion phosphodiester linkage are presented. It is concluded that a highly conserved bubble-intruding region (BIR) mediates stabilization of the open form of CPD DNA when complexed with class II CPD photolyases.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyribodipyrimidine photolyaseAB482Methanosarcina mazeiMutation(s): 1 
EC: 4.1.99.3
Find proteins for Q8PYK9 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PYK9 
Go to UniProtKB:  Q8PYK9
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3'C, E14synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3'D, F14synthetic construct
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      FAD
      Query on FAD

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      A, B
      FLAVIN-ADENINE DINUCLEOTIDE
      C27 H33 N9 O15 P2
      VWWQXMAJTJZDQX-UYBVJOGSSA-N
       Ligand Interaction
      SO4
      Query on SO4

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      A
      SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      ACT
      Query on ACT

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      A
      ACETATE ION
      C2 H3 O2
      QTBSBXVTEAMEQO-UHFFFAOYSA-M
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.70 Å
      • R-Value Free: 0.257 
      • R-Value Work: 0.214 
      • R-Value Observed: 0.216 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 71.1α = 90
      b = 114.42β = 90
      c = 166.42γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      XDSdata reduction
      XSCALEdata scaling
      PHASERphasing

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2018-08-22
        Type: Initial release
      • Version 1.1: 2018-10-03
        Changes: Data collection, Database references