9KYH

Crystal structure of E.coli ac4C amidohydrolase YqfB in complex with ac4C

This is a non-PDB format compatible entry.

Summary for 9KYH

• Entry DOI: 10.2210/pdb9kyh/pdb
• Descriptor: N(4)-acetylcytidine amidohydrolase, 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: n4-acetylcytidine, rna modification, amidohydrolase, cytidine, complex, hydrolase
• Biological source: Escherichia coli BL21(DE3)
• Total number of polymer chains: 2
• Total formula weight: 24357.48

Authors

Guo, W.T.,Meng, C.Y.,Wen, Y.,Wu, B.X. (deposition date: 2024-12-09, release date: 2025-08-20, Last modification date: 2025-09-24)

Primary citation

Meng, C.,Shi, X.,Guo, W.,Jian, X.,Zhao, J.,Wen, Y.,Wang, R.,Li, Y.,Xu, S.,Chen, H.,Zhang, J.,Chen, M.,Chen, H.,Wu, B.
Structural analysis of ASCH domain-containing proteins and their implications for nucleotide processing.
Structure, 2025

PubMed Abstract: ASC-1 homology (ASCH) domain family proteins are believed to play essential roles in RNA metabolism, but detailed structural and functional information is limited. Research has shown that the E. coli enzyme YqfB, which contains an ASCH domain, has amidohydrolase activity, converting N-acetylcytidine (acC) RNA nucleoside into cytidine. Here, we present the crystal structures of EcYqfB both in its unbound state and bound to a substrate. Our analysis reveals how the substrate interacts with the enzyme, offering insights into its catalytic mechanism. In vivo experiments further show that deleting EcYqfB does not change overall acC levels across various RNA types, indicating that EcYqfB specifically functions in acC nucleoside metabolism. We also determined the structures of two homologous proteins: mouse EOLA1 and the human TRIP4-ASCH domain, highlighting differences in their substrate preferences. These findings offer important insights for future research into the structure and function of the ASCH domain protein family.

PubMed: 40939588
DOI: 10.1016/j.str.2025.08.015

Experimental method

X-RAY DIFFRACTION (1.54 Å)