Proton-Transfer-Steered Mechanism of Photolesion Repair by (6–4)-Photolyases

Abstract

DNA (6−4)-photolyases are enzymes initiating cleavage of mutagenic pyrimidine (6−4) pyrimidone photolesions by a photoinitiated electron transfer from flavin adenine dinucleotide to the lesion. Using state-of-the-art quantum chemical calculations, we present the first energetically feasible molecular repair mechanism. The initial step is electron transfer coupled to proton transfer from the protonated His345 to the N3′ nitrogen of the pyrimidone thymine of the lesion, which proceeds simultaneously with intramolecular OH transfer in a concerted reaction without formation of an oxetane or isolated water molecule intermediate. In contrast to previously suggested mechanisms, this newly identified pathway requires neither a two-photon process nor electronic excitation of the photolesion. Indeed, the recognition that the initial electron transfer is coupled to the proton transfer was critically important for clarification of the mechanism. SECTION: Biophysical Chemistry

Photolyase: Dynamics and electron-transfer mechanisms of DNA repair

“…11E are triggered by the excitation of only one initial photon, which has also been supported by theoretical calculations [104, 107, 108, 113]. Recently, a two-photon repair mechanism of 6-4PP was suggested [111] by experiment [110] and some theoretical work [109].…”

“…Also, a two-photon repair mechanism has been proposed [110, 111]. Various theoretical calculations were carried out and several repair models have been suggested [104, 107–109, 112, 113]. Most of these proposed models invoke one proton transfer from a neighboring histidine residue at the active site (Fig.…”

Excited-State Proton Transfer and Phototautomerism in Nucleobase and Nucleoside Analogs: A Mini-Review

“…The concept of ESPT may be also useful for the interpretation of the modified RNA/DNA fluorescence, [52,103,104] and recently was postulated to explain the mechanism of 4-6 photolyases. [105] Intermolecular ESPT and phototautomerism are common phenomena in this class of compounds, and many other examples are likely to be found in the near future. One simple clue to identification of such systems may be finding of the large Stokes' shifts in their fluorescence in the acidic conditions (see, e.g., refs.…”

Characterization of the Intermediate in and Identification of the Repair Mechanism of (6‐4) Photolesions by Photolyases

“…(Figure ). Experimental and theoretical studies have been performed intensively over the past years, to trace all steps of the repair. While the functional mechanism of CPD photolyases has been identified, the details of the repair mechanism operating in (6‐4) photolyases is still a matter of ongoing debate.…”

“…Here, 6‐4PP is assumed to be converted to an oxetane ring, which requires the attack of the O4′ oxygen at the C4′ carbon involving intermediate I (Figure ). II) The transient water mechanism, in which the nearby His365 residue plays a crucial role, since proton transfer from this protonated His365 to O4′ is postulated to precede the cleavage of H 2 O4′ from the 5′ thymine involving intermediate IIb (Figure ). III) The so‐called proton transfer steered mechanism, in which proton transfer from the protonated His365 to the N3′ nitrogen of the 3′ thymine occurs simultaneously with an oxetane‐like transition state involving intermediates IIIa and IIIb (Figure ).…”