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Literature summary for 4.1.99.3 extracted from
- Mechanisms of DNA repair by photolyase and excision nuclease (Nobel lecture) (2016), Angew. Chem. Int. Ed. Engl., 55, 8502-8527 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| recombinant overexpression in Escherichia coli | Escherichia coli |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| crystal structure of Escherichia coli photolyase, overview | Escherichia coli |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | the entire catalytic cycle is complete in 1.2 ns, and the enzyme repairs thymine dimer with a quantum yield of 0.9 | Escherichia coli |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| cyclobutadipyrimidine (in DNA) | Escherichia coli | - |
2 pyrimidine residues (in DNA) | - |
? |  |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Escherichia coli | P00914 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant enzyme from Escherichia coli overproducing cells | Escherichia coli |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) | radical mechanism through a cyclic redox reaction. Photolyase binds DNA containing a CPD because the thymine dimer distorts the backbone of the DNA. Upon binding to damaged DNA, through ionic interactions between the positively charged groove on the photolyase surface and negatively charged DNA phosphodiester backbone the enzyme pulls the thymine dimer out from within the helix and into the core of the enzyme so that the thymine dimer is within Van der Waals contact with FADH-. It makes a very staple complex, and nothing happens until folate absorbs a photon and transfers the excitation energy to the flavin cofactor. The excited-state flavin, FADH- radical, repairs the thymine dimer by a cyclic redox reaction, and then the enzyme dissociates from the DNA to go on in search of other damage sites to carry out the repair reactions again | Escherichia coli |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| cyclobutadipyrimidine (in DNA) | - |
Escherichia coli | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | the entire catalytic cycle is complete in 1.2 ns, and the enzyme repairs thymine dimer with a quantum yield of 0.9 | Escherichia coli | 2 pyrimidine residues (in DNA) | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| photolyase | - |
Escherichia coli |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| FAD | catalytic cofactor, 4 different redox states of flavin, overview | Escherichia coli | |
| methenyltetrahydrofolate | is the solar panel or photoantenna of the enzyme | Escherichia coli | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| additional information | during purification, the flavin undergoes changes in oxidation state and as a consequence the enzyme may exhibit colors ranging from purple to orange. Three-dimensional structure and structural basis for the proposed reaction mechanism, overview | Escherichia coli |
| physiological function | UV irradiation converts two adjacent pyrimidines, including thymines, to a cyclobutane pyrimidine dimer (CPD), and the enzyme photolyase uses blue light energy to break the two abnormal bonds joining the thymines and thus converts the thymine dimer to two normal thymines. Photolyase therefore repairs DNA and eliminates the harmful effects of UV light. The blue light-absorbing component of photolyase are chromophores. Photolyase from Escherichia coli contains two chromophores, which are two-electron reduced flavin adenine dinucleotide (FADH-) and methenyltetrahydrofolate (folate). The folate acts like a solar panel, absorbing light and transferring the excitation energy to FADH-. The flavin is the actual catalyst, and upon excitation by energy transfer from folate (and less efficiently by direct absorption of a photon) it carries out the repair reaction on the CPD by a radical mechanism through a cyclic redox reaction | Escherichia coli |
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