1ATI

CRYSTAL STRUCTURE OF GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus.

Logan, D.T.Mazauric, M.H.Kern, D.Moras, D.

(1995) EMBO J. 14: 4156-4167


  • PubMed Abstract: 
  • The sequence and crystal structure at 2.75 A resolution of the homodimeric glycyl-tRNA synthetase from Thermus thermophilus, the first representative of the last unknown class II synthetase subgroup, have been determined. The three class II synthetas ...

    The sequence and crystal structure at 2.75 A resolution of the homodimeric glycyl-tRNA synthetase from Thermus thermophilus, the first representative of the last unknown class II synthetase subgroup, have been determined. The three class II synthetase sequence motifs are present but the structure was essential for identification of motif 1, which does not possess the proline previously believed to be an essential class II invariant. Nevertheless, crucial contacts with the active site of the other monomer involving motif 1 are conserved and a more comprehensive description of class II now becomes possible. Each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel beta-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA synthetase due to the conserved nature of the class II active site.


    Related Citations: 
    • 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

    Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCYL-TRNA SYNTHETASE
A, B
505Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLYCYL-tRNA SYNTHETASE
C
37N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GLYCYL-tRNA SYNTHETASE
D
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
C, D
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.227 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 126.900α = 90.00
b = 255.300β = 90.00
c = 105.000γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
CCP4data scaling
MOSFLMdata reduction
X-PLORmodel building
ROTAVATA)data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance