8OY4

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

Summary for 8OY4

• Entry DOI: 10.2210/pdb8oy4/pdb
• Descriptor: Deoxyribodipyrimidine photo-lyase, CPD-COMPRISING OLIGONUCLEOTIDE, COUNTERSTRAND-OLIGONUCLEOTIDE, ... (6 entities in total)
• Functional Keywords: dna binding protein, dna repair enzyme, flavoprotein, photoenzyme, lyase
• Biological source: Methanosarcina mazei Go1; More
• Total number of polymer chains: 6
• Total formula weight: 132875.81

Authors

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. (deposition date: 2023-05-03, release date: 2023-11-22, Last modification date: 2023-12-13)

Primary citation

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.
Time-resolved crystallography captures light-driven DNA repair.
Science, 382:1015-1020, 2023

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.

PubMed: 38033070
DOI: 10.1126/science.adj4270

Experimental method

X-RAY DIFFRACTION (2.35 Å)