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 
  • R-Value Observed: 0.161 

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
  • Primary Citation of Related Structures:  
    4H3S

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamine-tRNA ligaseA817Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GLN4O3601YOR168W
EC: 6.1.1.18
UniProt
Find proteins for P13188 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13188 
Go to UniProtKB:  P13188
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTT
Query on DTT

Download Ideal Coordinates CCD File 
Q [auth A]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download Ideal Coordinates CCD File 
K [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
ZN
Query on ZN

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B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
M [auth A], N [auth A], O [auth A], P [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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 
  • R-Value Observed: 0.161 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.611α = 90
b = 176.611β = 90
c = 72.188γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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