2W40

Crystal structure of Plasmodium falciparum glycerol kinase with bound glycerol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure and Non-Essential Function of Glycerol Kinase in Plasmodium Falciparum Blood Stages.

Schnick, C., Polley, S.D., Fivelman, Q.L., Ranford-Cartwright, L., Wilkinson, S.R., Brannigan, J.A., Wilkinson, A.J., Baker, D.A.

(2009) Mol Microbiol 71: 533

  • DOI: 10.1111/j.1365-2958.2008.06544.x
  • Primary Citation of Related Structures:  
    2W40, 2W41

  • PubMed Abstract: 

    • Malaria pathology is caused by multiplication of asexual parasites within erythrocytes, whereas mosquito transmission of malaria is mediated by sexual precursor cells (gametocytes). Microarray analysis identified glycerol kinase (GK) as the second most highly upregulated gene in Plasmodium falciparum gametocytes with no expression detectable in asexual blood stage parasites ...

    Malaria pathology is caused by multiplication of asexual parasites within erythrocytes, whereas mosquito transmission of malaria is mediated by sexual precursor cells (gametocytes). Microarray analysis identified glycerol kinase (GK) as the second most highly upregulated gene in Plasmodium falciparum gametocytes with no expression detectable in asexual blood stage parasites. Phosphorylation of glycerol by GK is the rate-limiting step in glycerol utilization. Deletion of this gene from P. falciparum had no effect on asexual parasite growth, but surprisingly also had no effect on gametocyte development or exflagellation, suggesting that these life cycle stages do not utilize host-derived glycerol as a carbon source. Kinetic studies of purified PfGK showed that the enzyme is not regulated by fructose 1,6 bisphosphate. The high-resolution crystal structure of P. falciparum GK, the first of a eukaryotic GK, reveals two domains embracing a capacious ligand-binding groove. In the complexes of PfGK with glycerol and ADP, we observed closed and open forms of the active site respectively. The 27 degree domain opening is larger than in orthologous systems and exposes an extensive surface with potential for exploitation in selective inhibitor design should the enzyme prove to be essential in vivo either in the human or in the mosquito.

    Organizational Affiliation: 

    Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCEROL KINASE, PUTATIVEA, B, C, D503Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1351600
EC: 2.7.1.30
UniProt
Find proteins for Q8IDI4 (Plasmodium falciparum (isolate 3D7))
Explore Q8IDI4 
Go to UniProtKB:  Q8IDI4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IDI4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
EB [auth C],
FB [auth C],
GB [auth C],
HB [auth C],
IB [auth C],
EB [auth C],
FB [auth C],
GB [auth C],
HB [auth C],
IB [auth C],
JA [auth B],
JB [auth C],
KA [auth B],
KB [auth C],
N [auth A],
O [auth A],
ZB [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth B],
AB [auth C],
BA [auth B],
BB [auth C],
CA [auth B],
AA [auth B],
AB [auth C],
BA [auth B],
BB [auth C],
CA [auth B],
CB [auth C],
DA [auth B],
DB [auth C],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
K [auth A],
L [auth A],
LA [auth C],
LB [auth D],
M [auth A],
MA [auth C],
MB [auth D],
NA [auth C],
NB [auth D],
OA [auth C],
OB [auth D],
P [auth B],
PA [auth C],
PB [auth D],
Q [auth B],
QA [auth C],
QB [auth D],
R [auth B],
RA [auth C],
RB [auth D],
S [auth B],
SA [auth C],
SB [auth D],
T [auth B],
TA [auth C],
TB [auth D],
U [auth B],
UA [auth C],
UB [auth D],
V [auth B],
VA [auth C],
VB [auth D],
W [auth B],
WA [auth C],
WB [auth D],
X [auth B],
XA [auth C],
XB [auth D],
Y [auth B],
YA [auth C],
YB [auth D],
Z [auth B],
ZA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.915α = 90
b = 100.717β = 92.56
c = 107.812γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance