4TS1

CRYSTAL STRUCTURE OF A DELETION MUTANT OF A TYROSYL-T/RNA SYNTHETASE COMPLEXED WITH TYROSINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a deletion mutant of a tyrosyl-tRNA synthetase complexed with tyrosine.

Brick, P.Blow, D.M.

(1987) J.Mol.Biol. 194: 287-297


  • PubMed Abstract: 
  • The crystal structure of a deletion mutant of tyrosyl-tRNA synthetase from Bacillus stearothermophilus has been determined at 2.5 A resolution using molecular replacement techniques. The genetically engineered molecule catalyses the activation of tyr ...

    The crystal structure of a deletion mutant of tyrosyl-tRNA synthetase from Bacillus stearothermophilus has been determined at 2.5 A resolution using molecular replacement techniques. The genetically engineered molecule catalyses the activation of tyrosine with kinetic properties similar to those of the wild-type enzyme but no longer binds tRNATyr. It contains 319 residues corresponding to the region of the polypeptide chain for which interpretable electron density is present in crystals of the wild-type enzyme. The partly refined model of the wild-type enzyme was used as a starting point in determining the structure of the truncated mutant. The new crystals are of space group P2(1) and contain the molecular dimer within the asymmetric unit. The refined model has a crystallographic R-factor of 18.7% for all reflections between 8 and 2.5 A. Each subunit contains two structural domains: the alpha/beta domain (residues 1 to 220) containing a six-stranded beta-sheet and the alpha-helical domain (residues 248 to 319) containing five helices. The alpha/beta domains are related by a non-crystallographic dyad while the alpha-helical domains are in slightly different orientations in the two subunits. The tyrosine substrate binds in a slot at the bottom of a deep active site cleft in the middle of the alpha/beta domain. It is surrounded by polar side-chains and water molecules that are involved in an intricate hydrogen bonding network. Both the alpha-amino and hydroxyl groups of the substrate make good hydrogen bonds with the protein. The amino group forms hydrogen bonds with Tyr169-OH, Asp78-OD1 and Gln173-OE1. The phenolic hydroxyl group forms hydrogen bonds with Asp76-OD1 and Tyr34-OH. In contrast, the substrate carboxyl group makes no direct interactions with the enzyme. The results of both substrate inhibition studies and site-directed mutagenesis experiments have been examined in the light of the refined structure.


    Related Citations: 
    • Tyrosyl-T/RNA Synthetase Forms a Mononucleotide-Binding Fold
      Bhat, T.N.,Blow, D.M.,Brick, P.,Nyborg, J.
      (1982) J.Mol.Biol. 158: 699
    • Interaction of Crystalline Tyrosol-T/RNA Synthetase with Adenosine, Adenosine Monophosphate, Adenosine Triphosphate and Pyrophosphate in the Presence of Tyrosinol
      Monteilhet, C.,Blow, D.M.,Brick, P.
      (1984) J.Mol.Biol. 173: 477
    • Deletion Mutagenesis Using an M13 Splint. The N-Terminal Structural Domain of Tyrosyl-T/RNA Synthetase (B. Stearothermophilus) Catalyses the Formation of Tyrosyl Adenylate
      Waye, M.M.Y.,Winter, G.,Wilkinson, A.J.,Fersht, A.R.
      (1983) Embo J. 2: 1827
    • Binding of Tyrosine, Adenosine Triphosphate and Analogues to Crystalline Tyrosyl Transfer RNA Synthetase
      Monteilhet, C.,Blow, D.M.
      (1978) J.Mol.Biol. 122: 407
    • Structure of Tyrosyl-T/RNA Synthetase Refined at 2.3 Angstroms Resolution. Interaction of the Enzyme with the Tyrosyl Adenylate Intermediate
      Brick, P.,Bhat, T.N.,Blow, D.M.
      (1989) J.Mol.Biol. 208: 83



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYROSYL-tRNA SYNTHETASE
A, B
319Geobacillus stearothermophilusMutation(s): 0 
Gene Names: tyrS
EC: 6.1.1.1
Find proteins for P00952 (Geobacillus stearothermophilus)
Go to UniProtKB:  P00952
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYR
Query on TYR

Download SDF File 
Download CCD File 
A, B
TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TYRKd: 11600 nM BINDINGMOAD
TYRKd: 11600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 95.460α = 90.00
b = 67.060β = 90.78
c = 61.370γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1989-06-29 
  • Released Date: 1989-10-15 
  • Deposition Author(s): Brick, P., Blow, D.M.

Revision History 

  • Version 1.0: 1989-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance