7F8T | pdb_00007f8t

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

• PDB DOI: https://doi.org/10.2210/pdb7F8T/pdb

• Classification: LYASE
• Organism(s): Methanosarcina mazei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-07-02 Released: 2022-03-09 
• Deposition Author(s): 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.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2XRY

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

• PubMed: 35393554 
• DOI: https://doi.org/10.1038/s41557-022-00922-3
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan.
RIKEN SPring-8 Center, Sayo, Hyogo, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, Japan.
Department of Chemistry, Philipps University Marburg, Marburg, Germany.
Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan.
Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan.
Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem,, Jerusalem, Israel.
Dipartamento di Scienze e tecnologie, Universita degli studi del Sannio, Benevento, Italy.
Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France.
European Synchrotron Radiation Facility, Grenoble, France.
Department of Chemistry, Philipps University Marburg, Marburg, Germany. [e-mail].
Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan. [e-mail].
RIKEN SPring-8 Center, Sayo, Hyogo, Japan. [e-mail].
Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan. [e-mail].
Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 56.96 kDa 
• Atom Count: 4,270 
• Modeled Residue Count: 458 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribodipyrimidine photolyase	A	482	Methanosarcina mazei	Mutation(s): 1  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	M [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.77	α = 90
b = 69.77	β = 90
c = 243.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-09 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	AS-KPQ-105-TPP
Japan Society for the Promotion of Science (JSPS)	Japan	16K01942

Revision History  

• 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