9Q8F | pdb_00009q8f

Structure of the (6-4) photolyase of Caulobacter crescentus with K48A mutation in its dark adapted and oxidized state determined by synchrotron

• PDB DOI: https://doi.org/10.2210/pdb9Q8F/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Caulobacter vibrioides
• Expression System: Escherichia coli B
• Mutation(s): Yes 


• Deposited: 2025-02-24 Released: 2025-05-07 
• Deposition Author(s): Po Hsun, W., Maestre-Reyna, M., Essen, L.-O.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.165 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Redox-State-Dependent Structural Changes within a Prokaryotic 6-4 Photolyase.

Wang, P.H., Hosokawa, Y., C Soares, J., Emmerich, H.J., Fuchs, V., Caramello, N., Engilberge, S., Bologna, A., Rosner, C.J., Nakamura, M., Watad, M., Luo, F., Owada, S., Tosha, T., Kang, J., Tono, K., Bessho, Y., Nango, E., Pierik, A.J., Royant, A., Tsai, M.D., Yamamoto, J., Maestre-Reyna, M., Essen, L.O.

(2025) J Am Chem Soc 147: 16084-16098

• PubMed: 40298610 
• DOI: https://doi.org/10.1021/jacs.4c18116
• Primary Citation Related Structures: 
  9HNK, 9HNL, 9HNM, 9HNN, 9HNO, 9Q8F


• PubMed Abstract: 
  

  Photolyases repair UV damage to DNA by using absorbed blue light. Within the photolyase/cryptochrome superfamily (PCSf), a major subgroup consists of prokaryotic (6-4) photolyases. These enzymes rely on flavin adenine dinucleotide (FAD) as a catalytic cofactor, besides an ancillary antenna chromophore, and a [4Fe-4S] cluster with yet unknown function. For the prokaryotic 6-4 photolyase of Caulobacter crescentus , we investigated structural changes associated with its different redox states by damage-free crystallography using X-ray free-electron lasers. EPR and optical spectroscopy confirmed redox-dependent structural transitions, including the formation of an oxidized [4Fe-4S] ³⁺ cluster with the dynamic cleavage of a single iron-sulfur bond. Photoreduction to the catalytic FADH ^- state alters the flavin binding site at the proximal aromatic pair Y390/F394 that is part of the electron transport pathway. Upon oxidation, the observable structural transitions of the protein matrix around the [4Fe-4S] cluster may affect DNA binding and are consistent with the much-debated role of the iron-sulfur cluster in DNA-binding proteins for quenching electron holes.

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Organizational Affiliation: 
• Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany.
Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan.
Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan.
Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
Biochemistry, Faculty of Chemistry, University of Kaiserslautern, Kaiserslautern D-67663, Germany.
European Synchrotron Radiation Facility, 38043 Grenoble, France.
Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany.
Univ. Grenoble Alpes, CNRS, CEA Institut de Biologie Structurale, 38044 Grenoble, France.
Department of Science and Technology, University of Sannio, Via Francesco de Sanctis, snc, 82100 Benevento, Italy.
Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan.
Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-43 1 Katahira, Aoba-ku, Sendai 980-8577, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.24 kDa 
• Atom Count: 5,001 
• Modeled Residue Count: 509 
• Deposited Residue Count: 509 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cryptochrome/photolyase family protein	A	509	Caulobacter vibrioides	Mutation(s): 1  Gene Names: CC_0646
UniProt
Find proteins for Q9AAF5 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9AAF5  Go to UniProtKB:  Q9AAF5

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SF4 (Subject of Investigation/LOI)	D [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
DLZ (Subject of Investigation/LOI)	C [auth A]	1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol C13 H18 N4 O6 SXDXRJZUAJBNFL-XKSSXDPKSA-N
SO4 (Subject of Investigation/LOI)	L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)	M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.165 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.984	α = 90
b = 102.102	β = 90
c = 102.944	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Po Hsun, W., Maestre-Reyna, M., Essen, L.-O.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	ES152/18

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Database references