1TYD

STRUCTURE OF TYROSYL-TRNA SYNTHETASE REFINED AT 2.3 ANGSTROMS RESOLUTION. INTERACTION OF THE ENZYME WITH THE TYROSYL ADENYLATE INTERMEDIATE


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

Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate.

Brick, P.Bhat, T.N.Blow, D.M.

(1989) J.Mol.Biol. 208: 83-98

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of tyrosyl-tRNA synthetase (EC 6.1.1.1) from Bacillus stearothermophilus has been refined to a crystallographic R-factor of 22.6% at 2.3 A resolution using a restrained least-squares procedure. In the final model the root-mean-s ...

    The crystal structure of tyrosyl-tRNA synthetase (EC 6.1.1.1) from Bacillus stearothermophilus has been refined to a crystallographic R-factor of 22.6% at 2.3 A resolution using a restrained least-squares procedure. In the final model the root-mean-square deviation from ideality for bond distances is 0.018 A and for angle distances is 0.044 A. Each monomer consists of three domains: an alpha/beta domain (residues 1 to 220) containing a six-stranded beta-sheet, an alpha-helical domain (248 to 318) containing five helices, and a disordered C-terminal domain (319 to 418) for which the electron density is very weak and where it has not been possible to trace the polypeptide chain. Complexes of the enzyme with the catalytic intermediate tyrosyl adenylate and the inhibitor tyrosinyl adenylate have also been refined to R-factors of 23.9% at 2.8 A resolution and 21.0% at 2.7 A resolution, respectively. Formation of the complexes results in some crystal cracking, but there is no significant difference in the conformation of the polypeptide chain of the three structures described here. The relative orientation of the alpha/beta and alpha-helical domains is similar to that previously observed for the "A" subunit of a deletion mutant lacking the C-terminal domain. Differences between these structures are confined to surface loops that are involved in crystal packing. Tyrosyl adenylate and tyrosinyl adenylate bind in similar conformations within a deep cleft in the alpha/beta domain. The tyrosine moiety is in the equivalent position to that occupied by tyrosine in crystals of the truncated mutant and makes similar strong polar interactions with the enzyme. The alpha-phosphate group interacts with the main-chain nitrogen of Asp38. The two hydroxyl groups of the ribose form strong interactions with the protein. The 2'-hydroxyl group interacts with the carboxylate of Asp194 and the main-chain nitrogen of Gly192 while the 3'-hydroxyl interacts with a tightly bound water molecule (Wat326). The adenine moiety appears to make no significant polar interactions with the protein. The results of site-directed mutagenesis studies are examined in the light of these refined structures.


    Related Citations: 
    • Fine Structure-Activity Analysis of Mutations at Position 51 of Tyrosyl-tRNA Synthetase
      Fersht, A.R.,Wilkinson, A.J.,Carter, P.,Winter, G.
      (1985) Biochemistry 24: 5858
    • Natural Variation of Tyrosyl-tRNA Synthetase and Comparison with Engineered Mutants
      Jones, M.D.,Lowe, D.M.,Borgford, T.,Fersht, A.R.
      (1986) Biochemistry 25: 11887
    • 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
    • Crystal Structure of a Deletion Mutant of a Tyrosyl-T/RNA Synthetase Complexed with Tyrosine
      Brick, P.,Blow, D.M.
      (1987) J.Mol.Biol. 194: 287
    • Structure of Aminoacyl T/RNA Synthetases
      Blow, D.M.,Monteilhet, C.,Rubin, J.R.
      (1978) Proc.FEBS Meet. 52: 59
    • The Peptide Chain of Tyrosyl T/RNA Synthetase. No Evidence for a Super-Secondary Structure of Four Alpha-Helices
      Blow, D.M.,Irwin, M.J.,Nyborg, J.
      (1977) Biochem.Biophys.Res.Commun. 76: 728
    • 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
    • The Crystal Structure of Tyrosyl-Transfer RNA Synthetase at 2.7 Angstroms Resolution
      Irwin, M.J.,Nyborg, J.,Reid, B.R.,Blow, D.M.
      (1976) J.Mol.Biol. 105: 577
    • Structure of a Mutant of Tyrosyl-tRNA Synthetase with Enhanced Catalytic Properties
      Brown, K.A.,Brick, P.,Blow, D.M.
      (1987) Nature 326: 416
    • Internal Thermodynamics of Position 51 Mutants and Natural Variants of Tyrosyl-tRNA Synthetase
      Ho, C.K.,Fersht, A.R.
      (1986) Biochemistry 25: 1891
    • Crystallization and Preliminary X-Ray Diffraction Studies on Tyrosyl-Transfer RNA Synthetase from Bacillus Stearothermophilus
      Reid, B.R.,Koch, G.L.E.,Boulanger, Y.,Hartley, B.S.,Blow, D.M.
      (1973) J.Mol.Biol. 80: 199
    • A Large Increase in Enzyme-Substrate Affinity by Protein Engineering
      Wilkinson, A.J.,Fersht, A.R.,Blow, D.M.,Carter, P.,Winter, G.
      (1984) Nature 307: 187
    • The Use of Double Mutants to Detect Structural Changes in the Active Site of the Tyrosyl-tRNA Synthetase (Bacillus Stearothermophilus)
      Carter, P.J.,Winter, G.,Wilkinson, A.J.,Fersht, A.R.
      (1984) Cell 38: 835
    • A Density-Modification Method for the Improvement of Poorly Resolved Protein Electron-Density Maps
      Bhat, T.N.,Blow, D.M.
      (1982) Acta Crystallogr.,Sect.A 38: 21
    • Binding of Tyrosine, Adenosine Triphosphate and Analogues to Crystalline Tyrosyl Transfer RNA Synthetase
      Monteilhet, C.,Blow, D.M.
      (1978) J.Mol.Biol. 122: 407
    • Use of Binding Energy in Catalysis Analyzed by Mutagenesis of the Tyrosyl-tRNA Synthetase
      Wells, T.N.C.,Fersht, A.R.
      (1986) Biochemistry 25: 1881


    Organizational Affiliation

    Blackett Laboratory, Imperial College, London, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYROSYL-tRNA SYNTHETASE
E
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 
E
TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 64.460α = 90.00
b = 64.460β = 90.00
c = 237.600γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance