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Structural basis for ligand binding modes of CTP synthase.

Xian Zhou1, Chen-Jun Guo1,2,3, Chia-Chun Chang1

  • 1School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.

Proceedings of the National Academy of Sciences of the United States of America
|July 24, 2021
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Summary

Cytidine triphosphate synthase (CTPS) activity regulation was elucidated using cryo-EM. GTP stabilizes the ammonia tunnel, while noncanonical CTP binding reveals feedback inhibition in CTP biosynthesis.

Keywords:
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Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • Cytidine triphosphate synthase (CTPS) is crucial for de novo CTP biosynthesis, involving ammonia ligase and glutamine amidotransferase domains.
  • CTPS activity is allosterically regulated by nucleotides (GTP, ATP, UTP) and glutamine, but precise binding modes and conformational changes remain unclear.

Purpose of the Study:

  • To determine the near-atomic resolution structures of Drosophila CTPS bound to all substrates and regulatory nucleotides.
  • To elucidate the molecular mechanisms underlying GTP-mediated allosteric activation and substrate binding in CTPS.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) was employed to resolve the structure of Drosophila CTPS.
  • The structures were determined in the presence of four nucleotides (GTP, ATP, UTP) and a glutamine analog (6-diazo-5-oxo-L-norleucine).

Main Results:

  • Near-atomic resolution structures revealed specific binding modes of GTP, ATP, and UTP, along with a glutamine analog.
  • GTP binding was shown to stabilize the ammonia tunnel, coordinating reactions across both CTPS domains and preventing ammonia leakage.
  • An ATP-dependent UTP phosphorylation intermediate was observed, and a noncanonical CTP binding mode at the ATP site indicated feedback inhibition.

Conclusions:

  • The study provides unprecedented structural insights into CTPS with all substrates bound, clarifying allosteric regulation mechanisms.
  • Findings reveal how GTP allosterically activates CTPS and how CTP binding can inhibit the enzyme, completing the understanding of CTP synthesis regulation.