9XUB | pdb_00009xub

Crystal Structure of Thioredoxin reductase from Mycobacterium tuberculosis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.232 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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Literature

Structural and Mechanistic Characterization of Mycobacterium tuberculosis TrxR Inhibition by Glutathione-Coated Gold Nanocluster.

Li, Z.Niu, W.Xia, D.Chen, Y.Chen, S.Zhang, B.Wang, J.Zhu, H.Yang, H.Xie, F.Zhou, Y.Gong, Y.Xu, Y.Cao, P.

(2026) Int J Mol Sci 27

  • DOI: https://doi.org/10.3390/ijms27031209
  • Primary Citation of Related Structures:  
    9XUB

  • PubMed Abstract: 

    Mycobacterium tuberculosis ( M. tuberculosis ) relies on the thioredoxin (Trx)-thioredoxin reductase (TrxR) system to maintain intracellular redox homeostasis and to support Trx-dependent DNA synthesis and repair, making TrxR a potential target for anti-tuberculosis therapy. Gold nanoclusters have been reported to inhibit human TrxR and suppress tumor growth, suggesting that gold-based nanomaterials can modulate TrxR activity. In this study, we report a previously uncharacterized oxidized crystal structure of M. tuberculosis TrxR containing two dimers in the asymmetric unit and use this structure to investigate inhibition by a glutathione-coated gold nanocluster (GSH-AuNC). Biolayer interferometry and enzymatic assays show that GSH-AuNC binds directly to M. tuberculosis TrxR and efficiently inhibits its catalytic activity at the purified enzyme level. Molecular dynamics simulations indicate that GSH-AuNC can occupy a surface pocket proximal to the active site, providing a plausible structural basis for enzyme engagement. AlphaFold3 modeling of the M. tuberculosis TrxR-Trx heterodimeric complex defines the interaction interface required for productive electron transfer and provides a structural hypothesis for how GSH-AuNC disrupts this process. Together, these results provide structural and mechanistic insights into the biochemical modulation of M. tuberculosis TrxR by GSH-AuNC, while the antimycobacterial activity of GSH-AuNC remains to be evaluated in future studies.


  • Organizational Affiliation
    • Beijing Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Innovation and Translation, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin reductase
A, B, C, D
309Mycobacterium tuberculosis CDC1551Mutation(s): 0 
Gene Names: trxBtrxB2MT4032
EC: 1.8.1.9
UniProt
Find proteins for P9WHH0 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore P9WHH0 
Go to UniProtKB:  P9WHH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHH0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.232 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.354α = 90
b = 107.6β = 90
c = 220.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaKZ202210005001

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-04
    Type: Initial release
  • Version 1.1: 2026-02-25
    Changes: Database references