8PRY | pdb_00008pry

Crystal structure of Trypanosoma cruzi glycerol kinase

• PDB DOI: https://doi.org/10.2210/pdb8PRY/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-12 Released: 2024-07-24 
• Deposition Author(s): Lipinski, O., Sonani, R.R., Dubin, G.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of glycerol kinase from Trypanosoma cruzi, a potential molecular target in Chagas disease.

Lipinski, O., Sonani, R.R., Dubin, G.

(2024) Acta Crystallogr D Struct Biol 80: 629-638

• PubMed: 39052317 
• DOI: https://doi.org/10.1107/S2059798324006594
• Primary Citation of Related Structures:  
  8PRY


• PubMed Abstract: 
  

  Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. It bears a significant global health burden with limited treatment options, thus calling for the development of new and effective drugs. Certain trypanosomal metabolic enzymes have been suggested to be druggable and valid for subsequent inhibition. In this study, the crystal structure of glycerol kinase from T. cruzi, a key enzyme in glycerol metabolism in this parasite, is presented. Structural analysis allowed a detailed description of the glycerol binding pocket, while comparative assessment pinpointed a potential regulatory site which may serve as a target for selective inhibition. These findings advance the understanding of glycerol metabolism in eukaryotes and provide a solid basis for the future treatment of Chagas disease.

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Organizational Affiliation: 
• Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 233.45 kDa 
• Atom Count: 16,378 
• Modeled Residue Count: 2,046 
• Deposited Residue Count: 2,092 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerol kinase	A, B, C, D	523	Trypanosoma cruzi	Mutation(s): 0  Gene Names: C4B63_2g784 EC: 2.7.1.30
UniProt
Find proteins for V5BY50 (Trypanosoma cruzi Dm28c) Explore V5BY50  Go to UniProtKB:  V5BY50

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.779	α = 117.35
b = 89.321	β = 88.99
c = 97.155	γ = 93.68

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Lipinski, O., Sonani, R.R., Dubin, G.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2020/39/B/NZ1/01551

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary
• Version 1.2: 2025-02-05
  Changes: Database references