5UJJ

Crystal structure of human H130R tryptophanyl-tRNA synthetase in complex with TrpAMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1080/15476286.2017.1377868
  • Primary Citation of Related Structures:  

  • 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 throug ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptophan--tRNA ligase, cytoplasmic
A, B
484Homo sapiensMutation(s): 1 
Gene Names: WARS (IFI53, WRS)
EC: 6.1.1.2
Find proteins for P23381 (Homo sapiens)
Go to Gene View: WARS
Go to UniProtKB:  P23381
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TYM
Query on TYM

Download SDF File 
Download CCD File 
A, B
TRYPTOPHANYL-5'AMP
C21 H24 N7 O8 P
IFQVDHDRFCKAAW-SQIXAUHQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.352α = 90.00
b = 95.277β = 130.46
c = 99.623γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-01-18 
  • Released Date: 2018-01-17 
  • Deposition Author(s): Xu, X., Yang, X.-L.

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Data collection, Database references