4WIN

Crystal structure of the GATase domain from Plasmodium falciparum GMP synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Active site coupling in Plasmodium falciparum GMP synthetase is triggered by domain rotation.

Ballut, L.Violot, S.Shivakumaraswamy, S.Thota, L.P.Sathya, M.Kunala, J.Dijkstra, B.W.Terreux, R.Haser, R.Balaram, H.Aghajari, N.

(2015) Nat Commun 6: 8930-8930

  • DOI: 10.1038/ncomms9930
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • GMP synthetase (GMPS), a key enzyme in the purine biosynthetic pathway performs catalysis through a coordinated process across two catalytic pockets for which the mechanism remains unclear. Crystal structures of Plasmodium falciparum GMPS in conjunct ...

    GMP synthetase (GMPS), a key enzyme in the purine biosynthetic pathway performs catalysis through a coordinated process across two catalytic pockets for which the mechanism remains unclear. Crystal structures of Plasmodium falciparum GMPS in conjunction with mutational and enzyme kinetic studies reported here provide evidence that an 85° rotation of the GATase domain is required for ammonia channelling and thus for the catalytic activity of this two-domain enzyme. We suggest that conformational changes in helix 371-375 holding catalytic residues and in loop 376-401 along the rotation trajectory trigger the different steps of catalysis, and establish the central role of Glu374 in allostery and inter-domain crosstalk. These studies reveal the mechanism of domain rotation and inter-domain communication, providing a molecular framework for the function of all single polypeptide GMPSs and form a solid basis for rational drug design targeting this therapeutically important enzyme.


    Organizational Affiliation

    BioCrystallography and Structural Biology of Therapeutic Targets Group, Molecular and Structural Bases of Infectious Systems, UMR5086 CNRS-University of Lyon 1, 7 passage du Vercors, 69367 Lyon Cedex 07, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GMP synthetase
A, B
249Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 6.3.5.2
Find proteins for Q8IJR9 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IJR9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download SDF File 
Download CCD File 
A, B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.820α = 90.00
b = 74.210β = 90.00
c = 91.590γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references