Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes

@article{Hitomi2009FunctionalMI,
  title={Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes},
  author={K. Hitomi and Luciano DiTacchio and A. Arvai and J. Yamamoto and Sang-Tae Kim and T. Todo and J. Tainer and S. Iwai and S. Panda and E. Getzoff},
  journal={Proceedings of the National Academy of Sciences},
  year={2009},
  volume={106},
  pages={6962 - 6967}
}
Homologous flavoproteins from the photolyase (PHR)/cryptochrome (CRY) family use the FAD cofactor in PHRs to catalyze DNA repair and in CRYs to tune the circadian clock and control development. To help address how PHR/CRY members achieve these diverse functions, we determined the crystallographic structure of Arabidopsis thaliana (6-4) PHR (UVR3), which is strikingly (>65%) similar in sequence to human circadian clock CRYs. The structure reveals a substrate-binding cavity specific for the UV… Expand
Structural role of two histidines in the (6-4) photolyase reaction
TLDR
It is reported that both H354A and H358A mutants of Xenopus (6-4) PHR still maintain their repair activity, although the efficiency is much lower than that of the wild type. Expand
Structure of Full-length Drosophila Cryptochrome
TLDR
A 2.3-Å resolution crystal structure of Drosophila CRY with an intact C terminus is reported, demonstrating how conserved protein architecture and photochemistry can be elaborated into a range of light-driven functions. Expand
Residues at a Single Site Differentiate Animal Cryptochromes from Cyclobutane Pyrimidine Dimer Photolyases by Affecting the Proteins' Preferences for Reduced FAD
TLDR
It is speculated that the residues at site 377 play a key role in the different preferences of CPF proteins for reduced FAD, which differentiate animal CRYs from CPD photolyases. Expand
Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore
TLDR
A prokaryotic (6-4) photolyase, PhrB from Agrobacterium tumefaciens, is reported and it is proposed that the proKaryotic photolyases are the ancestors of the cryptochrome/photolyase family. Expand
Folding kinetics of recognition loop peptides from a photolyase and cryptochrome-DASH.
TLDR
The results suggest that evolution of protein dynamics, through local sequence tuning in the recognition loop, may be an important mechanism for functional diversification in PL and CRY. Expand
Key Amino Acids in the Bacterial (6-4) Photolyase PhrB from Agrobacterium fabrum
Photolyases can repair pyrimidine dimers on the DNA that are formed during UV irradiation. PhrB from Agrobacterium fabrum represents a new group of prokaryotic (6–4) photolyases which contain anExpand
Key dynamics of conserved asparagine in a cryptochrome/photolyase family protein by fourier transform infrared spectroscopy.
TLDR
This study investigated light-induced conformational changes of a cyanobacterium Cry/Phr-like protein with UV-visible and Fourier transform infrared (FTIR) spectroscopy and characterized an asparagine-to-cysteine mutant of SCry-DASH, which mimics an insect specific Cry. Expand
Light-induced conformational change and product release in DNA repair by (6-4) photolyase.
TLDR
To decipher pivotal reactions of the common FAD cofactor, time-resolved measurements of radical formation, diffusion, and protein conformational changes during light-dependent repair by full-length (6-4) photolyase on DNA carrying a single UV-induced damage are accomplished. Expand
Structural Changes of the Active Center during the Photoactivation of Xenopus (6-4) Photolyase.
TLDR
Light-induced difference Fourier transform infrared (FTIR) spectra corresponding to the photoactivation process of Xenopus (6-4) PHR suggested restructuring of the binding pocket of the DNA lesion in the process of photoactivation. Expand
Key interactions with deazariboflavin cofactor for light-driven energy transfer in Xenopus (6-4) photolyase.
  • Ayaka Morimoto, Y. Hosokawa, +4 authors J. Yamamoto
  • Medicine
  • Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology
  • 2021
TLDR
This study comprehensively characterized the binding of 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF) to Xenopus (6-4) photolyase and obtained new insights into binding of the natural antenna molecule that will be helpful for the development of artificial light-harvesting chromophores and future characterization of the energy transfer in ( 6-4), by spectroscopic studies. Expand
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TLDR
The crystal structure of the photolyase-like domain of CRY-1 from Arabidopsis thaliana is presented, and a single molecule of an ATP analog bound in the aforementioned surface cavity, near the bound FAD cofactor is observed. Expand
Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor.
TLDR
The crystal structure of the St-photolyase protein is determined to confirm its structural features and to investigate the mechanism of the archaeal DNA repair system with light energy, suggesting that FAD works as a novel light-harvesting cofactor of photolyase. Expand
Functional Evolution of the Photolyase/Cryptochrome Protein Family: Importance of the C Terminus of Mammalian CRY1 for Circadian Core Oscillator Performance
TLDR
It is shown that the C-terminal extension of mCRy1 harbors a nuclear localization signal and a putative coiled-coil domain that drive nuclear localization via two independent mechanisms and shift the equilibrium of shuttling mammalian CRY1 (mCRY1)/mammalian PER2 (mPER2) complexes towards the nucleus. Expand
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TLDR
The three-dimensional crystallographic structure of DNA photolyase from Escherichia coli is presented and the atomic model was refined to an R value of 0.172 at 2.3 A resolution, suggesting that the Pyr<> Pyr "flips out" of the helix to fit into this hole, and that electron transfer between the flavin and the Pyr <> Pyr occurs over van der Waals contact distance. Expand
Electron Nuclear Double Resonance Differentiates Complementary Roles for Active Site Histidines in (6-4) Photolyase*
TLDR
Shifts in the hyperfine couplings as a function of structural modifications induced by point mutations and pH changes distinguish the protonation states of two highly conserved histidines, His354 and His358, in Xenopus laevis (6-4) photolyase, which are proposed to catalyze formation of the oxetane intermediate that precedes light-initiated DNA repair. Expand
Active site of Escherichia coli DNA photolyase: Asn378 is crucial both for stabilizing the neutral flavin radical cofactor and for DNA repair.
TLDR
It is concluded that the Asn378 residue of E. coli photolyase is crucial both for stabilizing the neutral flavin radical cofactor and for catalysis. Expand
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TLDR
The whole genome transcriptional profiling together with experimental confirmation of DNA binding indicated that Synechocystis cryptochrome DASH functions as a transcriptional repressor, suggesting that cryptochromes evolved before the divergence of eukaryotes and prokaryotes. Expand
Role of Two Histidines in the (6-4) Photolyase Reaction*
TLDR
A mechanism in which histidines catalyze the formation of the four-membered ring intermediate in the repair process of this enzyme is proposed and the proton transfer shown by this isotope effect supports the proposed mechanism. Expand
Binding and Catalytic Properties of Xenopus (6-4) Photolyase*
TLDR
It is demonstrated that cis,syn-cyclobutane pyrimidine dimer photolyase and (6-4) photoly enzyme are quite similar, but they are different with regard to the binding properties. Expand
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TLDR
The direct comparison of cryptochrome to photolyase in terms of photoreactivity and mechanism has to be made with caution, as little is known about the pathway from light absorption to signal transduction on the molecular level. Expand
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