7VJB

class II photolyase MmCPDII semiquinone to fully reduced TR-SFX studies (30 ns time-point)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme.

Maestre-Reyna, M.Yang, C.H.Nango, E.Huang, W.C.Ngurah Putu, E.P.G.Wu, W.J.Wang, P.H.Franz-Badur, S.Saft, M.Emmerich, H.J.Wu, H.Y.Lee, C.C.Huang, K.F.Chang, Y.K.Liao, J.H.Weng, J.H.Gad, W.Chang, C.W.Pang, A.H.Sugahara, M.Owada, S.Hosokawa, Y.Joti, Y.Yamashita, A.Tanaka, R.Tanaka, T.Luo, F.Tono, K.Hsu, K.C.Kiontke, S.Schapiro, I.Spadaccini, R.Royant, A.Yamamoto, J.Iwata, S.Essen, L.O.Bessho, Y.Tsai, M.D.

(2022) Nat Chem 14: 677-685

  • DOI: https://doi.org/10.1038/s41557-022-00922-3
  • Primary Citation of Related Structures:  
    7F8T, 7VIW, 7VIX, 7VIY, 7VIZ, 7VJ0, 7VJ1, 7VJ2, 7VJ3, 7VJ4, 7VJ5, 7VJ6, 7VJ7, 7VJ8, 7VJ9, 7VJA, 7VJB, 7VJC, 7VJE, 7VJG, 7VJH, 7VJI, 7VJJ, 7VJK

  • PubMed Abstract: 

    Flavin coenzymes are universally found in biological redox reactions. DNA photolyases, with their flavin chromophore (FAD), utilize blue light for DNA repair and photoreduction. The latter process involves two single-electron transfers to FAD with an intermittent protonation step to prime the enzyme active for DNA repair. Here we use time-resolved serial femtosecond X-ray crystallography to describe how light-driven electron transfers trigger subsequent nanosecond-to-microsecond entanglement between FAD and its Asn/Arg-Asp redox sensor triad. We found that this key feature within the photolyase-cryptochrome family regulates FAD re-hybridization and protonation. After first electron transfer, the FAD •- isoalloxazine ring twists strongly when the arginine closes in to stabilize the negative charge. Subsequent breakage of the arginine-aspartate salt bridge allows proton transfer from arginine to FAD •- . Our molecular videos demonstrate how the protein environment of redox cofactors organizes multiple electron/proton transfer events in an ordered fashion, which could be applicable to other redox systems such as photosynthesis.


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA photolyase482Methanosarcina mazei Go1Mutation(s): 1 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.52α = 90
b = 70.52β = 90
c = 246.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)TaiwanAS-KPQ-105-TPP
Japan Society for the Promotion of Science (JSPS)Japan16K01942

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references
  • Version 1.2: 2022-06-22
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description