Crystal structure of trypanosoma brucei gambiense glycerol kinase complex with adp, mg2+, and glycerol

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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Molecular basis for the reverse reaction of African human trypanosomes glycerol kinase.

Balogun, E.O.Inaoka, D.K.Shiba, T.Kido, Y.Tsuge, C.Nara, T.Aoki, T.Honma, T.Tanaka, A.Inoue, M.Matsuoka, S.Michels, P.A.Kita, K.Harada, S.

(2014) Mol Microbiol 94: 1315-1329

  • DOI: https://doi.org/10.1111/mmi.12831
  • Primary Citation of Related Structures:  
    3WXI, 3WXJ, 3WXK, 3WXL

  • PubMed Abstract: 

    The glycerol kinase (GK) of African human trypanosomes is compartmentalized in their glycosomes. Unlike the host GK, which under physiological conditions catalyzes only the forward reaction (ATP-dependent glycerol phosphorylation), trypanosome GK can additionally catalyze the reverse reaction. In fact, owing to this unique reverse catalysis, GK is potentially essential for the parasites survival in the human host, hence a promising drug target. The mechanism of its reverse catalysis was unknown; therefore, it was not clear if this ability was purely due to its localization in the organelles or whether structure-based catalytic differences also contribute. To investigate this lack of information, the X-ray crystal structure of this protein was determined up to 1.90 Å resolution, in its unligated form and in complex with three natural ligands. These data, in conjunction with results from structure-guided mutagenesis suggests that the trypanosome GK is possibly a transiently autophosphorylating threonine kinase, with the catalytic site formed by non-conserved residues. Our results provide a series of structural peculiarities of this enzyme, and gives unexpected insight into the reverse catalysis mechanism. Together, they provide an encouraging molecular framework for the development of trypanosome GK-specific inhibitors, which may lead to the design of new and safer trypanocidal drug(s).

  • Organizational Affiliation

    Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; Department of Biochemistry, Ahmadu Bello University, Zaria, 2222, Nigeria.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol kinase
A, B, C, D
518Trypanosoma brucei gambienseMutation(s): 0 
Gene Names: gk
Find proteins for D3KVM3 (Trypanosoma brucei gambiense)
Explore D3KVM3 
Go to UniProtKB:  D3KVM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3KVM3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
I [auth B],
O [auth D],
P [auth D]
C10 H15 N5 O10 P2
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
G [auth B]
K [auth C]
L [auth C]
M [auth C]
E [auth A],
G [auth B],
K [auth C],
L [auth C],
M [auth C],
N [auth D]
C3 H8 O3
Query on MG

Download Ideal Coordinates CCD File 
J [auth B],
Q [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.115α = 90
b = 153.84β = 89.95
c = 120.098γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations