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Model Studies on the Photoreduction of the 5-Hydroxy-5,6-dihydrothymine and 5-Methyl-2-pyrimidone Moieties of (6-4) Photoproducts by Photolyase.

ABSTRACT: Photorepair mechanism of (6-4) photoproducts (6-4PP) by photolyase has been the subject of active debate over the years. The initial rationalization based on electron transfer to an oxetane or azetidine intermediate formed upon binding to the enzyme has been questioned, and there is now a more general consensus that the lesion is directly reduced from the excited flavin cofactor. However, the accepting moiety, i.e. the 5-methyl-2-pyrimidone or 5-hydroxy-5,6-dihydrothymine, has not been fully identified yet. In this work, spectroscopic experiments have been run to determine which of the 5'- or 3'-base of 6-4PP is more prone to be reduced. For this aim, the two building blocks of 6-4PP were synthesized and used as electron acceptors. Instead of the short-lived photolyase cofactor, which does not provide a time window compatible with diffusion-controlled intermolecular processes, carbazole, 2-methoxynaphthalene and phenanthrene have been selected as electron donors due to their appropriate singlet lifetimes and reduction potentials. Steady-state and time-resolved fluorescence revealed that, in solution, the pyrimidone chromophore is the most easily reduced moiety. This was confirmed by transient absorption experiments consisting of quenching of the solvated electron by the two moieties of 6-4PP.

SUBMITTER: Rodriguez-Muniz GM

PROVIDER: S-EPMC9304215 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Determining complete electron flow in the cofactor photoreduction of oxidized photolyase.

Project description:The flavin cofactor in photoenzyme photolyase and photoreceptor cryptochrome may exist in an oxidized state and should be converted into reduced state(s) for biological functions. Such redox changes can be efficiently achieved by photoinduced electron transfer (ET) through a series of aromatic residues in the enzyme. Here, we report our complete characterization of photoreduction dynamics of photolyase with femtosecond resolution. With various site-directed mutations, we identified all possible electron donors in the enzyme and determined their ET timescales. The excited cofactor behaves as an electron sink to draw electron flow from a series of encircling aromatic molecules in three distinct layers from the active site in the center to the protein surface. The dominant electron flow follows the conserved tryptophan triad in a hopping pathway across the layers with multiple tunneling steps. These ET dynamics occur ultrafast in less than 150 ps and are strongly coupled with local protein and solvent relaxations. The reverse electron flow from the flavin is slow and in the nanosecond range to ensure high reduction efficiency. With 12 experimentally determined elementary ET steps and 6 ET reaction pairs, the enzyme exhibits a distinct reduction-potential gradient along the same aromatic residues with favorable reorganization energies to drive a highly unidirectional electron flow toward the active-site center from the protein surface.

| S-EPMC3740875 | biostudies-literature

Photoreduction of the folate cofactor in members of the photolyase family.

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| S-EPMC2755890 | biostudies-literature

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| S-EPMC9774824 | biostudies-literature

2-Methyl-5,6-dinitro-benzimidazolium chloride.

Project description:In the title compound, C(8)H(7)N(4)O(4) (+)·Cl(-), the cation possesses twofold symmetry, with the twofold axis bis-ecting the 2-methyl-5,6-dinitro-benzimidazolium cation. The methyl H atoms are disordered about this twofold axis and were assigned equal half-occupancies. The chloride anion also lies on a twofold axis. In the crystal, N-H?Cl and C-H?O hydrogen bonds link the ions to form a three-dimensional network.

| S-EPMC3100037 | biostudies-literature

The class III cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways.

Project description:Photolyases are proteins with an FAD chromophore that repair UV-induced pyrimidine dimers on the DNA in a light-dependent manner. The cyclobutane pyrimidine dimer class III photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. Here we present the crystal structure of a class III photolyase termed photolyase-related protein A (PhrA) of Agrobacterium tumefaciens at 1.67-Å resolution. PhrA contains 5,10-methenyltetrahydrofolate (MTHF) as an antenna chromophore with a unique binding site and mode. Two Trp residues play pivotal roles for stabilizing MTHF by a double π-stacking sandwich. Plant cryptochrome I forms a pocket at the same site that could accommodate MTHF or a similar molecule. The PhrA structure and mutant studies showed that electrons flow during FAD photoreduction proceeds via two Trp triads. The structural studies on PhrA give a clearer picture on the evolutionary transition from photolyase to photoreceptor.

| S-EPMC4416854 | biostudies-literature

2-Methyl-5,6-methyl-enedi-oxy-3-phenyl-sulfonyl-1-benzofuran.

Project description:The title compound, C(16)H(12)O(5)S, was prepared by oxidation of 2-methyl-5,6-methyl-ene-di-oxy-3-phenyl-sulfanyl-1-benzo-furan with 3-chloro-peroxy-benzoic acid. The phenyl ring makes a dihedral angle of 83.64?(4)° with the mean plane of the 5,6-(methyl-ene-di-oxy)-benzo-furan fragment. The crystal structure is stabilized by C-H?? inter-actions between a benzene H atom of the 5,6-(methyl-ene-di-oxy)-benzo-furan unit and the phenyl ring of the phenyl-sulfonyl substituent. Additionally, the crystal structure exhibits inter- and intra-molecular C-H?O inter-actions.

| S-EPMC2961259 | biostudies-literature

5,6-Dichloro-2-(2-hydroxy-phen-yl)-iso-indoline-1,3-dione.

Project description:In the mol-ecule of the title compound, C(14)H(7)Cl(2)NO(3), the phthalimide ring system is virtually planar, with a dihedral angle between the fused five- and six-membered rings of 4.02?(3)°. In the crystal structure, inter-molecular C-H?O and O-H?O hydrogen bonds and C-Cl?O close contacts [Cl?O = 3.0123?(13)?Å and C-Cl?O = 171.14?(7)°] link the mol-ecules, generating R(2) (2)(16), R(4) (2)(19) and R(4) (4)(22) ring motifs by C(6) chains to form a three-dimensional network. A weak ?-? inter-action between the six-membered rings of the phthalimide ring systems further stabilizes the structure, with a centroid-centroid distance of 3.666?(3)?Å and an interplanar separation of 3.568?Å.

| S-EPMC2961102 | biostudies-literature

2-(4-Fluoro-phen-yl)-5,6-methyl-enedi-oxy-3-methyl-sulfinyl-1-benzofuran.

Project description:In the title compound, C(16)H(11)FO(4)S, the O atom and the methyl group of the methyl-sulfinyl substituent are located on opposite sides of the mean plane through the 5,6-(methyl-enedi-oxy)benzofuran fragment. The 4-fluoro-phenyl ring is rotated out of the 5,6-(methyl-enedi-oxy)benzofuran plane, making a dihedral angle of 29.90?(6)°. In the crystal structure, both inter-molecular C-H?O hydrogen bonds link the mol-ecules into centrosymmetric dimers. The combination of C-H?O hydrogen bonds result in chains running along [1].

| S-EPMC2983733 | biostudies-literature

Crystal structures of 5,5'-bis(-hydroxy-methyl)-3,3'-biisoxazole and 4,4',5,5'-tetrakis-(hydroxy-methyl)-3,3'-biisoxazole.

Project description:The mol-ecular structure of 5,5'-bis(-hydroxy-methyl)-3,3'-biisoxazole, C8H8N2O4 (1), is composed of two trans planar isoxazole rings [r.m.s deviation = 0.006 (1) Å], each connected with a methyl hydroxyl group. Similarly, the structure of 4,4',5,5'-tetrakis-(hydroxy-methyl)-3,3'-biisoxazole, C10H12N2O6 (2), is composed of two planar isoxazole rings [r.m.s. deviation = 0.002 (1) Å], but with four hydroxymethyl groups as substituents. Both mol-ecules sit on a center of inversion, thus Z' = 0.5. The crystal structures are stabilized by networks of O-H⋯N [for (1)] and O-H⋯O hydrogen-bonding inter-actions [for (2)], giving rise to corrugated supra-molecular planes. The isoxazole rings are packed in a slip-stacked fashion, with centroid-to-centroid distances of 4.0652 (1) Å for (1) (along the b-axis direction) and of 4.5379 (Å) for (2) (along the a-axis direction).

| S-EPMC5956336 | biostudies-literature

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