2ALY

Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with 5'-O-[N-(L-tyrosyl)sulphamoyl]adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for Discrimination of L-Phenylalanine from L-Tyrosine by Phenylalanyl-tRNA Synthetase

Kotik-Kogan, O.M.Moor, N.A.Tworowski, D.E.Safro, M.G.

(2005) Structure 13: 1799-1807

  • DOI: 10.1016/j.str.2005.08.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aminoacyl-tRNA synthetases (aaRSs) exert control over the faithful transfer of amino acids onto cognate tRNAs. Since chemical structures of various amino acids closely resemble each other, it is difficult to discriminate between them. Editing activit ...

    Aminoacyl-tRNA synthetases (aaRSs) exert control over the faithful transfer of amino acids onto cognate tRNAs. Since chemical structures of various amino acids closely resemble each other, it is difficult to discriminate between them. Editing activity has been evolved by certain aaRSs to resolve the problem. In this study, we determined the crystal structures of complexes of T. thermophilus phenylalanyl-tRNA synthetase (PheRS) with L-tyrosine, p-chloro-phenylalanine, and a nonhydrolyzable tyrosyl-adenylate analog. The structures demonstrate plasticity of the synthetic site capable of binding substrates larger than phenylalanine and provide a structural basis for the proofreading mechanism. The editing site is localized at the B3/B4 interface, 35 A from the synthetic site. Glubeta334 plays a crucial role in the specific recognition of the Tyr moiety in the editing site. The tyrosyl-adenylate analog binds exclusively in the synthetic site. Both structural data and tyrosine-dependent ATP hydrolysis enhanced by tRNA(Phe) provide evidence for a preferential posttransfer editing pathway in the phenylalanine-specific system.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylalanyl-tRNA synthetase alpha chain
A
266Thermus thermophilusMutation(s): 0 
Gene Names: pheS
EC: 6.1.1.20
Find proteins for P27001 (Thermus thermophilus)
Go to UniProtKB:  P27001
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phenylalanyl-tRNA synthetase beta chain
B
785Thermus thermophilusMutation(s): 0 
Gene Names: pheT
EC: 6.1.1.20
Find proteins for P27002 (Thermus thermophilus)
Go to UniProtKB:  P27002
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
YSA
Query on YSA

Download SDF File 
Download CCD File 
A
5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE
TYROSYLADENYLATE
C19 H23 N7 O8 S
MJZAZMKENKZBAJ-QTOWJTHWSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.228 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 173.640α = 90.00
b = 173.640β = 90.00
c = 139.810γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description