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Structural analysis of ASCH domain-containing proteins and their implications for nucleotide processing
Chunyan Meng1, Xiaoyan Shi2, Wenting Guo3
1China-New Zealand Joint Laboratory on Biomedicine and Health, Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China.
Structure (London, England : 1993)
|September 12, 2025
Summary
The E. coli enzyme YqfB, containing an ASCH domain, metabolizes N4-acetylcytidine (ac4C) nucleosides. Structural and in vivo studies reveal its specific function in ac4C metabolism and substrate preferences in related proteins.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- ASC-1 homology (ASCH) domain proteins are implicated in RNA metabolism, yet their structures and functions remain poorly understood.
- The E. coli enzyme YqfB, possessing an ASCH domain, exhibits amidohydrolase activity, converting N4-acetylcytidine (ac4C) RNA nucleosides to cytidine.
Purpose of the Study:
- To elucidate the structural basis of EcYqfB's amidohydrolase activity and its interaction with N4-acetylcytidine.
- To investigate the in vivo function of EcYqfB in ac4C metabolism.
- To explore the structural and functional diversity within the ASCH domain protein family through homologous proteins.
Main Methods:
- X-ray crystallography was employed to determine the structures of EcYqfB in unbound and substrate-bound states.
- In vivo experiments involving gene deletion were conducted to assess the physiological role of EcYqfB.
- Structural determination of homologous proteins, mouse EOLA1 and human TRIP4-ASCH domain, was performed.
Main Results:
- Crystal structures revealed the detailed interaction between EcYqfB and its substrate, providing insights into the catalytic mechanism.
- In vivo studies demonstrated that EcYqfB deletion does not affect global ac4C levels, indicating a specific role in nucleoside metabolism rather than RNA modification.
- Structural analysis of EOLA1 and TRIP4-ASCH domain highlighted variations in substrate preferences among ASCH domain proteins.
Conclusions:
- EcYqfB specifically functions in the metabolism of ac4C nucleosides, not in the direct modification of RNA.
- The study provides crucial structural insights into the ASCH domain family, paving the way for future functional characterization.
- Comparative structural analysis reveals potential differences in substrate specificity within the ASCH domain protein family.
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