8RVR | pdb_00008rvr

Crystal structure of Trypanosoma congolense pyruvate kinase in complex with a single-domain antibody (TcoPYK-sdAb42) in the presence of sulfate

PDB DOI: https://doi.org/10.2210/pdb8RVR/pdb

Classification: TRANSFERASE
Organism(s): Trypanosoma congolense, Vicugna pacos
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-02 Released: 2025-04-16
Deposition Author(s): Sterckx, Y.G.-J.
Funding Organization(s): Ghent University Special Research Fund (BOF), Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free:
0.275 (Depositor), 0.272 (DCC)
R-Value Work:
0.221 (Depositor), 0.223 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Allosteric inhibition of trypanosomatid pyruvate kinases by a camelid single-domain antibody.

Pinto Torres, J.E., Claes, M., Hendrickx, R., Yuan, M., Smiejkowska, N., Van Wielendaele, P., Hacisuleyman, A., De Winter, H., Muyldermans, S., Michels, P.A.M., Walkinshaw, M.D., Versees, W., Caljon, G., Magez, S., Sterckx, Y.G.

(2025) Elife 13

PubMed: 40163365 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.7554/eLife.100066
Primary Citation of Related Structures:
8RTF, 8RVR

PubMed Abstract:
African trypanosomes are the causative agents of neglected tropical diseases affecting both humans and livestock. Disease control is highly challenging due to an increasing number of drug treatment failures. African trypanosomes are extracellular, blood-borne parasites that mainly rely on glycolysis for their energy metabolism within the mammalian host. Trypanosomal glycolytic enzymes are therefore of interest for the development of trypanocidal drugs. Here, we report the serendipitous discovery of a camelid single-domain antibody (sdAb aka Nanobody) that selectively inhibits the enzymatic activity of trypanosomatid (but not host) pyruvate kinases through an allosteric mechanism. By combining enzyme kinetics, biophysics, structural biology, and transgenic parasite survival assays, we provide a proof-of-principle that the sdAb-mediated enzyme inhibition negatively impacts parasite fitness and growth.

Organizational Affiliation

Laboratory for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB), Brussel, Belgium.

Macromolecule Content

Total Structure Weight: 439.11 kDa
Atom Count: 25,987
Modeled Residue Count: 3,476
Deposited Residue Count: 3,978
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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	514	Trypanosoma congolense	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0UYF4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Camelid single-domain antibody 42 (sdAb42)	G, H, I, J, K G, H, I, J, K, L	149	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLU Query on GLU Download Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain R [auth C] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C]	R [auth C], W [auth D]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain R [auth C] Focus chain W [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain V [auth C] SDF format, chain N [auth B] SDF format, chain M [auth A] SDF format, chain CA [auth F] SDF format, chain BA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain V [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth E]	BA [auth E] CA [auth F] M [auth A] N [auth B] V [auth C] BA [auth E], CA [auth F], M [auth A], N [auth B], V [auth C], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth E] Focus chain CA [auth F] Focus chain M [auth A] Focus chain N [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth F] Focus chain M [auth A] Focus chain N [auth B] Focus chain V [auth C] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain GA [auth J] SDF format, chain FA [auth I] SDF format, chain EA [auth H] SDF format, chain DA [auth G] SDF format, chain AA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain GA [auth J] MOL2 format, chain FA [auth I] MOL2 format, chain EA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain AA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain GA [auth J] mmCIF format, chain FA [auth I] mmCIF format, chain EA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain AA [auth E]	AA [auth E] DA [auth G] EA [auth H] FA [auth I] GA [auth J] AA [auth E], DA [auth G], EA [auth H], FA [auth I], GA [auth J], O [auth B], P [auth B], Q [auth B], S [auth C], T [auth C], U [auth C], X [auth D], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth G] Focus chain EA [auth H] Focus chain FA [auth I] Focus chain GA [auth J] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth G] Focus chain EA [auth H] Focus chain FA [auth I] Focus chain GA [auth J] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free: 0.275 (Depositor), 0.272 (DCC)
R-Value Work: 0.221 (Depositor), 0.223 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.52	α = 90
b = 168.42	β = 90
c = 177.13	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-16

Deposition Author(s):

Sterckx, Y.G.-J.

Funding Organization	Location	Grant Number
Ghent University Special Research Fund (BOF)	Belgium	BOF.STG.2018.0009.01/01N01518
Research Foundation - Flanders (FWO)	Belgium	G013518N
Research Foundation - Flanders (FWO)	Belgium	1137622N