1B76

GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.5 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:  
    1B76, 1GGM

  • 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 cocrystallized with glycine and ATP, which were transformed by the enzyme into glycyl-adenylate and thus gave the enzyme-product complex ...

    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: 
    • Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus.
      Logan, D.T., Mazauric, M.H., Kern, D., Moras, D.
      (1995) EMBO J 14: 4156
    • Crystallisation of the glycyl-tRNA synthetase from Thermus thermophilus and initial crystallographic data.
      Logan, D.T., Cura, V., Touzel, J.P., Kern, D., Moras, D.
      (1994) J Mol Biol 241: 732

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycine--tRNA ligaseA, B442Thermus thermophilus HB8Mutation(s): 0 
Gene Names: glyQSglySTTHA0543
EC: 6.1.1.14
UniProt
Find proteins for P56206 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P56206 
Go to UniProtKB:  P56206
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.227 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.8α = 90
b = 250.9β = 90
c = 105.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
AUTOMARdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-28
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-05-31
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2019-10-30
    Changes: Data collection, Database references