8I4I

The asymmetric structure of homodimeric E. coli TrpRS bound with tryptophanyl adenylate and L-tryptophan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening.

Xiang, M.Xia, K.Chen, B.Luo, Z.Yu, Y.Jiang, L.Zhou, H.

(2023) Nucleic Acids Res 51: 4637-4649

  • DOI: https://doi.org/10.1093/nar/gkad278
  • Primary Citation of Related Structures:  
    8I1W, 8I1Y, 8I1Z, 8I27, 8I2A, 8I2C, 8I2J, 8I2L, 8I2M, 8I4I

  • PubMed Abstract: 

    Tryptophanyl-tRNA synthetase (TrpRS) links tryptophan to tRNATrp, thereby playing an indispensable role in protein translation. Unlike most class I aminoacyl-tRNA synthetases (AARSs), TrpRS functions as a homodimer. Herein, we captured an 'open-closed' asymmetric structure of Escherichia coli TrpRS (EcTrpRS) with one active site occupied by a copurified intermediate product and the other remaining empty, providing structural evidence for the long-discussed half-of-the-sites reactivity of bacterial TrpRS. In contrast to its human counterpart, bacterial TrpRS may rely on this asymmetric conformation to functionally bind with substrate tRNA. As this asymmetric conformation is probably a dominant form of TrpRS purified from bacterial cells, we performed fragment screening against asymmetric EcTrpRS to support antibacterial discovery. Nineteen fragment hits were identified, and 8 of them were successfully cocrystallized with EcTrpRS. While a fragment named niraparib bound to the L-Trp binding site of the 'open' subunit, the other 7 fragments all bound to an unprecedented pocket at the interface between two TrpRS subunits. Binding of these fragments relies on residues specific to bacterial TrpRS, avoiding undesired interactions with human TrpRS. These findings improve our understanding of the catalytic mechanism of this important enzyme and will also facilitate the discovery of bacterial TrpRS inhibitors with therapeutic potential.


  • Organizational Affiliation

    Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery and Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong510006, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan--tRNA ligase
A, B
340Escherichia coli K-12Mutation(s): 0 
Gene Names: trpSb3384JW3347
EC: 6.1.1.2
UniProt
Find proteins for P00954 (Escherichia coli (strain K12))
Explore P00954 
Go to UniProtKB:  P00954
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00954
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.664α = 90
b = 80.048β = 106.2
c = 77.435γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
CrysalisProdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22177140

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2023-06-07
    Changes: Database references
  • Version 1.3: 2024-05-29
    Changes: Data collection