3IAL

Giardia lamblia Prolyl-tRNA synthetase in complex with prolyl-adenylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the prolyl-tRNA synthetase from the eukaryotic pathogen Giardia lamblia.

Larson, E.T.Kim, J.E.Napuli, A.J.Verlinde, C.L.Fan, E.Zucker, F.H.Van Voorhis, W.C.Buckner, F.S.Hol, W.G.Merritt, E.A.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1194-1200

  • DOI: 10.1107/S0907444912024699
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The genome of the human intestinal parasite Giardia lamblia contains only a single aminoacyl-tRNA synthetase gene for each amino acid. The Giardia prolyl-tRNA synthetase gene product was originally misidentified as a dual-specificity Pro/Cys enzyme, ...

    The genome of the human intestinal parasite Giardia lamblia contains only a single aminoacyl-tRNA synthetase gene for each amino acid. The Giardia prolyl-tRNA synthetase gene product was originally misidentified as a dual-specificity Pro/Cys enzyme, in part owing to its unexpectedly high off-target activation of cysteine, but is now believed to be a normal representative of the class of archaeal/eukaryotic prolyl-tRNA synthetases. The 2.2 Å resolution crystal structure of the G. lamblia enzyme presented here is thus the first structure determination of a prolyl-tRNA synthetase from a eukaryote. The relative occupancies of substrate (proline) and product (prolyl-AMP) in the active site are consistent with half-of-the-sites reactivity, as is the observed biphasic thermal denaturation curve for the protein in the presence of proline and MgATP. However, no corresponding induced asymmetry is evident in the structure of the protein. No thermal stabilization is observed in the presence of cysteine and ATP. The implied low affinity for the off-target activation product cysteinyl-AMP suggests that translational fidelity in Giardia is aided by the rapid release of misactivated cysteine.


    Organizational Affiliation

    Medical Structural Genomics of Pathogenic Protozoa, http://msgpp.org, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prolyl-tRNA synthetaseA, B518Giardia lamblia ATCC 50803Mutation(s): 0 
Gene Names: GL50803_15983ProRSGL50803_0015983
EC: 6.1.1.15
Find proteins for A8BR89 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
Explore A8BR89 
Go to UniProtKB:  A8BR89
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PR8
Query on PR8

Download CCD File 
A, B
5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine
C15 H21 N6 O8 P
KQFKHTAASHMYDJ-TWBCTODHSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.338α = 90
b = 87.624β = 90
c = 142.41γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-11-14
    Changes: Database references