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 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1107/S0907444912024699
  • Primary Citation of Related Structures:  
    3IAL

  • 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, 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prolyl-tRNA synthetase
A, B
518Giardia lamblia ATCC 50803Mutation(s): 0 
Gene Names: GL50803_15983ProRS
EC: 6.1.1.15
UniProt
Find proteins for A8BR89 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
Explore A8BR89 
Go to UniProtKB:  A8BR89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8BR89
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PR8
Query on PR8

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

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
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

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description