6SU2 | pdb_00006su2

Trypanosoma congolense pyruvate kinase in complex with citrate and glycerol

• PDB DOI: https://doi.org/10.2210/pdb6SU2/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma congolense IL3000
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-09-12 Released: 2020-03-04 
• Deposition Author(s): Sterckx, Y.G.-J., Pinto Torres, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.284 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Literature

Structural and kinetic characterization of Trypanosoma congolense pyruvate kinase.

Pinto Torres, J.E., Yuan, M., Goossens, J., Versees, W., Caljon, G., Michels, P.A., Walkinshaw, M.D., Magez, S., Sterckx, Y.G.

(2020) Mol Biochem Parasitol 236: 111263-111263

• PubMed: 32084384 
• DOI: https://doi.org/10.1016/j.molbiopara.2020.111263
• Primary Citation of Related Structures:  
  6SU1, 6SU2


• PubMed Abstract: 
  

  Trypanosoma are blood-borne parasites and are the causative agents of neglected tropical diseases (NTDs) affecting both humans and animals. These parasites mainly rely on glycolysis for their energy production within the mammalian host, which is why trypanosomal glycolytic enzymes have been pursued as interesting targets for the development of trypanocidal drugs. The structure-function relationships of pyruvate kinases (PYKs) from trypanosomatids (Trypanosoma and Leishmania) have been well-studied within this context. In this paper, we describe the structural and enzymatic characterization of PYK from T. congolense (TcoPYK), the main causative agent of Animal African Trypanosomosis (AAT), by employing a combination of enzymatic assays, thermal unfolding studies and X-ray crystallography.

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Organizational Affiliation: 
• Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Michael Swann Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom.
VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
Laboratory of Microbiology, Parasitology and Hygiene (LMPH) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium.
Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Ghent University Global Campus, Songdomunhwa-Ro 119, Yeonsu-Gu, 406-840 Incheon, South Korea.
Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 227.15 kDa 
• Atom Count: 14,203 
• Modeled Residue Count: 1,974 
• Deposited Residue Count: 2,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B, C, D	514	Trypanosoma congolense IL3000	Mutation(s): 0  Gene Names: TCIL3000_10_12020 EC: 2.7.1.40
UniProt
Find proteins for G0UYF4 (Trypanosoma congolense (strain IL3000)) Explore G0UYF4  Go to UniProtKB:  G0UYF4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FBP (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], K [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N
MG (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.284 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.77	α = 90
b = 182.46	β = 90
c = 244.85	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Sterckx, Y.G.-J., Pinto Torres, J.E.

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2020-03-11
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references, Structure summary