1R6U

Crystal structure of an active fragment of human tryptophanyl-tRNA synthetase with cytokine activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Functional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase

Yang, X.-L.Guo, M.Kapoor, M.Ewalt, K.L.Otero, F.J.Skene, R.J.McRee, D.E.Schimmel, P.

(2007) Structure 15: 793-805

  • DOI: 10.1016/j.str.2007.05.009

  • PubMed Abstract: 
  • Higher eukaryote tRNA synthetases have expanded functions that come from enlarged, more differentiated structures that were adapted to fit aminoacylation function. How those adaptations affect catalytic mechanisms is not known. Presented here is the ...

    Higher eukaryote tRNA synthetases have expanded functions that come from enlarged, more differentiated structures that were adapted to fit aminoacylation function. How those adaptations affect catalytic mechanisms is not known. Presented here is the structure of a catalytically active natural splice variant of human tryptophanyl-tRNA synthetase (TrpRS) that is a potent angiostatic factor. This and related structures suggest that a eukaryote-specific N-terminal extension of the core enzyme changed substrate recognition by forming an active site cap. At the junction of the extension and core catalytic unit, an arginine is recruited to replace a missing landmark lysine almost 200 residues away. Mutagenesis, rapid kinetic, and substrate binding studies support the functional significance of the cap and arginine recruitment. Thus, the enzyme function of human TrpRS has switched more to the N terminus of the sequence. This switch has the effect of creating selective pressure to retain the N-terminal extension for functional expansion.


    Organizational Affiliation

    The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. xlyang@scripps.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptophanyl-tRNA synthetase
A, B
437Homo sapiensMutation(s): 2 
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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TYM
Query on TYM

Download SDF File 
Download CCD File 
A
TRYPTOPHANYL-5'AMP
C21 H24 N7 O8 P
IFQVDHDRFCKAAW-SQIXAUHQSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.658α = 90.00
b = 96.460β = 129.90
c = 97.132γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
Blu-Icedata collection
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance