PDBsum entry 3h46

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protein ligands Protein-protein interface(s) links
Transferase PDB id
Protein chains
500 a.a. *
SO4 ×2
GOL ×2
EDO ×2
Waters ×193
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Glycerol kinase h232e with glycerol
Structure: Glycerol kinase. Chain: x, o. Synonym: atp:glycerol 3-phosphotransferase, glycerokinase, engineered: yes. Mutation: yes
Source: Enterococcus casseliflavus. Enterococcus flavescens. Organism_taxid: 37734. Gene: glpk. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.75Å     R-factor:   0.194     R-free:   0.228
Authors: J.I.Yeh,R.D.Kettering
Key ref: J.I.Yeh et al. (2009). Structural characterizations of glycerol kinase: unraveling phosphorylation-induced long-range activation. Biochemistry, 48, 346-356. PubMed id: 19102629
17-Apr-09     Release date:   02-Jun-09    
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Protein chains
Pfam   ArchSchema ?
O34153  (GLPK_ENTCA) -  Glycerol kinase
506 a.a.
500 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Glycerol kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + glycerol = ADP + sn-glycerol 3-phosphate
Bound ligand (Het Group name = GOL)
corresponds exactly
+ sn-glycerol 3-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   5 terms 
  Biochemical function     nucleotide binding     6 terms  


Biochemistry 48:346-356 (2009)
PubMed id: 19102629  
Structural characterizations of glycerol kinase: unraveling phosphorylation-induced long-range activation.
J.I.Yeh, R.Kettering, R.Saxl, A.Bourand, E.Darbon, N.Joly, P.Briozzo, J.Deutscher.
Glycerol metabolism provides a central link between sugar and fatty acid catabolism. In most bacteria, glycerol kinase plays a crucial role in regulating channel/facilitator-dependent uptake of glycerol into the cell. In the firmicute Enterococcus casseliflavus, this enzyme's activity is enhanced by phosphorylation of the histidine residue (His232) located in its activation loop, approximately 25 A from its catalytic cleft. We reported earlier that some mutations of His232 altered enzyme activities; we present here the crystal structures of these mutant GlpK enzymes. The structure of a mutant enzyme with enhanced enzymatic activity, His232Arg, reveals that residues at the catalytic cleft are more optimally aligned to bind ATP and mediate phosphoryl transfer. Specifically, the position of Arg18 in His232Arg shifts by approximately 1 A when compared to its position in wild-type (WT), His232Ala, and His232Glu enzymes. This new conformation of Arg18 is more optimally positioned at the presumed gamma-phosphate location of ATP, close to the glycerol substrate. In addition to structural changes exhibited at the active site, the conformational stability of the activation loop is decreased, as reflected by an approximately 35% increase in B factors ("thermal factors") in a mutant enzyme displaying diminished activity, His232Glu. Correlating conformational changes to alteration of enzymatic activities in the mutant enzymes identifies distinct localized regions that can have profound effects on intramolecular signal transduction. Alterations in pairwise interactions across the dimer interface can communicate phosphorylation states over 25 A from the activation loop to the catalytic cleft, positioning Arg18 to form favorable interactions at the beta,gamma-bridging position with ATP. This would offset loss of the hydrogen bonds at the gamma-phosphate of ATP during phosphoryl transfer to glycerol, suggesting that appropriate alignment of the second substrate of glycerol kinase, the ATP molecule, may largely determine the rate of glycerol 3-phosphate production.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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