Crystal structure of the aminoacylation catalytic fragment of human tryptophanyl-tRNA synthetase

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

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Crystal Structure of Human Tryptophanyl-tRNA Synthetase Catalytic Fragment

Yu, Y.Liu, Y.Shen, N.Xu, X.Xu, F.Jia, J.Jin, Y.Arnold, E.Ding, J.

(2004) J Biol Chem 279: 8378-8388

  • DOI: https://doi.org/10.1074/jbc.M311284200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human tryptophanyl-tRNA synthetase (hTrpRS) produces a full-length and three N terminus-truncated forms through alternative splicing and proteolysis. The shortest fragment that contains the aminoacylation catalytic fragment (T2-hTrpRS) exhibits the most potent angiostatic activity. We report here the crystal structure of T2-hTrpRS at 2.5 A resolution, which was solved using the multi-wavelength anomalous diffraction method. T2-hTrpRS shares a very low sequence homology of 22% with Bacillus stearothermophilus TrpRS (bTrpRS); however, their overall structures are strikingly similar. Structural comparison of T2-hTrpRS with bTrpRS reveals substantial structural differences in the substrate-binding pocket and at the entrance to the pocket that play important roles in substrate binding and tRNA binding. T2-hTrpRS has a wide opening to the active site and adopts a compact conformation similar to the closed conformation of bTrpRS. These results suggest that mammalian and bacterial TrpRSs might use different mechanisms to recognize the substrate. Modeling studies indicate that tRNA binds with the dimeric enzyme and interacts primarily with the connective polypeptide 1 of hTrpRS via its acceptor arm and the alpha-helical domain of hTrpRS via its anticodon loop. Our results also suggest that the angiostatic activity is likely located at the alpha-helical domain, which resembles the short chain cytokines.

  • Organizational Affiliation

    Key Laboratory of Proteomics and State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophanyl-tRNA synthetase378Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P23381 (Homo sapiens)
Explore P23381 
Go to UniProtKB:  P23381
PHAROS:  P23381
GTEx:  ENSG00000140105 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23381
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.24α = 90
b = 82.24β = 90
c = 263.56γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references