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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.199
R-Value Work: 0.170
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan.

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

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribodipyrimidine photolyase	A	482	Methanosarcina mazei	Mutation(s): 1
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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8PYK9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] 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		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A]	K [auth A], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]