1GGM

GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH GLYCYL-ADENYLATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine.

Arnez, J.G.Dock-Bregeon, A.C.Moras, D.

(1999) J.Mol.Biol. 286: 1449-1459

  • DOI: 10.1006/jmbi.1999.2562
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of glycyl-tRNA synthetase (GlyRS) from Thermus thermophilus, a homodimeric class II enzyme, were determined in the enzyme-substrate and enzyme-product states corresponding to the first step of aminoacylation. GlyRS was cocrysta ...

    The crystal structures of glycyl-tRNA synthetase (GlyRS) from Thermus thermophilus, a homodimeric class II enzyme, were determined in the enzyme-substrate and enzyme-product states corresponding to the first step of aminoacylation. GlyRS was cocrystallized with glycine and ATP, which were transformed by the enzyme into glycyl-adenylate and thus gave the enzyme-product complex. To trap the enzyme-substrate complex, the enzyme was combined with the glycine analog ethanolamine and ATP. The ligands are bound in fixed orientations in the substrate-binding pocket of the N-terminal active site domain, which contains the classical class II aminoacyl-tRNA synthetase (aaRS) fold. Since glycine does not possess a side-chain, much of the specificity of the enzyme is directed toward excluding any additional atoms beyond the alpha-carbon atom. Several carboxylate residues of GlyRS line the glycine binding pocket; two of them interact directly with the alpha-ammonium group. In addition, the enzyme utilizes the acidic character of the pro-L alpha-hydrogen atom by contacting it via a glutamate carboxylic oxygen atom. A guanidino eta-nitrogen atom of the class II aaRS-conserved motif 2 arginine interacts with the substrate carbonyl oxygen atom. These features serve to attract the small amino acid substrate into the active site and to position it in the correct orientation. GlyRS uses class II-conserved residues to interact with the ATP and the adenosine-phosphate moiety of glycyl-adenylate. On the basis of this similarity, we propose that GlyRS utilizes the same general mechanism as that employed by other class II aminoacyl-tRNA synthetases.


    Related Citations: 
    • Crystallisation of the Glycyl-tRNA Synthetase from Thermus Thermophilus and Initial Crystallographic Data
      Logan, D.,Cura, V.,Touzel, J.-P.,Kern, D.,Moras, D.
      (1994) J.Mol.Biol. 241: 732
    • Crystal Structure of Glycyl-tRNA Synthetase from Thermus Thermophilus: New Functional Domains and Substrate Specificity
      Logan, D.T.,Mazauric, M.H.,Kern, D.,Moras, D.
      (1995) Embo J. 14: 4156


    Organizational Affiliation

    Laboratoire de Biologie Structurale, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch Cedex, 67404, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycine--tRNA ligase
A, B
442Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: glyQS (glyS)
EC: 6.1.1.14
Find proteins for P56206 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P56206
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAP
Query on GAP

Download SDF File 
Download CCD File 
A, B
GLYCYL-ADENOSINE-5'-PHOSPHATE
C12 H17 N6 O8 P
HROXHMRQKGGIFT-JJNLEZRASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.242 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 122.500α = 90.00
b = 250.100β = 90.00
c = 106.000γ = 90.00
Software Package:
Software NamePurpose
AUTOMARdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-01-27 
  • Released Date: 1999-01-28 
  • Deposition Author(s): Arnez, J.G., Moras, D.

Revision History 

  • Version 1.0: 1999-01-28
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-05-31
    Type: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2017-10-04
    Type: Refinement description