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Structure paper

TitleStructural Basis of Bifunctional CTP/dCTP Synthase.
Journal, issue, pagesJ Mol Biol, Vol. 436, Issue 20, Page 168750, Year 2024
Publish dateOct 15, 2024
AuthorsChen-Jun Guo / Zherong Zhang / Jia-Li Lu / Jiale Zhong / Yu-Fen Wu / Shu-Ying Guo / Ji-Long Liu /
PubMed AbstractThe final step in the de novo synthesis of cytidine 5'-triphosphate (CTP) is catalyzed by CTP synthase (CTPS), which can form cytoophidia in all three domains of life. Recently, we have discovered ...The final step in the de novo synthesis of cytidine 5'-triphosphate (CTP) is catalyzed by CTP synthase (CTPS), which can form cytoophidia in all three domains of life. Recently, we have discovered that CTPS binds to ribonucleotides (NTPs) to form filaments, and have successfully resolved the structures of Drosophila melanogaster CTPS bound with NTPs. Previous biochemical studies have shown that CTPS can bind to deoxyribonucleotides (dNTPs) to produce 2'-deoxycytidine-5'-triphosphate (dCTP). However, the structural basis of CTPS binding to dNTPs is still unclear. In this study, we find that Drosophila CTPS can also form filaments with dNTPs. Using cryo-electron microscopy, we are able to resolve the structure of Drosophila melanogaster CTPS bound to dNTPs with a resolution of up to 2.7 Å. By combining these structural findings with biochemical analysis, we compare the binding and reaction characteristics of NTPs and dNTPs with CTPS. Our results indicate that the same enzyme can act bifunctionally as CTP/dCTP synthase in vitro, and provide a structural basis for these activities.
External linksJ Mol Biol / PubMed:39173734
MethodsEM (single particle)
Resolution2.73 - 2.79 Å
Structure data

61008

9iz1

EMDB-61008, PDB-9iz1:
dmCTPS tetramer with dATP dUTP dGTP and DON
Method: EM (single particle) / Resolution: 2.73 Å

61009

9iz2

EMDB-61009, PDB-9iz2:
Focus refinement dmCTPS bound with dATP dUTP dGTP and DON
Method: EM (single particle) / Resolution: 2.79 Å

Chemicals

ChemComp-DON:
6-DIAZENYL-5-OXO-L-NORLEUCINE

ChemComp-MG:
Unknown entry

ChemComp-DAT:
2'-DEOXYADENOSINE-5'-DIPHOSPHATE

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

ChemComp-5ZL:
[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

Source
  • drosophila melanogaster (fruit fly)
KeywordsLIGASE / filament / CTPS / inhibitor / substrates / intermediate

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