Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 126219.35 
• Atom Count: 8179 
• Residue Count: 1135 
• Unique protein chains: 2

1B70

PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINE

• DOI: 10.2210/pdb1B70/pdb

• Classification: LIGASE
• Organism(s): Thermus thermophilus


• Deposited: 1999-01-26 Released: 2000-02-09 
• Deposition Author(s): Reshetnikova, L., Moor, N., Lavrik, O., Vassylyev, D.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.256 
• R-Value Work: 0.224 

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

• PubMed: 10092459 
• DOI: 10.1006/jmbi.1999.2617
• Primary Citation of Related Structures:  
  1B7Y


• 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 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.

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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




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Organizational Affiliation: 

Institute of Molecular Biology, Moscow, 117984, Russia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PHENYLALANYL-TRNA SYNTHETASE	A	350	Thermus thermophilus	Mutation(s): 0  Gene Names: pheS EC: 6.1.1.20
Find proteins for P27001 (Thermus thermophilus) Go to UniProtKB:  P27001

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PHENYLALANYL-TRNA SYNTHETASE	B	785	Thermus thermophilus	Mutation(s): 0  Gene Names: pheT EC: 6.1.1.20
Find proteins for P27002 (Thermus thermophilus) Go to UniProtKB:  P27002

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PHE	A	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.256 
• R-Value Work: 0.224 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 174.000	α = 90.00
b = 174.000	β = 90.00
c = 140.400	γ = 120.00

Software Package:

Software Name	Purpose
DENZO	data reduction
X-PLOR	phasing
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-01-26 
• Released Date: 2000-02-09 
• Deposition Author(s): Reshetnikova, L., Moor, N., Lavrik, O., Vassylyev, D.G.

Revision History 

• Version 1.0: 2000-02-09
  Type: Initial release
• Version 1.1: 2008-04-26
  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