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Literature summary for 4.1.99.14 extracted from

  • Kneuttinger, A.C.; Heil, K.; Kashiwazaki, G.; Carell, T.
    The radical SAM enzyme spore photoproduct lyase employs a tyrosyl radical for DNA repair (2013), Chem. Commun. (Camb. ), 49, 722-724.
    View publication on PubMed

Protein Variants

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 [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

Metals/Ions Comment Organism Structure
Fe2+ contains a [4Fe-4S] cluster Geobacillus thermodenitrificans

Natural Substrates/ Products (Substrates)

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

Organism UniProt Comment Textmining
Geobacillus thermodenitrificans
-
-
-

Reaction

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 and Products (Substrate)

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

Synonyms Comment Organism
SPL
-
Geobacillus thermodenitrificans
spore photoproduct lyase
-
Geobacillus thermodenitrificans

Cofactor

Cofactor Comment Organism Structure
S-adenosyl-L-methionine a radical SAM enzyme Geobacillus thermodenitrificans

General Information

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