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Literature summary for 4.1.99.13 extracted from
- Repair of (6-4) lesions in DNA by (6-4) photolyase 20 years of quest for the photoreaction mechanism (2017), Photochem. Photobiol., 93, 51-66 .
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| additional information | repair is triggered by non-saturating 100-ps laser flashes | Arabidopsis thaliana | |
| additional information | repair is triggered by non-saturating 100-ps laser flashes | Xenopus laevis | |
| additional information | repair is triggered by non-saturating 100-ps laser flashes | Drosophila melanogaster |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| determination of a crystal structure of Drosophila melanogaster (6-4) PL (Dm64) bound to a 15-mer DNA duplex containing a central T(6-4)T lesion | Drosophila melanogaster |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| H354A | site-directed mutagenesis, the mutant shows reduced repair activity compared to the wild-type enzyme | Xenopus laevis |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| (6-4) photoproduct (in DNA) | Arabidopsis thaliana | - |
2 pyrimidine residues (in DNA) | - |
? |  |
| (6-4) photoproduct (in DNA) | Xenopus laevis | - |
2 pyrimidine residues (in DNA) | - |
? | |
| (6-4) photoproduct (in DNA) | Drosophila melanogaster | - |
2 pyrimidine residues (in DNA) | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Arabidopsis thaliana | O48652 | - |
- |
| Drosophila melanogaster | Q0E8P0 | - |
- |
| Xenopus laevis | Q9I910 | - |
- |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| (6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA) | in the formation of the (6-4) PPs, a Paterno-Buechi reaction first yields an oxetane-bridged (or azetidine-bridged for cytosine at 3') intermediate. This structure is thermodynamically unstable and rearranges to form a (6-4) PP. During this reaction, the O4' (or N4'H) in the 3' component is transferred to the 5'-component and has thus to be returned to 3' during the repair reaction. Reaction mechanism of repair of (6-4) lesions by (6-4) photolyase, detailed overview. The repair-active redox state of the FAD cofactor is fully reduced FADH- and (6-4) PP-containing substrates are bound in a specific manner. No thermal oxetane formation | Drosophila melanogaster | |
| (6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA) | reaction mechanism of repair of (6-4) lesions by (6-4) photolyase, detailed overview. The repair-active redox state of the FAD cofactor is fully reduced FADH- and (6-4) PP-containing substrates are bound in a specific manner | Arabidopsis thaliana | |
| (6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA) | reaction mechanism of repair of (6-4) lesions by (6-4) photolyase, detailed overview. The repair-active redox state of the FAD cofactor is fully reduced FADH- and (6-4) PP-containing substrates are bound in a specific manner. Occurrence of a two-photon mechanism for the repair of a T(6-4)T lesion by the (6-4) PL of Xenopus laevis | Xenopus laevis |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| (6-4) photoproduct (in DNA) | - |
Arabidopsis thaliana | 2 pyrimidine residues (in DNA) | - |
? | |
| (6-4) photoproduct (in DNA) | - |
Xenopus laevis | 2 pyrimidine residues (in DNA) | - |
? | |
| (6-4) photoproduct (in DNA) | - |
Drosophila melanogaster | 2 pyrimidine residues (in DNA) | - |
? | |
| additional information | analysis of the repair of a T(6-4)T lesion by the (6-4) PL of Arabidopsis thaliana (At64) by ultrafast fluorescence and transient absorption spectroscopy between 315 and 800 nm. About 90% of the FADH- radicals formed by this primary electron transfer are re-reduced very quickly | Arabidopsis thaliana | ? | - |
? | |
| additional information | inability of (6-4) PL to repair the Dewar photoproduct T(Dew) T lesion (formed via an electrocyclic reaction of the 3' pyrimidone ring in (6-4) PPs upon photoexcitation in the 325-nm band of the (6-4) PP), which cannot be attributed to poor substrate binding, as a high affinity for T(Dew)T-containing substrates has been demonstrated. Rather, reversion of the T(Dew)T to the T(6-4)T lesion appears to be inhibited, either by an unfavorable electron transfer from photoexcited FADH- to T(Dew)T. QM/MM calculations of the absorption spectra of different potential reaction intermediates | Xenopus laevis | ? | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| (6-4) photolyase | - |
Arabidopsis thaliana |
| (6-4) photolyase | - |
Xenopus laevis |
| (6-4) photolyase | - |
Drosophila melanogaster |
| (6-4) PL | - |
Arabidopsis thaliana |
| (6-4) PL | - |
Xenopus laevis |
| (6-4) PL | - |
Drosophila melanogaster |
| (6-4) PP-specific PL | - |
Arabidopsis thaliana |
| (6-4) PP-specific PL | - |
Xenopus laevis |
| (6-4) PP-specific PL | - |
Drosophila melanogaster |
| At64 | - |
Arabidopsis thaliana |
| Dm64 | - |
Drosophila melanogaster |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| FAD | - |
Arabidopsis thaliana | |
| FAD | - |
Xenopus laevis | |
| FAD | - |
Drosophila melanogaster | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| additional information | residues H354 and H358 are important in catalysis of Xenopus laevis (6-4) PL | Xenopus laevis |
| additional information | residues H365 and H369 are important in catalysis of enzyme (6-4) PL, structure of a complex between the (6-4) PL of Drosophila melanogaster and a double-stranded DNA substrate containing a T(6-4)T lesion, overview | Drosophila melanogaster |
| additional information | two His residues are important in catalysis of enzyme (6-4) PL | Arabidopsis thaliana |
| physiological function | exposure of DNA to ultraviolet (UV) light from the sun or from other sources causes the formation of harmful and carcinogenic crosslinks between adjacent pyrimidine nucleobases, namely cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts. Unique flavoenzymes, called DNA photolyases, utilize blue light, that is photons of lower energy than those of the damaging light, to repair these lesions. The chemically challenging repair of the (6-4) photoproducts by (6-4) photolyase and reaction mechanisms, overview | Arabidopsis thaliana |
| physiological function | exposure of DNA to ultraviolet (UV) light from the sun or from other sources causes the formation of harmful and carcinogenic crosslinks between adjacent pyrimidine nucleobases, namely cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts. Unique flavoenzymes, called DNA photolyases, utilize blue light, that is photons of lower energy than those of the damaging light, to repair these lesions. The chemically challenging repair of the (6-4) photoproducts by (6-4) photolyase and reaction mechanisms, overview | Xenopus laevis |
| physiological function | exposure of DNA to ultraviolet (UV) light from the sun or from other sources causes the formation of harmful and carcinogenic crosslinks between adjacent pyrimidine nucleobases, namely cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts. Unique flavoenzymes, called DNA photolyases, utilize blue light, that is photons of lower energy than those of the damaging light, to repair these lesions. The chemically challenging repair of the (6-4) photoproducts by (6-4) photolyase and reaction mechanisms, overview | Drosophila melanogaster |
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