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PDBsum entry 2w41

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protein ligands Protein-protein interface(s) links
Transferase PDB id
2w41
Jmol
Contents
Protein chains
506 a.a. *
Ligands
ADP ×2
EDO ×21
Waters ×307
* Residue conservation analysis
PDB id:
2w41
Name: Transferase
Title: Crystal structure of plasmodium falciparum glycerol kinase with adp
Structure: Glycerol kinase, putative. Chain: a, b. Engineered: yes
Source: Plasmodium falciparum. Organism_taxid: 36329. Strain: 3d7. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
2.41Å     R-factor:   0.200     R-free:   0.258
Authors: C.Schnick,S.D.Polley,Q.L.Fivelman,L.Ranford-Cartwright, S.R.Wilkinson,J.A.Brannigan,A.J.Wilkinson,D.A.Baker
Key ref: C.Schnick et al. (2009). Structure and non-essential function of glycerol kinase in Plasmodium falciparum blood stages. Mol Microbiol, 71, 533-545. PubMed id: 19040641
Date:
18-Nov-08     Release date:   02-Dec-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8IDI4  (Q8IDI4_PLAF7) -  Glycerol kinase, putative
Seq:
Struc:
501 a.a.
506 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.30  - Glycerol kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + glycerol = ADP + sn-glycerol 3-phosphate
ATP
+ glycerol
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+
sn-glycerol 3-phosphate
Bound ligand (Het Group name = EDO)
matches with 40.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   4 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
Mol Microbiol 71:533-545 (2009)
PubMed id: 19040641  
 
 
Structure and non-essential function of glycerol kinase in Plasmodium falciparum blood stages.
C.Schnick, S.D.Polley, Q.L.Fivelman, L.C.Ranford-Cartwright, S.R.Wilkinson, J.A.Brannigan, A.J.Wilkinson, D.A.Baker.
 
  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. 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20823846 G.Plata, T.L.Hsiao, K.L.Olszewski, M.Llinás, and D.Vitkup (2010).
Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network.
  Mol Syst Biol, 6, 408.  
20586726 V.Polonais, and D.Soldati-Favre (2010).
Versatility in the acquisition of energy and carbon sources by the Apicomplexa.
  Biol Cell, 102, 435-445.  
19819219 D.W.Pettigrew (2009).
Oligomeric interactions provide alternatives to direct steric modes of control of sugar kinase/actin/hsp70 superfamily functions by heterotropic allosteric effectors: inhibition of E. coli glycerol kinase.
  Arch Biochem Biophys, 492, 29-39.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.