Protein Variants | Comment | Organism |
---|---|---|
C140A | site-directed mutagenesis, the mutant still shows catalytic turnover, but reduced activity, due to a replacement of the thiyl radical by a thermodynamically comparable glycyl radical16 in the catalytic cycle | Geobacillus thermodenitrificans |
C140G | site-directed mutagenesis, the mutant still shows catalytic turnover, but reduced activity, due to a replacement of the thiyl radical by a thermodynamically comparable glycyl radical16 in the catalytic cycle | Geobacillus thermodenitrificans |
Y98F | the mutant shows in addition a reduced substrate binding affinity, which indicates that the phenolic hydroxyl group is important to organize the substrate in the active site | Geobacillus thermodenitrificans |
KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
0.0009 | - |
5-(alpha-thyminyl)-5,6-dihydrothymidine | wild-type enzyme, pH and temperature not specified in the publication | Geobacillus thermodenitrificans | |
0.0011 | - |
5-(alpha-thyminyl)-5,6-dihydrothymidine | mutant C140A, pH and temperature not specified in the publication | Geobacillus thermodenitrificans | |
0.0113 | - |
5-(alpha-thyminyl)-5,6-dihydrothymidine | mutant Y98F, pH and temperature not specified in the publication | Geobacillus thermodenitrificans |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Fe2+ | contains a [4Fe-4S] cluster | Geobacillus thermodenitrificans |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine | Geobacillus thermodenitrificans | the enzyme establishes a complex radical transfer cascade and creates a cysteine and a tyrosyl radical dyade to establish repair. This allows the enzyme to solve topological and energetic problems associated with the radical based repair reaction | thymidylyl-(3'-5')-thymidylate | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Geobacillus thermodenitrificans | - |
- |
- |
Reaction | Comment | Organism | Reaction ID |
---|---|---|---|
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA) | reaction mechanism, two different routes, overview | Geobacillus thermodenitrificans |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine | the enzyme establishes a complex radical transfer cascade and creates a cysteine and a tyrosyl radical dyade to establish repair. This allows the enzyme to solve topological and energetic problems associated with the radical based repair reaction | Geobacillus thermodenitrificans | thymidylyl-(3'-5')-thymidylate | - |
? | |
5-(alpha-thyminyl)-5,6-dihydrothymidine | the enzyme repairs 5-(alpha-thyminyl)-5,6-dihydrothymidine in DNA | Geobacillus thermodenitrificans | thymidylyl-(3'-5')-thymidylate | - |
? |
Synonyms | Comment | Organism |
---|---|---|
SPL | - |
Geobacillus thermodenitrificans |
spore photoproduct lyase | - |
Geobacillus thermodenitrificans |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
S-adenosyl-L-methionine | a radical SAM enzyme | Geobacillus thermodenitrificans |
General Information | Comment | Organism |
---|---|---|
additional information | residues Cys140 and Tyr98 are important for establishing catalytic turnover. While the allyl radical is situated and reduced at the 3'-side, transfer of the radical center back to the 5'-dAdoH requires moving the radical back to the 50-part in the active side over a distance of roughly 10 A. This creates next to a topological problem also an energetic obstacle, because regeneration of the adenosyl radical by the thiyl radical would be endothermic. The enzyme uses a further tyrosyl radical intermediate to solve the energetic and topological problem | Geobacillus thermodenitrificans |