9KYF | pdb_00009kyf

Crystal structure of E.coli ac4C amidohydrolase YqfB

• PDB DOI: https://doi.org/10.2210/pdb9KYF/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-09 Released: 2025-08-20 
• Deposition Author(s): Guo, W.T., Wu, B.X., Meng, C.Y., Wen, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: in silico

Literature

Structural analysis of ASCH domain-containing proteins and their implications for nucleotide processing.

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.

(2025) Structure 33: 2095-2108.e5

• PubMed: 40939588 
• DOI: https://doi.org/10.1016/j.str.2025.08.015
• Primary Citation Related Structures: 
  9KYF, 9KYG, 9KYH, 9KYI, 9KYJ, 9KYK, 9KYL


• 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 ⁴ -acetylcytidine (ac ⁴ C) 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 ac ⁴ C levels across various RNA types, indicating that EcYqfB specifically functions in ac ⁴ C 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.

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Organizational Affiliation: 
• China-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.
Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, China.
Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China.
School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China.
China-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. Electronic address: [e-mail].
College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: [e-mail].
Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, China. Electronic address: [e-mail].
China-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. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.84 kDa 
• Atom Count: 1,988 
• Modeled Residue Count: 203 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N(4)-acetylcytidine amidohydrolase	A, B	103	Escherichia coli BL21(DE3)	Mutation(s): 0  Gene Names: ECBD_0837 EC: 3.5.1.135
UniProt
Find proteins for P67603 (Escherichia coli (strain K12)) Explore P67603  Go to UniProtKB:  P67603

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.306	α = 90
b = 30.55	β = 93.897
c = 61.949	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Guo, W.T., Wu, B.X., Meng, C.Y., Wen, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release
  
• Version 1.1: 2025-09-24
  Changes: Database references
• Version 1.2: 2025-12-24
  Changes: Database references