8OYC

Time-resolved SFX structure of the class II photolyase complexed with a thymine dimer (100 microsecond timpeoint)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.371 
  • R-Value Work: 0.304 
  • R-Value Observed: 0.307 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Time-resolved crystallography captures light-driven DNA repair.

Christou, N.E.Apostolopoulou, V.Melo, D.V.M.Ruppert, M.Fadini, A.Henkel, A.Sprenger, J.Oberthuer, D.Gunther, S.Pateras, A.Rahmani Mashhour, A.Yefanov, O.M.Galchenkova, M.Reinke, P.Y.A.Kremling, V.Scheer, T.E.S.Lange, E.R.Middendorf, P.Schubert, R.De Zitter, E.Lumbao-Conradson, K.Herrmann, J.Rahighi, S.Kunavar, A.Beale, E.V.Beale, J.H.Cirelli, C.Johnson, P.J.M.Dworkowski, F.Ozerov, D.Bertrand, Q.Wranik, M.Bacellar, C.Bajt, S.Wakatsuki, S.Sellberg, J.A.Huse, N.Turk, D.Chapman, H.N.Lane, T.J.

(2023) Science 382: 1015-1020

  • DOI: https://doi.org/10.1126/science.adj4270
  • Primary Citation of Related Structures:  
    8OET, 8OY3, 8OY4, 8OY5, 8OY6, 8OY7, 8OY8, 8OY9, 8OYA, 8OYB, 8OYC

  • PubMed Abstract: 

    Photolyase is an enzyme that uses light to catalyze DNA repair. To capture the reaction intermediates involved in the enzyme's catalytic cycle, we conducted a time-resolved crystallography experiment. We found that photolyase traps the excited state of the active cofactor, flavin adenine dinucleotide (FAD), in a highly bent geometry. This excited state performs electron transfer to damaged DNA, inducing repair. We show that the repair reaction, which involves the lysis of two covalent bonds, occurs through a single-bond intermediate. The transformation of the substrate into product crowds the active site and disrupts hydrogen bonds with the enzyme, resulting in stepwise product release, with the 3' thymine ejected first, followed by the 5' base.


  • Organizational Affiliation

    Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyribodipyrimidine photo-lyase
A, B
498Methanosarcina mazei Go1Mutation(s): 0 
Gene Names: MM_0852
EC: 4.1.99.3
UniProt
Find proteins for Q8PYK9 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PYK9 
Go to UniProtKB:  Q8PYK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PYK9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
CPD-COMPRISING OLIGONUCLEOTIDE
C, E
14synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
COUNTERSTRAND-OLIGONUCLEOTIDE
D, F
14synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.2α = 90
b = 117.76β = 90
c = 170.47γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Database references