8I9O

ecCTPS filament bound with CTP, NADH, DON

Summary for 8I9O

• Entry DOI: 10.2210/pdb8i9o/pdb
• EMDB information: 35278
• Descriptor: CTP synthase, ADENINE, 5-OXO-L-NORLEUCINE, ... (5 entities in total)
• Functional Keywords: inhibitor, metabolic filament, ctp synthase, hydrolase
• Biological source: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
• Total number of polymer chains: 4
• Total formula weight: 244422.18

Authors

Guo, C.J.,Liu, J.L. (deposition date: 2023-02-07, release date: 2024-02-14, Last modification date: 2024-07-24)

Primary citation

Guo, C.,Wang, Z.,Liu, J.L.
Filamentation and inhibition of prokaryotic CTP synthase with ligands.
Mlife, 3:240-250, 2024

PubMed Abstract: Cytidine triphosphate synthase (CTPS) plays a pivotal role in the de novo synthesis of cytidine triphosphate (CTP), a fundamental building block for RNA and DNA that is essential for life. CTPS is capable of directly binding to all four nucleotide triphosphates: adenine triphosphate, uridine triphosphate, CTP, and guanidine triphosphate. Furthermore, CTPS can form cytoophidia in vivo and metabolic filaments in vitro, undergoing regulation at multiple levels. CTPS is considered a potential therapeutic target for combating invasions or infections by viral or prokaryotic pathogens. Utilizing cryo-electron microscopy, we determined the structure of CTPS (ecCTPS) filament in complex with CTP, nicotinamide adenine dinucleotide (NADH), and the covalent inhibitor 6-diazo-5-oxo- l-norleucine (DON), achieving a resolution of 2.9 Å. We constructed a phylogenetic tree based on differences in filament-forming interfaces and designed a variant to validate our hypothesis, providing an evolutionary perspective on CTPS filament formation. Our computational analysis revealed a solvent-accessible ammonia tunnel upon DON binding. Through comparative structural analysis, we discern a distinct mode of CTP binding of ecCTPS that differs from eukaryotic counterparts. Combining biochemical assays and structural analysis, we determined and validated the synergistic inhibitory effects of CTP with NADH or adenine on CTPS. Our results expand our comprehension of the diverse regulatory aspects of CTPS and lay a foundation for the design of specific inhibitors targeting prokaryotic CTPS.

PubMed: 38948148
DOI: 10.1002/mlf2.12119

Experimental method

ELECTRON MICROSCOPY (2.9 Å)