9VTV | pdb_00009vtv

Chitinase TfeC from Yersinia pseudotuberculosis

• PDB DOI: https://doi.org/10.2210/pdb9VTV/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia pseudotuberculosis YPIII
• Expression System: Escherichia
• Mutation(s): No 


• Deposited: 2025-07-11 Released: 2025-11-05 
• Deposition Author(s): Zhu, L.F., Zuo, Y.X., Cui, R., Li, D.F., Liu, S.J., Shen, X.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.208 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Interkingdom sensing of fungal tyrosol promotes bacterial antifungal T6SS activity in the murine gut.

Zhu, L., Zuo, Y., Cui, R., Fu, P., Liu, Y., Wang, Z., He, X., Yu, D., Wei, Z., Li, S., Wang, Y., Li, C., Wang, Y., Li, D.F., Liu, S.J., Shen, X.

(2026) Nat Microbiol 11: 240-255

• PubMed: 41350923 
• DOI: https://doi.org/10.1038/s41564-025-02208-z
• Primary Citation Related Structures: 
  9VTV


• PubMed Abstract: 
  

  Type VI secretion systems (T6SSs) are molecular machines used by bacteria to release effectors that target either host cells, competing bacteria or fungi. Regulatory mechanisms underlying antifungal T6SS activity remain unexplored. Here we show, using mouse infection with wild-type and T6SS mutant bacteria, that T6SS activity of the enteropathogen, Yersinia pseudotuberculosis (Yptb), reduces fungal prevalence in the gut microbiota and has direct activity on Candida albicans. Screening of bacterial effector mutant strains, and structural and biochemical analyses identify TfeC as an antifungal chitinase T6SS effector that can kill C. albicans. In vivo experiments confirm that TfeC expression promotes Yptb colonization and reduces C. albicans abundance. We also show that Yptb senses the fungal quorum-sensing molecule, tyrosol, through the two-component system, EnvZ-OmpR, and responds by activating T6SS4. Our findings suggest that Yptb modulates its antifungal activities by detecting changes in fungal population density cues, revealing a mechanism of fungal-bacterial interkingdom communication mediated by fungal quorum-sensing molecules.

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Organizational Affiliation: 
• State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, P. R. China.
College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, P. R. China.
State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
School of Life Sciences, University of Chinese Academy of Sciences, Beijing, P. R. China.
State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China. [e-mail].
School of Life Sciences, University of Chinese Academy of Sciences, Beijing, P. R. China. [e-mail].
State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China. [e-mail].
School of Life Sciences, University of Chinese Academy of Sciences, Beijing, P. R. China. [e-mail].
State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China. [e-mail].
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, P. R. China. [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: 60.14 kDa 
• Atom Count: 3,838 
• Modeled Residue Count: 420 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF3142 domain-containing protein	A, B	262	Yersinia pseudotuberculosis YPIII	Mutation(s): 0  Gene Names: YPK_0957
UniProt
Find proteins for A0A0H3B0R1 (Yersinia pseudotuberculosis serotype O:3 (strain YPIII)) Explore A0A0H3B0R1  Go to UniProtKB:  A0A0H3B0R1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRT	C [auth A], D [auth B]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.208 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.913	α = 90
b = 63.926	β = 90.18
c = 77.947	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Zhu, L.F., Zuo, Y.X., Cui, R., Li, D.F., Liu, S.J., Shen, X.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	92051101

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release
  
• Version 1.1: 2026-05-27
  Changes: Database references