7ZZI

Plasmodium falciparum hexokinase complexed with glucose and citrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural Analysis of Plasmodium falciparum Hexokinase Provides Novel Information about Catalysis Due to a Plasmodium -Specific Insertion.

Dillenberger, M.Werner, A.D.Velten, A.S.Rahlfs, S.Becker, K.Fritz-Wolf, K.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms241612739
  • Primary Citation of Related Structures:  
    7ZZI

  • PubMed Abstract: 

    The protozoan parasite Plasmodium falciparum is the causative pathogen of the most severe form of malaria, for which novel strategies for treatment are urgently required. The primary energy supply for intraerythrocytic stages of Plasmodium is the production of ATP via glycolysis. Due to the parasite's strong dependence on this pathway and the significant structural differences of its glycolytic enzymes compared to its human counterpart, glycolysis is considered a potential drug target. In this study, we provide the first three-dimensional protein structure of P. falciparum hexokinase ( Pf HK) containing novel information about the mechanisms of Pf HK. We identified for the first time a Plasmodium -specific insertion that lines the active site. Moreover, we propose that this insertion plays a role in ATP binding. Residues of the insertion further seem to affect the tetrameric interface and therefore suggest a special way of communication among the different monomers. In addition, we confirmed that Pf HK is targeted and affected by oxidative posttranslational modifications (oxPTMs). Both S-glutathionylation and S-nitrosation revealed an inhibitory effect on the enzymatic activity of Pf HK.


  • Organizational Affiliation

    Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, D-35392 Giessen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphotransferase
A, B
493PlasmodiumMutation(s): 0 
Gene Names: CK202_5141PFNF54_05159
EC: 2.7.1
UniProt
Find proteins for W7JZC2 (Plasmodium falciparum (isolate NF54))
Explore W7JZC2 
Go to UniProtKB:  W7JZC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW7JZC2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT (Subject of Investigation/LOI)
Query on CIT

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
I [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
J [auth B],
K [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.206 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.24α = 90
b = 125.24β = 90
c = 120.93γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyBE1540/23 2

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Database references