3E0V

Crystal structure of pyruvate kinase from Leishmania mexicana in complex with sulphate ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Sulphate removal induces a major conformational change in Leishmania mexicana pyruvate kinase in the crystalline state.

Tulloch, L.B.Morgan, H.P.Hannaert, V.Michels, P.A.Fothergill-Gilmore, L.A.Walkinshaw, M.D.

(2008) J.Mol.Biol. 383: 615-626

  • DOI: 10.1016/j.jmb.2008.08.037
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report X-ray structures of pyruvate kinase from Leishmania mexicana (LmPYK) that are trapped in different conformations. These, together with the previously reported structure of LmPYK in its inactive (T-state) conformation, allow comparisons of t ...

    We report X-ray structures of pyruvate kinase from Leishmania mexicana (LmPYK) that are trapped in different conformations. These, together with the previously reported structure of LmPYK in its inactive (T-state) conformation, allow comparisons of three different conformers of the same species of pyruvate kinase (PYK). Four new site point mutants showing the effects of side-chain alteration at subunit interfaces are also enzymatically characterised. The LmPYK tetramer crystals grown with ammonium sulphate as precipitant adopt an active-like conformation, with sulphate ions at the active and effector sites. The sulphates occupy positions similar to those of the phosphates of ligands bound to active (R-state) and constitutively active (nonallosteric) PYKs from several species, and provide insight into the structural roles of the phosphates of the substrates and effectors. Crystal soaking in sulphate-free buffers was found to induce major conformational changes in the tetramer. In particular, the unwinding of the Aalpha6' helix and the inward hinge movement of the B domain are coupled with a significant widening (4 A) of the tetramer caused by lateral movement of the C domains. The two new LmPYK structures and the activity studies of site point mutations described in this article are consistent with a developing picture of allosteric activity in which localised changes in protein flexibility govern the distribution of conformer families adopted by the tetramer in its active and inactive states.


    Organizational Affiliation

    Institute of Structural and Molecular Biology, The University of Edinburgh, Michael Swann Building, The King's Buildings, Edinburgh, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate kinase
A, B, C, D, E, F
539Leishmania mexicanaMutation(s): 1 
Gene Names: PYK
EC: 2.7.1.40
Find proteins for Q27686 (Leishmania mexicana)
Go to UniProtKB:  Q27686
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.227 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 261.955α = 90.00
b = 261.955β = 90.00
c = 185.541γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
SCALAdata scaling
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance