6SU1 | pdb_00006su1

Trypanosoma congolense pyruvate kinase in complex with citrate and glycerol

PDB DOI: https://doi.org/10.2210/pdb6SU1/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.257 (Depositor), 0.285 (DCC)
R-Value Work:
0.208 (Depositor)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.molbiopara.2020.111263
Primary Citation 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.

Organizational Affiliation

Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.

Macromolecule Content

Total Structure Weight: 453.72 kDa
Atom Count: 28,228
Modeled Residue Count: 3,765
Deposited Residue Count: 4,112
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B, C, D, E A, B, C, D, E, F, G, H	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0UYF4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT (Subject of Investigation/LOI) Query on CIT Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain Y [auth H] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain Y [auth H] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain Y [auth H]	K [auth B] M [auth C] P [auth D] R [auth E] T [auth F] K [auth B], M [auth C], P [auth D], R [auth E], T [auth F], Y [auth H]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain Y [auth H] Interactions & Density Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain Y [auth H]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain V [auth F] MOL2 format, chain V [auth F] mmCIF format, chain V [auth F]	V [auth F]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain V [auth F] Interactions & Density Focus chain V [auth F]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain W [auth F] MOL2 format, chain W [auth F] mmCIF format, chain W [auth F]	W [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain W [auth F] Interactions & Density Focus chain W [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain U [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] SDF format, chain S [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain U [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] MOL2 format, chain S [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain U [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H] mmCIF format, chain S [auth E]	I [auth A] J [auth A] L [auth B] N [auth C] O [auth C] I [auth A], J [auth A], L [auth B], N [auth C], O [auth C], Q [auth D], S [auth E], U [auth F], X [auth G], Z [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain X [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.257 (Depositor), 0.285 (DCC)
R-Value Work: 0.208 (Depositor)
R-Value Observed: 0.210 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.45	α = 109.74
b = 107.15	β = 90.51
c = 148	γ = 106.78

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-03-04

Deposition Author(s):

Sterckx, Y.G.-J.

Pinto Torres, J.E.

Revision History (Full details and data files)

Version 1.0: 2020-03-04
Type: Initial release
Version 1.1: 2020-03-11
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description