8C1U

SFX structure of D.m(6-4)photolyase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

Starting Model: experimental
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Literature

Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography.

Cellini, A.Shankar, M.K.Nimmrich, A.Hunt, L.A.Monrroy, L.Mutisya, J.Furrer, A.Beale, E.V.Carrillo, M.Malla, T.N.Maj, P.Vrhovac, L.Dworkowski, F.Cirelli, C.Johnson, P.J.M.Ozerov, D.Stojkovic, E.A.Hammarstrom, L.Bacellar, C.Standfuss, J.Maj, M.Schmidt, M.Weinert, T.Ihalainen, J.A.Wahlgren, W.Y.Westenhoff, S.

(2024) Nat Chem 16: 624-632

  • DOI: https://doi.org/10.1038/s41557-023-01413-9
  • Primary Citation of Related Structures:  
    8C1U, 8C69, 8C6A, 8C6B, 8C6C, 8C6F, 8C6H

  • PubMed Abstract: 

    Charge-transfer reactions in proteins are important for life, such as in photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report the structural changes that take place while electrons transfer along a chain of four conserved tryptophans in the Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at a key asparagine, at a conserved salt bridge, and by rearrangements of nearby water molecules. We detect charge-induced structural changes close to the second tryptophan from 1 ps to 20 ps, identifying a nearby methionine as an active participant in the redox chain, and from 20 ps around the fourth tryptophan. The photolyase undergoes highly directed and carefully timed adaptations of its structure. This questions the validity of the linear solvent response approximation in Marcus theory and indicates that evolution has optimized fast protein fluctuations for optimal charge transfer.


  • Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cryptochrome-1500Drosophila melanogasterMutation(s): 0 
Gene Names: phr6-4CG2488
UniProt
Find proteins for Q8SXK5 (Drosophila melanogaster)
Explore Q8SXK5 
Go to UniProtKB:  Q8SXK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8SXK5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.9α = 90
b = 103.9β = 90
c = 52.19γ = 90
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references