7YEK

TR-SFX MmCPDII-DNA complex: 500 ns time-point collected in SACLA. Includes 500 ns, dark, and extrapolated structure factors

Summary for 7YEK

• Entry DOI: 10.2210/pdb7yek/pdb
• Related: 7YC7 7YCM 7YCP 7YCR 7YD6 7YD7 7YD8 7YDZ 7YE0 7YEB 7YEC 7YEE 7YEI 7YEJ
• Descriptor: Deoxyribodipyrimidine photo-lyase, CPD photolesion containing DNA after repair, complementary oligonucleotide to the CPD containing DNA, ... (6 entities in total)
• Functional Keywords: flavoprotein, photolyase, light driven electron transfer, dna repair, time-resolved serial crystallography., dna binding protein
• Biological source: Methanosarcina mazei; More
• Total number of polymer chains: 6
• Total formula weight: 128412.85

Authors

Maestre-Reyna, M.,Wang, P.-H.,Nango, E.,Hosokawa, Y.,Saft, M.,Furrer, A.,Yang, C.-H.,Ngura Putu, E.P.G.,Wu, W.-J.,Emmerich, H.-J.,Engilberge, S.,Caramello, N.,Wranik, M.,Glover, H.L.,Franz-Badur, S.,Wu, H.-Y.,Lee, C.-C.,Huang, W.-C.,Huang, K.-F.,Chang, Y.-K.,Liao, J.-H.,Weng, J.-H.,Gad, W.,Chang, C.-W.,Pang, A.H.,Gashi, D.,Beale, E.,Ozerov, D.,Milne, C.,Cirelli, C.,Bacellar, C.,Sugahara, M.,Owada, S.,Joti, Y.,Yamashita, A.,Tanaka, R.,Tanaka, T.,Luo, F.J.,Tono, K.,Kiontke, S.,Spadaccini, R.,Royant, A.,Yamamoto, J.,Iwata, S.,Standfuss, J.,Essen, L.-O.,Bessho, Y.,Tsai, M.-D. (deposition date: 2022-07-06, release date: 2023-11-22, Last modification date: 2024-03-13)

Primary citation

Maestre-Reyna, M.,Wang, P.H.,Nango, E.,Hosokawa, Y.,Saft, M.,Furrer, A.,Yang, C.H.,Gusti Ngurah Putu, E.P.,Wu, W.J.,Emmerich, H.J.,Caramello, N.,Franz-Badur, S.,Yang, C.,Engilberge, S.,Wranik, M.,Glover, H.L.,Weinert, T.,Wu, H.Y.,Lee, C.C.,Huang, W.C.,Huang, K.F.,Chang, Y.K.,Liao, J.H.,Weng, J.H.,Gad, W.,Chang, C.W.,Pang, A.H.,Yang, K.C.,Lin, W.T.,Chang, Y.C.,Gashi, D.,Beale, E.,Ozerov, D.,Nass, K.,Knopp, G.,Johnson, P.J.M.,Cirelli, C.,Milne, C.,Bacellar, C.,Sugahara, M.,Owada, S.,Joti, Y.,Yamashita, A.,Tanaka, R.,Tanaka, T.,Luo, F.,Tono, K.,Zarzycka, W.,Muller, P.,Alahmad, M.A.,Bezold, F.,Fuchs, V.,Gnau, P.,Kiontke, S.,Korf, L.,Reithofer, V.,Rosner, C.J.,Seiler, E.M.,Watad, M.,Werel, L.,Spadaccini, R.,Yamamoto, J.,Iwata, S.,Zhong, D.,Standfuss, J.,Royant, A.,Bessho, Y.,Essen, L.O.,Tsai, M.D.
Visualizing the DNA repair process by a photolyase at atomic resolution.
Science, 382:eadd7795-eadd7795, 2023

PubMed Abstract: Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.

PubMed: 38033054
DOI: 10.1126/science.add7795

Experimental method

X-RAY DIFFRACTION (2.4 Å)