4H3S

The Structure of Glutaminyl-tRNA Synthetase from Saccharomyces Cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Structure of Yeast Glutaminyl-tRNA Synthetase and Modeling of Its Interaction with tRNA.

Grant, T.D.Luft, J.R.Wolfley, J.R.Snell, M.E.Tsuruta, H.Corretore, S.Quartley, E.Phizicky, E.M.Grayhack, E.J.Snell, E.H.

(2013) J.Mol.Biol. 425: 2480-2493

  • DOI: 10.1016/j.jmb.2013.03.043

  • PubMed Abstract: 
  • Eukaryotic glutaminyl-tRNA synthetase (GlnRS) contains an appended N-terminal domain (NTD) whose precise function is unknown. Although GlnRS structures from two prokaryotic species are known, no eukaryotic GlnRS structure has been reported. Here we p ...

    Eukaryotic glutaminyl-tRNA synthetase (GlnRS) contains an appended N-terminal domain (NTD) whose precise function is unknown. Although GlnRS structures from two prokaryotic species are known, no eukaryotic GlnRS structure has been reported. Here we present the first crystallographic structure of yeast GlnRS, finding that the structure of the C-terminal domain is highly similar to Escherichia coli GlnRS but that 214 residues, including the NTD, are crystallographically disordered. We present a model of the full-length enzyme in solution, using the structures of the C-terminal domain, and the isolated NTD, with small-angle X-ray scattering data of the full-length molecule. We proceed to model the enzyme bound to tRNA, using the crystallographic structures of GatCAB and GlnRS-tRNA complex from bacteria. We contrast the tRNA-bound model with the tRNA-free solution state and perform molecular dynamics on the full-length GlnRS-tRNA complex, which suggests that tRNA binding involves the motion of a conserved hinge in the NTD.


    Organizational Affiliation

    Hauptman Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamine-tRNA ligase
A
817Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: GLN4
EC: 6.1.1.18
Find proteins for P13188 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P13188
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

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A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
DTT
Query on DTT

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A
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.160 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 176.611α = 90.00
b = 176.611β = 90.00
c = 72.188γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PHENIXphasing
Blu-Icedata collection
PHENIXmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references
  • Version 1.2: 2014-11-12
    Type: Structure summary
  • Version 1.3: 2014-11-26
    Type: Other