6KSH

Crystal structure of pyruvate kinase (PYK) from Plasmodium falciparum in complex with oxalate and ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pyruvate kinase from Plasmodium falciparum: Structural and kinetic insights into the allosteric mechanism.

Zhong, W.Li, K.Cai, Q.Guo, J.Yuan, M.Wong, Y.H.Walkinshaw, M.D.Fothergill-Gilmore, L.A.Michels, P.A.M.Dedon, P.C.Lescar, J.

(2020) Biochem Biophys Res Commun 532: 370-376

  • DOI: 10.1016/j.bbrc.2020.08.048
  • Primary Citation of Related Structures:  
    6KSH

  • PubMed Abstract: 
  • During its intra-erythrocytic growth phase, the malaria parasite Plasmodium falciparum relies heavily on glycolysis for its energy requirements. Pyruvate kinase (PYK) is essential for regulating glycolytic flux and for ATP production, yet the allosteric mechanism of P ...

    During its intra-erythrocytic growth phase, the malaria parasite Plasmodium falciparum relies heavily on glycolysis for its energy requirements. Pyruvate kinase (PYK) is essential for regulating glycolytic flux and for ATP production, yet the allosteric mechanism of P. falciparum PYK (PfPYK) remains poorly understood. Here we report the first crystal structure of PfPYK in complex with substrate analogues oxalate and the ATP product. Comparisons of PfPYK structures in the active R-state and inactive T-state reveal a 'rock-and-lock' allosteric mechanism regulated by rigid-body rotations of each subunit in the tetramer. Kinetic data and structural analysis indicate glucose 6-phosphate is an activator by increasing the apparent maximal velocity of the enzyme. Intriguingly, the trypanosome drug suramin inhibits PfPYK, which points to glycolysis as a set of potential therapeutic targets against malaria.


    Organizational Affiliation

    Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore. Electronic address: julien@ntu.edu.sg.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate kinaseA, B, C, D514Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0626800
EC: 2.7.1.40
UniProt
Find proteins for C6KTA4 (Plasmodium falciparum (isolate 3D7))
Explore C6KTA4 
Go to UniProtKB:  C6KTA4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
G [auth A], L [auth B], Q [auth C], V [auth D]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
OXL
Query on OXL

Download Ideal Coordinates CCD File 
I [auth A], N [auth B], S [auth C], X [auth D]OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
H [auth A], M [auth B], R [auth C], W [auth D]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], J [auth B], K [auth B], O [auth C], P [auth C], T [auth D], U [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.41α = 90
b = 139.41β = 90
c = 453.156γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Singapore)SingaporeS916137

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2020-10-28
    Changes: Database references