PDBsum entry 1r59

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Transferase PDB id
Protein chains
480 a.a. *
Waters ×102
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Enterococcus casseliflavus glycerol kinase
Structure: Glycerol kinase. Chain: o, x. Fragment: glycerol kinase. Synonym: atp:glycerol 3-phosphotransferase, glycerokinase, gk. Engineered: yes
Source: Enterococcus casseliflavus. Organism_taxid: 37734. Gene: glpk. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.50Å     R-factor:   0.221     R-free:   0.243
Authors: J.I.Yeh,V.Charrier,J.Paulo,L.Hou,E.Darbon,A.Claiborne, W.G.Hol,J.Deutscher
Key ref:
J.I.Yeh et al. (2004). Structures of enterococcal glycerol kinase in the absence and presence of glycerol: correlation of conformation to substrate binding and a mechanism of activation by phosphorylation. Biochemistry, 43, 362-373. PubMed id: 14717590 DOI: 10.1021/bi034258o
09-Oct-03     Release date:   12-Oct-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O34153  (GLPK_ENTCA) -  Glycerol kinase
506 a.a.
480 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Glycerol kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + glycerol = ADP + sn-glycerol 3-phosphate
+ glycerol
+ 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  


DOI no: 10.1021/bi034258o Biochemistry 43:362-373 (2004)
PubMed id: 14717590  
Structures of enterococcal glycerol kinase in the absence and presence of glycerol: correlation of conformation to substrate binding and a mechanism of activation by phosphorylation.
J.I.Yeh, V.Charrier, J.Paulo, L.Hou, E.Darbon, A.Claiborne, W.G.Hol, J.Deutscher.
The first structure of a glycerol kinase from a Gram-positive organism, Enterococcus casseliflavus, has been determined to 2.8 A resolution in the presence of glycerol and to 2.5 A resolution in the absence of substrate. The substrate-induced closure of 7 degrees is significantly smaller than that reported for hexokinase, a model for substrate-mediated domain closure that has been proposed for glycerol kinase. Despite the 78% level of sequence identity and conformational similarity in the catalytic cleft regions of the En. casseliflavus and Escherichia coli glycerol kinases, remarkable structural differences have now been identified. These differences correlate well with their divergent regulatory schemes of activation by phosphorylation in En. casseliflavus and allosteric inhibition in E. coli. On the basis of our structural results, we propose a mechanism by which the phosphorylation of a histidyl residue located 25 A from the active site results in a 10-15-fold increase in the activity of the enterococcal glycerol kinase.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19040641 C.Schnick, S.D.Polley, Q.L.Fivelman, L.C.Ranford-Cartwright, S.R.Wilkinson, J.A.Brannigan, A.J.Wilkinson, and D.A.Baker (2009).
Structure and non-essential function of glycerol kinase in Plasmodium falciparum blood stages.
  Mol Microbiol, 71, 533-545.
PDB codes: 2w40 2w41
19056335 D.W.Pettigrew (2009).
Amino acid substitutions in the sugar kinase/hsp70/actin superfamily conserved ATPase core of E. coli glycerol kinase modulate allosteric ligand affinity but do not alter allosteric coupling.
  Arch Biochem Biophys, 481, 151-156.  
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.  
18296637 J.I.Yeh, U.Chinte, and S.Du (2008).
Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.
  Proc Natl Acad Sci U S A, 105, 3280-3285.
PDB codes: 2qcu 2r45 2r46 2r4e 2r4j
18422647 Y.Koga, R.Katsumi, D.J.You, H.Matsumura, K.Takano, and S.Kanaya (2008).
Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form.
  FEBS J, 275, 2632-2643.
PDB code: 2zf5
17123542 E.Di Luccio, B.Petschacher, J.Voegtli, H.T.Chou, H.Stahlberg, B.Nidetzky, and D.K.Wilson (2007).
Structural and kinetic studies of induced fit in xylulose kinase from Escherichia coli.
  J Mol Biol, 365, 783-798.
PDB codes: 2itm 2nlx
17158705 J.Deutscher, C.Francke, and P.W.Postma (2006).
How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.
  Microbiol Mol Biol Rev, 70, 939.  
16009937 T.Hibuse, N.Maeda, T.Funahashi, K.Yamamoto, A.Nagasawa, W.Mizunoya, K.Kishida, K.Inoue, H.Kuriyama, T.Nakamura, T.Fushiki, S.Kihara, and I.Shimomura (2005).
Aquaporin 7 deficiency is associated with development of obesity through activation of adipose glycerol kinase.
  Proc Natl Acad Sci U S A, 102, 10993-10998.  
15231787 A.Mazé, G.Boël, S.Poncet, I.Mijakovic, Y.Le Breton, A.Benachour, V.Monedero, J.Deutscher, and A.Hartke (2004).
The Lactobacillus casei ptsHI47T mutation causes overexpression of a LevR-regulated but RpoN-independent operon encoding a mannose class phosphotransferase system.
  J Bacteriol, 186, 4543-4555.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.