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EC Number

Catalytic Site Atlas

CSA LITERATURE entry for 1tys

E.C. namethymidylate synthase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1tys
CSA Entries With UniProtID P0A884
CSA Entries With EC Number
PDBe Entry 1tys
PDBSum Entry 1tys
MACiE Entry 1tys

Literature Report

IntroductionThymidylate synthase (TS) from Escherichia coli catalyses the last step of the pathway for the biosynthesis of thymidine 5'-monophosphate (dTMP). dTMP is a nucleotide required for DNA synthesis. It is produced by the transfer of a methylene group from 5,10-methylene-6(R)-tetrahydrofolate to 2'-deoxyuridine 5'monophosphate (dUMP) accompanied by the reduction of the methylene group to a methyl group. TS is a highly conserved enzyme, and because of its essential role in cell division it has been identified as an important target for the development of clinically useful antineoplastic agents.
Mechansim1. Arg 166 activates Cys 146 for nucleophilic attack by interacting with it electrostatically. 2. The S atom of Cys 146 nucleophilically attacks the C6 atom of the dUMP substrate. 3. Protonated Glu 58 donates a proton to the subsequently negatively charged O4 atom of dUMP. 4. The cofactor CH2H4PteGlu is activated by the protonation at N5 by Asp 169, forming an iminium ion at N5. 5. Glu 58 then abstracts the same proton from O4 of dUMP, causing nucleophilic attack of C5 of dUMP on the methylene group of activated CH2H4PteGlu. 6. Tyr 94 abstracts a proton from C5 (either by itself or via water), and the subsequently negatively charged O4 atom of the intermediate is protonated by Glu 58. 7. Glu 58 then abstracts the same proton from O4, causing the beta-elimination of H4-folate. 8. H4-folate then donates a hydride to the 'new' methyl carbon of the substrate, causing the breaking of the C-S-Cys 146 bond, forming the products dTMP and H2PteGlu.

Catalytic Sites for 1tys

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluA5858macie:sideChainTransfers a proton to and from the O4 atom of dUMP in various steps of the mechanism.
ArgA166166macie:sideChainActivates Cys 146 for nucleophilic attack.
AspA169169macie:sideChainActivates the co-substrate CH2H4PteGlu by protonating the N5 atom.
SerA146146macie:sideChainActs as a nucleophile by attacking the C6 atom of dUMP.
TyrA9494macie:sideChainAbstracts a proton from C5 of dUMP either by itself, or via a water molecule.

Literature References

Notes:It is not known whether Tyr 94 abstracts a proton from C5 of dUMP by itself, or via a water molecule.
Finer-Moore JS
Lessons and conclusions from dissecting the mechanism of a bisubstrate enzyme: thymidylate synthase mutagenesis, function, and structure.
Biochemistry 2003 42 248-256
PubMed: 12525151
Saxl RL
Modification of Escherichia coli thymidylate synthase at tyrosine-94 by 5-imidazolylpropynyl-2'-deoxyuridine 5'-monophosphate.
Biochemistry 2003 42 4544-4551
PubMed: 12693951