8OY4 | pdb_00008oy4

Time-resolved SFX structure of the class II photolyase complexed with a thymine dimer (300 ps pump-probe delay)

• PDB DOI: https://doi.org/10.2210/pdb8OY4/pdb
• NAKB: 8OY4

• Classification: LYASE
• Organism(s): Methanosarcina mazei Go1, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-03 Released: 2023-11-22 
• Deposition Author(s): Lane, T.J., Christou, N.-E., Melo, D.V.M., Apostolopoulou, V., Pateras, A., Mashhour, A.R., Galchenkova, M., Gunther, S., Reinke, P., Kremling, V., Oberthuer, D., Henkel, A., Sprenger, J., Scheer, T.E.S., Lange, E., Yefanov, O.N., Middendorf, P., Sellberg, J.A., Schubert, R., Fadini, A., Cirelli, C., Beale, E.V., Johnson, P., Dworkowski, F., Ozerov, D., Bertrand, Q., Wranik, M., Zitter, E.D., Turk, D., Bajt, S., Chapman, H., Bacellar, C.
• Funding Organization(s): Helmholtz Association, Swiss National Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.373 (Depositor), 0.372 (DCC) 
• R-Value Work: 
  0.301 (Depositor), 0.301 (DCC) 
• R-Value Observed: 
  0.304 (Depositor) 

Starting Model: experimental

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

• PubMed: 38033070 
• DOI: https://doi.org/10.1126/science.adj4270
• Primary Citation 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.
The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.
European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany.
Institute for Nanostructure and Solid-State Physics, CFEL Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK.
Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France.
Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, CA 94025, USA.
Department of Structural Biology, Stanford University, 318 Campus Drive West, Stanford, CA 94305-5151, USA.
Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Aškerčeva 6, 1000 Ljubljana, Slovenia.
Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, CA 94025, USA.
Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden.
Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.
Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia.
Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 132.88 kDa 
• Atom Count: 8,557 
• Modeled Residue Count: 930 
• Deposited Residue Count: 1,050 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribodipyrimidine photo-lyase	A, B	498	Methanosarcina mazei Go1	Mutation(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 ID: 2
Molecule	Chains	Length	Organism	Image
CPD-COMPRISING OLIGONUCLEOTIDE	C, E	13	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
COUNTERSTRAND-OLIGONUCLEOTIDE	D, F	14	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDA	H [auth A], I [auth B]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C27 H35 N9 O15 P2 YPZRHBJKEMOYQH-UYBVJOGSSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.373 (Depositor), 0.372 (DCC) 
• R-Value Work:  0.301 (Depositor), 0.301 (DCC) 
• R-Value Observed: 0.304 (Depositor) 

Diffraction Data: https://doi.org/10.16907/87a9f7a4-073e-430c-aa7f-6a194897074f

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.2	α = 90
b = 117.76	β = 90
c = 170.47	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Lane, T.J., Christou, N.-E., Melo, D.V.M., Apostolopoulou, V., Pateras, A., Mashhour, A.R., Galchenkova, M., Gunther, S., Reinke, P., Kremling, V., Oberthuer, D., Henkel, A., Sprenger, J., Scheer, T.E.S., Lange, E., Yefanov, O.N., Middendorf, P., Sellberg, J.A., Schubert, R., Fadini, A., Cirelli, C., Beale, E.V., Johnson, P., Dworkowski, F., Ozerov, D., Bertrand, Q., Wranik, M., Zitter, E.D., Turk, D., Bajt, S., Chapman, H., Bacellar, C.

---

Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--
Swiss National Science Foundation	Switzerland	--

Revision History  

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