28DB | pdb_000028db

Crystal structure of the thioredoxin domain of Amuc_2173 from Akkermansia muciniphila

• PDB DOI: https://doi.org/10.2210/pdb28DB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Akkermansia muciniphila ATCC BAA-835
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-06-22 Released: 2026-07-15 
• Deposition Author(s): Wei, J., Wang, M.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.196 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: in silico

Literature

Functional and structural characterization of Akkermansia muciniphila thioredoxin domain-containing protein Amuc_2173.

Wei, J., Zhang, R., Xiao, Z., Li, Q., Wang, M.

(2026) Biochem Biophys Res Commun 830: 154247-154247

• PubMed: 42413442 
• DOI: https://doi.org/10.1016/j.bbrc.2026.154247
• Primary Citation Related Structures: 
  28DB


• PubMed Abstract: 
  

  Akkermansia muciniphila is a beneficial bacterium that colonizes the human intestinal mucosa. Its colonization and function require the assistance of antioxidant proteins to cope with oxidative stress. In this work, we demonstrated that the A. muciniphila thioredoxin domain-containing protein Amuc_2173 possesses thiol-disulfide oxidoreductase activity and that this activity does not require the involvement of its coiled-coil CTD. Further, we determined the structure of the thioredoxin domain of Amuc_2173, which adopts the thioredoxin fold of the ResA/DsbE subfamily. In addition, our activity assays of cysteine mutations demonstrated that the cysteine residues in the CXXC motif are crucial for the thiol-disulfide oxidoreductase activity of Amuc_2173. Our results provide experimental evidence for the antioxidant potential of Amuc_2173.

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Organizational Affiliation: 
• School of Life Sciences and Medical Engineering, Anhui University, Hefei, Anhui, 230601, China.
School of Life Sciences and Medical Engineering, Anhui University, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, 230601, 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: 36.09 kDa 
• Atom Count: 2,551 
• Modeled Residue Count: 273 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Redoxin domain protein	A, B	161	Akkermansia muciniphila ATCC BAA-835	Mutation(s): 0  Gene Names: Amuc_2173
UniProt
Find proteins for B2UPV2 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc)) Explore B2UPV2  Go to UniProtKB:  B2UPV2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.196 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.662	α = 93.24
b = 44.534	β = 110.14
c = 45.714	γ = 114.86

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-15 
Deposition Author(s): Wei, J., Wang, M.

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Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

• Version 1.0: 2026-07-15
  Type: Initial release
  
• Version 1.1: 2026-07-22
  Changes: Database references