9ILR | pdb_00009ilr

The structure of the GmvT-GmvA-AcCoA ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.227 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural insights into the Shigella flexneri GmvAT toxin-antitoxin system.

Chen, R.Zhao, H.Zhou, J.Liu, A.Guo, Y.Wu, K.Xiang, Y.Lei, J.Jiang, S.Xie, W.

(2025) FEBS Lett 599: 1246-1259

  • DOI: https://doi.org/10.1002/1873-3468.70015
  • Primary Citation of Related Structures:  
    9ILR, 9ILS

  • PubMed Abstract: 

    Toxin-antitoxin (TA) systems are common bicistronic gene elements in bacteria and are critical for stress responses. The toxin members of the GNAT/RHH TA family can acetylate certain aminoacylated tRNA molecules and inhibit global protein translation. One member named GmvT is important for virulence plasmid maintenance in Shigella flexneri, but the underlying mechanism remains poorly understood. Here, we report the cocrystal structures of GmvT in two forms. The binding of the antitoxin mainly relies on the backbone of the toxin while the cofactor is free of contacts with the antitoxin, supported by follow-up in vitro and in vivo studies. Our study provides insight into the protein-protein/protein-ligand interactions of the GmvAT pair and the structural basis for molecular recognition.


  • Organizational Affiliation
    • MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetyltransferase168Shigella sonneiMutation(s): 1 
Gene Names: CBL27_26410
UniProt
Find proteins for Q99Q62 (Shigella flexneri)
Explore Q99Q62 
Go to UniProtKB:  Q99Q62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99Q62
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUF1778 domain-containing protein42Shigella sonneiMutation(s): 0 
UniProt
Find proteins for Q99Q00 (Shigella flexneri)
Explore Q99Q00 
Go to UniProtKB:  Q99Q00
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99Q00
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.227 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.22α = 90
b = 67.22β = 90
c = 185.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Database references