7YCP image
Entry Detail
PDB ID:
7YCP
Title:
TR-SFX MmCPDII-DNA complex: 250 ps snapshot. Includes 250 ps, dark, and extrapolated structure factors
Biological Source:
PDB Version:
Deposition Date:
2022-07-01
Release Date:
2023-11-22
Method Details:
Experimental Method:
Resolution:
2.08 Å
R-Value Free:
0.23
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Deoxyribodipyrimidine photo-lyase
Mutations:M377T
Chain IDs:A, B
Chain Length:482
Number of Molecules:2
Biological Source:Methanosarcina mazei
Polymer Type:polydeoxyribonucleotide
Description:CPD photolesion containing DNA
Chain IDs:C, E
Chain Length:13
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:complementary oligonucleotide to the CPD containing DNA
Chain IDs:D, F
Chain Length:14
Number of Molecules:2
Biological Source:synthetic construct
Primary Citation

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures