9GMP | pdb_00009gmp

TKUL kinase domain from Leishmania mexicana

• PDB DOI: https://doi.org/10.2210/pdb9GMP/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Leishmania mexicana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-29 Released: 2025-09-24 
• Deposition Author(s): Fokkens, T.J., Wolter, M., Lorenz, S.
• Funding Organization(s): European Molecular Biology Organization (EMBO), Max Planck Society, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

A Leishmania virulence factor harnesses an allosteric kinase switch to regulate its ubiquitin ligase activity.

Fokkens, T.J., Rauh, E.T., Wolter, M., Sebald, H., Mitnacht, M., Ainatzi, S., Sprick, S., Teschke, L., Eisenhuth, N., Huibregtse, J.M., Butter, F., Urlaub, H., Karnkowska, A., Steinchen, W., Schleicher, U., Janzen, C.J., Lorenz, S.

(2025) Mol Cell 85: 3711-3728.e11

• PubMed: 40997810 
• DOI: https://doi.org/10.1016/j.molcel.2025.09.002
• Primary Citation Related Structures: 
  9GMP


• PubMed Abstract: 
  

  Stringent control of ubiquitylation is a central requirement of signaling specificity in eukaryotes. Here, we discover a domain module integrating protein kinase and ubiquitin ligase domains within a single protein. This module is widespread across unicellular eukaryotic lineages and particularly conserved in Leishmania, the causative agents of major neglected tropical diseases with a strong therapeutic need. We reveal that a gene encoding the module, tetratricopeptide repeat (TPR)-kinase-ubiquitin ligase (TKUL), is essential for L. mexicana to sustain macrophage infections and that TKUL can cooperate with parasite heat shock protein 70 (HSP70) to modify unfolded proteins with degradative ubiquitin chains. Intriguingly, the homologous to E6AP C-terminus (HECT)-type ubiquitin ligase activity of TKUL requires its atypical kinase domain, with kinase autophosphorylation triggering activating conformational changes across the catalytic module. Consistent with the ligase domain harnessing the kinase domain for regulation, TKUL-driven ubiquitylation can allosterically be suppressed by small-molecule kinase inhibitors. Together, this work establishes an unprecedented allosteric coupling mechanism in the realms of phosphorylation and ubiquitylation.

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Organizational Affiliation: 
• Research Group "Ubiquitin Signaling Specificity," Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.
Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97072 Würzburg, Germany.
Institut für Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.
Research Group "Bioanalytical Mass Spectrometry," Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Bioanalytics, University Medical Center, 37075 Göttingen, Germany.
Institute of Molecular Virology and Cell Biology, Friedrich Loeffler Institute, 17493 Greifswald, Germany.
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, 02-089 Warsaw, Poland.
Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany.
Research Group "Ubiquitin Signaling Specificity," Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.35 kDa 
• Atom Count: 1,972 
• Modeled Residue Count: 241 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein (Map kinase kinase-like protein)	A	285	Leishmania mexicana	Mutation(s): 0  Gene Names: LMXM_34_4000
UniProt
Find proteins for E9B6S8 (Leishmania mexicana (strain MHOM/GT/2001/U1103)) Explore E9B6S8  Go to UniProtKB:  E9B6S8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.092	α = 90
b = 74.565	β = 90
c = 77.734	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Fokkens, T.J., Wolter, M., Lorenz, S.

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Funding Organization	Location	Grant Number
European Molecular Biology Organization (EMBO)	European Union	439-2022
Max Planck Society	Germany	--
German Research Foundation (DFG)	Germany	GRK2243

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release
  
• Version 1.1: 2026-04-08
  Changes: Database references