1B7Y

PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue.

Reshetnikova, L.Moor, N.Lavrik, O.Vassylyev, D.G.

(1999) J.Mol.Biol. 287: 555-568

  • DOI: 10.1006/jmbi.1999.2617
  • Primary Citation of Related Structures:  1B70

  • PubMed Abstract: 
  • The crystal structures of Thermus thermophilus phenylalanyl-tRNA synthetase (PheRS) complexed with phenylalanine and phenylalaninyl-adenylate (PheOH-AMP), the synthetic analogue of phenylalanyl-adenylate, have been determined at 2.7A and 2.5A resolut ...

    The crystal structures of Thermus thermophilus phenylalanyl-tRNA synthetase (PheRS) complexed with phenylalanine and phenylalaninyl-adenylate (PheOH-AMP), the synthetic analogue of phenylalanyl-adenylate, have been determined at 2.7A and 2.5A resolution, respectively. Both Phe and PheOH-AMP are engulfed in the active site cleft of the catalytic alpha-subunit of PheRS, and neither makes contact with the PheRS beta-subunit. The conformations and binding of Phe are almost identical in both complexes. The recognition of Phe by PheRS is achieved through a mixture of multiple van der Waals interactions and hydrogen bonds. The side-chain of the Phe substrate is sandwiched between the hydrophobic side-chains of Phealpha258 and Phealpha260 on one side, and the main-chain atoms of the two adjacent beta-strands on the other. The side-chains of Valalpha261 and Alaalpha314 form the back wall of the amino acid binding pocket. In addition, PheRS residues (Trpalpha149, Seralpha180, Hisalpha178, Argalpha204, Glnalpha218, and Glualpha220) form a total of seven hydrogen bonds with the main-chain atoms of Phe. The conformation of PheOH-AMP and the network of interactions of its AMP moiety with PheRS are reminiscent of the other class II synthetases. The structural similarity between PheRS and histidyl-tRNA synthetase extends to the amino acid binding site, which is normally unique for each enzyme. The complex structures suggest that the PheRS beta-subunit may affect the first step of the reaction (formation of phenylalanyl-adenylate) through the metal-mediated conserved alpha/beta-subunit interface. The modeling of tyrosine in the active site of PheRS revealed no apparent close contacts between tyrosine and the PheRS residues. This result implies that the proofreading mechanism against activated tyrosine, rather than direct recognition, may play the major role in the PheRS specificity.


    Related Citations: 
    • Structure of Phenylalanyl-tRNA Synthetase from Thermus Thermophilus
      Mosyak, L.,Reshetnikova, L.,Goldgur, Y.,Delarue, M.,Safro, M.G.
      (1995) Nature New Biol. 2: 537
    • The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe.
      Goldgur, Y.,Mosyak, L.,Reshetnikova, L.,Ankilova, V.,Lavrik, O.,Khodyreva, S.,Safro, M.
      (1997) Structure 5: 59


    Organizational Affiliation

    Institute of Molecular Biology, Moscow, 117984, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PHENYLALANYL-TRNA SYNTHETASE)
A
350Thermus thermophilusGene Names: pheS
EC: 6.1.1.20
Find proteins for P27001 (Thermus thermophilus)
Go to UniProtKB:  P27001
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PHENYLALANYL-TRNA SYNTHETASE)
B
785Thermus thermophilusGene Names: pheT
EC: 6.1.1.20
Find proteins for P27002 (Thermus thermophilus)
Go to UniProtKB:  P27002
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FYA
Query on FYA

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE]
C19 H25 N6 O7 P
XNEAAYNJQROQFE-BPAMBQHCSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 174.500α = 90.00
b = 174.500β = 90.00
c = 140.200γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-26
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-02-15
    Type: Database references