5AZI

Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with 4NP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Glycerol kinase of African trypanosomes possesses an intrinsic phosphatase activity.

Balogun, E.O.Inaoka, D.K.Shiba, T.Tokuoka, S.M.Tokumasu, F.Sakamoto, K.Kido, Y.Michels, P.A.M.Watanabe, Y.I.Harada, S.Kita, K.

(2017) Biochim Biophys Acta Gen Subj 1861: 2830-2842

  • DOI: https://doi.org/10.1016/j.bbagen.2017.07.028
  • Primary Citation of Related Structures:  
    5AZI, 5AZJ

  • PubMed Abstract: 

    In general, glycerol kinases (GKs) are transferases that catalyze phospho group transfer from ATP to glycerol, and the mechanism was suggested to be random bi-bi. The reverse reaction i.e. phospho transfer from glycerol 3-phosphate (G3P) to ADP is only physiologically feasible by the African trypanosome GK. In contrast to other GKs the mechanism of Trypanosoma brucei gambiense glycerol kinase (TbgGK) was shown to be in an ordered fashion, and proceeding via autophosphorylation. From the unique reaction mechanism of TbgGK, we envisaged its potential to possess phosphatase activity in addition to being a kinase. Our hypothesis was tested by spectrophotometric and LC-MS/MS analyses using paranitrophenyl phosphate (pNPP) and TbgGK's natural substrate, G3P respectively. Furthermore, protein X-ray crystallography and site-directed mutagenesis were performed to examine pNPP binding, catalytic residues, and the possible reaction mechanism. In addition to its widely known and expected phosphotransferase (class II) activity, TbgGK can efficiently facilitate the hydrolytic cleavage of phosphoric anhydride bonds (a class III property). This phosphatase activity followed the classical Michaelis-Menten pattern and was competitively inhibited by ADP and G3P, suggesting a common catalytic site for both activities (phosphatase and kinase). The structure of the TGK-pNPP complex, and structure-guided mutagenesis implicated T276 to be important for the catalysis. Remarkably, we captured a crystallographic molecular snapshot of the phosphorylated T276 reaction intermediate. We conclude that TbgGK has both kinase and phosphatase activities. This is the first report on a bifunctional kinase/phosphatase enzyme among members of the sugar kinase family.


  • Organizational Affiliation

    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. Electronic address: balogun1@m.u-tokyo.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol kinase
A, C
518Trypanosoma brucei gambienseMutation(s): 0 
Gene Names: gk
EC: 2.7.1.30
UniProt
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol kinase
B, D
518Trypanosoma brucei gambienseMutation(s): 0 
Gene Names: gk
EC: 2.7.1.30
UniProt
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.669α = 90
b = 120.253β = 89.96
c = 154.593γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary