7F8T

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), 0.190 (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 of 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.

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 
• Modelled 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), 0.190 (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