8KCM | pdb_00008kcm

MmCPDII-DNA complex containing low-dosage, light induced repaired DNA.

• PDB DOI: https://doi.org/10.2210/pdb8KCM/pdb
• NAKB: 8KCM

• Classification: DNA BINDING PROTEIN
• Organism(s): Methanosarcina mazei Go1, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-08-08 Released: 2023-11-22 
• Deposition Author(s): 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.
• 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: 2.50 Å
• R-Value Free: 
  0.259 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Visualizing the DNA repair process by a photolyase at atomic resolution.

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.

(2023) Science 382: eadd7795-eadd7795

• PubMed: 38033054 
• DOI: https://doi.org/10.1126/science.add7795
• Primary Citation Related Structures: 
  7YC7, 7YCM, 7YCP, 7YCR, 7YD6, 7YD7, 7YD8, 7YDZ, 7YE0, 7YEB, 7YEC, 7YEE, 7YEI, 7YEJ, 7YEK, 7YEL, 7YEM, 8KCM


• 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.

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Organizational Affiliation: 
• 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.
RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.
Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany.
Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland.
European Synchrotron Radiation Facility, 38043 Grenoble, France.
Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany.
Department of Physics, The Ohio State University, Columbus, OH 43210, USA.
Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France.
Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
Dipartimento di Scienze e tecnologie, Universita degli studi del Sannio, Benevento, Italy.
Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
Center for Ultrafast Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China.
Institute of Biochemical Sciences, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 129.87 kDa 
• Atom Count: 8,706 
• Modeled Residue Count: 931 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribodipyrimidine photo-lyase	A, B	482	Methanosarcina mazei Go1	Mutation(s): 1  Gene Names:  DU34_19720, DU35_15210, DU36_16165, DU37_08235, DU38_17340, DU39_00605, DU41_17975, DU42_05505, DU44_19145, DU46_16260, DU48_13210, DU49_01325, DU51_15440, DU57_04540, DU59_03190, DU60_01690, DU61_08490, DU62_04430, DU63_10745, DU65_18915, DU69_04700, DU71_05355, DU72_08110, DU74_09110, FQU78_02295 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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Repaired DNA	C, E	14	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
complementary oligonucleotide to the repaired DNA	D, F	14	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.259 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.83	α = 90
b = 115.04	β = 90
c = 167.71	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	AS-KPQ-105-TPP
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	AS-KPQ-109-TPP2
Japan Society for the Promotion of Science (JSPS)	Japan	16K01942

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release
  
• Version 1.1: 2023-12-13
  Changes: Database references
• Version 1.2: 2024-03-13
  Changes: Source and taxonomy