3KT8

Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with L-tryptophanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

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


Literature

Crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase: new insights into the mechanism of tryptophan activation and implications for anti-fungal drug design

Zhou, M.Dong, X.Shen, N.Zhong, C.Ding, J.

(2010) Nucleic Acids Res 38: 3399-3413

  • DOI: https://doi.org/10.1093/nar/gkp1254
  • Primary Citation of Related Structures:  
    3KT0, 3KT3, 3KT6, 3KT8

  • PubMed Abstract: 

    Specific activation of amino acids by aminoacyl-tRNA synthetases is essential for maintaining translational fidelity. Here, we present crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase (sTrpRS) in apo form and in complexes with various ligands. In each complex, there is a sulfate ion bound at the active site which mimics the alpha- or beta-phosphate group of ATP during tryptophan activation. In particular, in one monomer of the sTrpRS-TrpNH(2)O complex, the sulfate ion appears to capture a snapshot of the alpha-phosphate of ATP during its movement towards tryptophan. Simulation study of a human TrpRS-Trp-ATP model shows that during the catalytic process the alpha-phosphate of ATP is driven to an intermediate position equivalent to that of the sulfate ion, then moves further and eventually fluctuates at around 2 A from the nucleophile. A conserved Arg may interact with the oxygen in the scissile bond at the transition state, indicating its critical role in the nucleophilic substitution. Taken together, eukaryotic TrpRSs may adopt an associative mechanism for tryptophan activation in contrast to a dissociative mechanism proposed for bacterial TrpRSs. In addition, structural analysis of the apo sTrpRS reveals a unique feature of fungal TrpRSs, which could be exploited in rational antifungal drug design.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology and Research Center for Structural Biology, Institute of Biochemistry and Cell Biology, Shanghai, Shanghai 200031, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophanyl-tRNA synthetase, cytoplasmic
A, B, C, D
438Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: trpS
EC: 6.1.1.2
UniProt
Find proteins for Q12109 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12109 
Go to UniProtKB:  Q12109
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12109
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LTN
Query on LTN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C],
P [auth D]
L-TRYPTOPHANAMIDE
C11 H13 N3 O
JLSKPBDKNIXMBS-VIFPVBQESA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 252.26α = 90
b = 252.26β = 90
c = 111.376γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description