What Is Adenine Doing in Photolyase?

Acocella, Angela; Jones, G.; Zerbetto, Francesco

doi:10.1021/jp101093z

Cited by 38 publications

(52 citation statements)

References 23 publications

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“…2A). 106, 126 Such a hybrid tunneling pathway mediated by the adenine moiety is also observed in 6–4 photoproduct repair by 6–4 photolyase. 27,33 …”

Section: Dynamics and Mechanism Of Cpd Repair By Photolyasementioning

confidence: 85%

Dynamics and mechanisms of DNA repair by photolyase

Liu

Wang

Zhong

2015

Phys. Chem. Chem. Phys.

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Photolyase, a class of flavoproteins, uses blue light to repair two types of ultraviolet-induced DNA damage, cyclobutane pyrimidine dimer (CPD) and pyrimidine-pyrimidone (6–4) photoproduct (6–4PP). In this perspective, we review the recent progress on the repair dynamics and mechanisms of both types of DNA restoration by photolyases. We first report the spectroscopic characterization of flavin in various redox states and the active-site solvation dynamics in photolyases. We then systematically summarize the detailed repair dynamics of damaged DNA by photolyases and a biomimetic system through resolving all elementary steps on the ultrafast timescales, including multiple intermolecular electron- and proton-transfer reactions and bond-breaking and -making processes. We determined the unique electron tunneling pathways, identified the key functional residues and revealed the molecular origin of high repair efficiency, and thus elucidate the molecular mechanisms and repair photocycles at the most fundamental level. We finally conclude that the active sites of photolyases, unlike aqueous solution for the biomimetic system, provide a unique electrostatic environment and local flexibility and thus a dedicated synergy for all elementary dynamics to maximize the repair efficiency. This repair photomachine is the first enzyme that the entire functional evolution is completely mapped out in real time.

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“…2A). 106, 126 Such a hybrid tunneling pathway mediated by the adenine moiety is also observed in 6–4 photoproduct repair by 6–4 photolyase. 27,33 …”

Section: Dynamics and Mechanism Of Cpd Repair By Photolyasementioning

confidence: 85%

Dynamics and mechanisms of DNA repair by photolyase

Liu

Wang

Zhong

2015

Phys. Chem. Chem. Phys.

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“…Intramolecular electron hopping from the isoalloxazine ring to the adenine moiety is unfavorable due to their redox potentials (ΔG ∼ þ0.1 eV) (14) and moreover we did not observe any fast quenching of FADH − Ã fluorescence without substrate (5). It is thought that the repair reaction by photolyase involves electron tunneling (15)(16)(17). However, the cyclic electrontunneling pathways, forward (k FET ) and backward (k BET ) or return (k ER ), are a matter of some debate.…”

Section: Electron-tunneling Pathways and Functional Role Of Adenine Mmentioning

confidence: 88%

“…One view is that the electron tunneling is mediated by the intervening adenine with a total distance of about 8 Å (15). An alternative model suggests that tunneling occurs directly from the o-xylene ring of FADH − to the 3′ side of CPD with a shortest distance of 4.3 Å (16,17). To test the electron-tunneling directionality, we used a series of substrates, UhiU, UhiT, ThiU and ThiT (chemical structures in Fig.…”

Section: Electron-tunneling Pathways and Functional Role Of Adenine Mmentioning

confidence: 99%

Dynamics and mechanism of cyclobutane pyrimidine dimer repair by DNA photolyase

Liu

Tan

Guo

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

147

250

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Photolyase uses blue light to restore the major ultraviolet (UV)-induced DNA damage, the cyclobutane pyrimidine dimer (CPD), to two normal bases by splitting the cyclobutane ring. Our earlier studies showed that the overall repair is completed in 700 ps through a cyclic electron-transfer radical mechanism. However, the two fundamental processes, electron-tunneling pathways and cyclobutane ring splitting, were not resolved. Here, we use ultrafast UV absorption spectroscopy to show that the CPD splits in two sequential steps within 90 ps and the electron tunnels between the cofactor and substrate through a remarkable route with an intervening adenine. Site-directed mutagenesis reveals that the active-site residues are critical to achieving high repair efficiency, a unique electrostatic environment to optimize the redox potentials and local flexibility, and thus balance all catalytic reactions to maximize enzyme activity. These key findings reveal the complete spatio-temporal molecular picture of CPD repair by photolyase and elucidate the underlying molecular mechanism of the enzyme's high repair efficiency.DNA repair photocycle | ultrafast enzyme dynamics | thymine dimer splitting | electron tunneling pathway | active-site mutation U ltraviolet (UV) component of sunlight irradiation causes DNA damage by inducing the formation of cyclobutane pyrimidine dimer (CPD), which is mutagenic and a leading cause of skin cancer (1-3). CPD can be completely restored by a photoenzyme, photolyase, through absorption of visible blue light (4). In our early work (5-7), we have observed a cyclic electron-transfer (ET) reaction in thymine dimer (ThiT) repair by photolyase and determined the time scale of 700 ps for the complete repair photocycle (7). However, the central questions of whether the splitting of the cyclobutane ring is synchronously or asynchronously concerted or stepwise and whether the cyclic ET involves specific tunneling pathways were not resolved. Furthermore, the molecular mechanism underlying the high repair efficiency has not been elucidated. Here, using femtosecond spectroscopy and site-directed mutagenesis, we are able to measure the dynamics of all initial reactants, reaction intermediates, and final products with different substrates and with wild-type and active-site mutant enzymes, and thus reveal the complete spatio-temporal molecular picture of thymine dimer repair by photolyase.Photolyase contains a fully reduced flavin adenine dinucleotide (FADH − ) as the catalytic cofactor and electron donor (4). Based on previous studies (4-10), a sequential repair mechanism of thymine dimer splitting is shown in Fig. 1. Previously, we found that the forward ET from FADH − Ã to ThiT occurs in 250 ps (1∕k FET ) and the total decay of intermediate FADH• in 700 ps (1∕k total ) (5, 7). These dynamics usually follow a stretched-exponential decay behavior, reflecting heterogeneous ET dynamics controlled by the active-site solvation (5, 6, 11). However, in that study, no thymine-related species could be detected in the vi...

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“…One view is that the electron tunnels through the intervening Ade to the 5′ side of CPD with a total distance of about 8 Å [97, 98]. An alternative model suggests that the electron directly travels through space from the o-xylene ring of FADH − to the 3′ side of CPD over a shorter distance of 4.3 Å [99, 100]. Given the different electron affinity of thymine and uracil [79], we designed different dimer substrates that consist of thymine and (deoxy)uracil, U<>T, U<>U, T<>U, and T<>T (chemical structures in Fig.…”

Section: Cpd Repair: Bifurcating Electron-transfer Pathways Determinementioning

confidence: 99%

Photolyase: Dynamics and electron-transfer mechanisms of DNA repair

Zhang

Wang

Zhong

2017

Archives of Biochemistry and Biophysics

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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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What Is Adenine Doing in Photolyase?

Cited by 38 publications

References 23 publications

Dynamics and mechanisms of DNA repair by photolyase

Dynamics and mechanisms of DNA repair by photolyase

Dynamics and mechanism of cyclobutane pyrimidine dimer repair by DNA photolyase

Photolyase: Dynamics and electron-transfer mechanisms of DNA repair

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