7F8T

Re-refinement of the 2XRY X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei

Summary for 7F8T

• Entry DOI: 10.2210/pdb7f8t/pdb
• Descriptor: Deoxyribodipyrimidine photolyase, SULFATE ION, GLYCEROL, ... (5 entities in total)
• Functional Keywords: oxidoreductase, redox state, photoreduction, dna binding protein, lyase
• Biological source: Methanosarcina mazei (Methanosarcina frisia)
• Total number of polymer chains: 1
• Total formula weight: 56957.79

Authors

Maestre-Reyna, M.,Yang, C.-H.,Huang, W.C.,Nango, E.,Gusti-Ngurah-Putu, E.-P.,Franz-Badur, S.,Wu, W.-J.,Wu, H.-Y.,Wang, P.-H.,Liao, J.-H.,Lee, C.-C.,Huang, K.-F.,Chang, Y.-K.,Weng, J.-H.,Sugahara, M.,Owada, S.,Joti, Y.,Tanaka, R.,Tono, K.,Kiontke, S.,Yamamoto, J.,Iwata, S.,Essen, L.-O.,Bessho, Y.,Tsai, M.-D. (deposition date: 2021-07-02, release date: 2022-03-09, Last modification date: 2023-11-29)

Primary citation

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.
Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme.
Nat.Chem., 14:677-685, 2022

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.

PubMed: 35393554
DOI: 10.1038/s41557-022-00922-3

Experimental method

X-RAY DIFFRACTION (1.5 Å)