Photolyase: Dynamics and electron-transfer mechanisms of DNA repair
Open accessAbstract
Photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) and pyrimidine-pyrimidone (6-4) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair. Here, we review our comprehensive characterization of the dynamics of flavin cofactor and its repair photocycles by different classes of photolyases on the most fundamental level. Using femtosecond spectroscopy and molecular biology, significant advances have recently been made to map out the entire dynamical evolution and determine actual timescales of all the catalytic processes in photolyases. The repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. The unified, bifurcated ET mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. For 6-4 photoproduct repair, a similar cyclic ET mechanism operates and a new cyclic proton transfer with a conserved histidine residue at the active site of (6-4) photolyases is revealed.
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CPDs and 6-4PPs are the two main types of photolesions repaired by photolyases.
“CPDs and 6-4PPs are the two main types of photolesions repaired by photolyases.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
In the absence of blue light, photolyases bind to CPDs and 6-4PPs.
“In the absence of blue light photolyases bind to CPDs, and 6-4PPs.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
Subsequent back electron transfer regenerates FADH, ensuring the proper FAD form for the next reaction.
“Subsequent back electron transfer regenerates the FADH, ensuring the proper FAD form for the next reaction.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
Absorption of light by the class-specific chromophore leads to its excitation.
“The absorption of light by the class specific chromophore (either 5,10-methyl tetrahydrofolate (MTHF) or 8-hydroxy-5-deazaflavin (8-HDF)) leads to its excitation.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
In many organisms, photolyases are the key enzymes that remove photo-damage.
“However, in many organisms, photolyases are the key enzymes that remove photo-damage.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
Placental mammals, including humans, lack photolyase activity, and repair of UV-induced damage is probably replaced by NER.
“Placental mammals (including humans) lack photolyase activity, and the repair of UV-induced damage is probably replaced by the activity of NER.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
Energy obtained through excitation of the chromophore is transferred to FADH, and photoexcited FADH provides energy for dimer-splitting.
“The energy obtained through excitation of chormophore is then transferred to important cofactor—reduced flavin adenine dinucleotide (FADH). Consequently, photoexcitated FADH provides energy for the dimer-splitting.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
A thymine pair is flipped back into the DNA duplex, and the hydrogen bond between thymine and adenine is formed.
“A thymine pair is consequently flipped back into the DNA duplex and the hydrogen bond between thymine and adenine is formed.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
Two classes of CPD photolyases with different electron transfer pathways and different mechanistic properties exist.
“Two classes of CPD photolyases with different pathway of electron transfer, and different mechanistic properties exist.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
Repair of 6-4PPs is different than CPDs and requires (6-4PP) photolyase and involves oxetane intermediate formation.
“The repair of 6-4PPs is different than CPDs and requires (6-4PPs) photolyase and involves oxetane intermediate formation.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
Covalent links between adjacent pyrimidines in dimers are broken, and proper DNA structure is restored.
“Again, the covalent links between adjacent pyrimidines in the dimers are broken, and the proper structure of DNA molecule is restored [77,78,79,80,81].”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
Conflicting results exist on oxetane formation during repair.
“However, conflicting results exist on the oxetane formation during repair.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [79]
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- Authors
- Zhang, M., Wang, L., & Zhong, D.
- Affiliations
- The Ohio State University (US)
- Corresponding author
- Zhong, Dongping
- Venue
- Archives of Biochemistry and Biophysics
- Publisher
- Elsevier BV
- Published
- 2017-10
- Volume
- 632
- Pages
- 158-174
- ISSN
- 0003-9861 (ISSN-L)
- PMC
- PMC5650541
- OpenAlex
- W2742166934
- Cited by
- 115
- References
- 116
- Citations by year
- 2026: 11 · 2025: 11 · 2024: 19 · 2023: 16 · 2022: 21 · 2021: 13 · 2020: 11 · 2019: 8 · 2018: 4 · 2017: 1
- FWCI
- 0.54
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Archives of Biochemistry and Biophysics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (GM118332)
- Topics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Photochemistry and Electron Transfer Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- photolyase, DNA repair, UV-induced DNA damage, cyclobutane pyrimidine dimers, 6-4 photoproducts, flavin adenine dinucleotide, electron transfer mechanism, photocycle, cryptochrome, proton transfer, femtosecond spectroscopy
- MeSH terms
- DNA Damage, Deoxyribodipyrimidine Photo-Lyase, DNA Repair, Electron Transport, Flavin-Adenine Dinucleotide, Flavoproteins, Pyrimidine Dimers, Ultraviolet Rays, Protein Folding, Catalytic Domain
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