5AZJ

Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with 4NP (with disulfide bridge)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.bbagen.2017.07.028
  • Structures With Same Primary Citation

  • 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 on ...

    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.


    Organizational Affiliation

    Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; School of Tropical Medicine and Global Health, Nagasaki University 1-12-4, Sakamoto, Nagasaki 852-8523, Japan. Electronic address: kitak@nagasaki-u.ac.jp.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol kinaseA, C518Trypanosoma brucei gambienseMutation(s): 0 
Gene Names: gk
EC: 2.7.1.30
Find proteins for D3KVM3 (Trypanosoma brucei gambiense)
Explore D3KVM3 
Go to UniProtKB:  D3KVM3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glycerol kinaseB, D518Trypanosoma brucei gambienseMutation(s): 0 
Gene Names: gk
EC: 2.7.1.30
Find proteins for D3KVM3 (Trypanosoma brucei gambiense)
Explore D3KVM3 
Go to UniProtKB:  D3KVM3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4NP
Query on 4NP

Download CCD File 
A, C
4-NITROPHENYL PHOSPHATE
C6 H6 N O6 P
XZKIHKMTEMTJQX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, C, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
B,DL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.737α = 90
b = 120.031β = 90.02
c = 154.706γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Data collection, Database references, Derived calculations