5UJI

Crystal structure of human T2-Tryptophanyl-tRNA synthetase with H130R mutation

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2017-01-18 Released: 2018-01-17 
  • Deposition Author(s): Xu, X., Yang, X.-L.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), Zhejiang Provincial Natural Science Foundation of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An alternative conformation of human TrpRS suggests a role of zinc in activating non-enzymatic function.

Xu, X.Zhou, H.Zhou, Q.Hong, F.Vo, M.N.Niu, W.Wang, Z.Xiong, X.Nakamura, K.Wakasugi, K.Schimmel, P.Yang, X.L.

(2018) RNA Biol 15: 649-658

  • DOI: https://doi.org/10.1080/15476286.2017.1377868
  • Primary Citation of Related Structures:  
    5UJI, 5UJJ

  • PubMed Abstract: 

    Tryptophanyl-tRNA synthetase (TrpRS) in vertebrates contains a N-terminal extension in front of the catalytic core. Proteolytic removal of the N-terminal 93 amino acids gives rise to T2-TrpRS, which has potent anti-angiogenic activity mediated through its extracellular interaction with VE-cadherin. Zinc has been shown to have anti-angiogenic effects and can bind to human TrpRS. However, the connection between zinc and the anti-angiogenic function of TrpRS has not been explored. Here we report that zinc binding can induce structural relaxation in human TrpRS to facilitate the proteolytic generation of a T2-TrpRS-like fragment. The zinc-binding site is likely to be contained within T2-TrpRS, and the zinc-bound conformation of T2-TrpRS is mimicked by mutation H130R. We determined the crystal structure of H130R T2-TrpRS at 2.8 Å resolution, which reveals drastically different conformation from that of wild-type (WT) T2-TrpRS. The conformational change creates larger binding surfaces for VE-cadherin as suggested by molecular dynamic simulations. Surface plasmon resonance analysis indicates more than 50-fold increase in binding affinity of H130R T2-TrpRS for VE-cadherin, compared to WT T2-TrpRS. The enhanced interaction is also confirmed by a cell-based binding analysis. These results suggest that zinc plays an important role in activating TrpRS for angiogenesis regulation.


  • Organizational Affiliation

    a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan--tRNA ligase, cytoplasmic
A, B
388Homo sapiensMutation(s): 1 
Gene Names: WARSIFI53WRS
EC: 6.1.1.2
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.888α = 90
b = 139.057β = 90
c = 146.724γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data processing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31400630
Zhejiang Provincial Natural Science Foundation of ChinaChinaLY14C050002

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description