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PDBsum entry 1bot

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1bot
Jmol
Contents
Protein chains
497 a.a. *
Ligands
EPE
GOL ×2
* Residue conservation analysis
PDB id:
1bot
Name: Transferase
Title: Crystal structure of the complex between escherichia coli gl kinase and the allosteric regulator fructose 1,6-bisphospha
Structure: Protein (glycerol kinase). Chain: o, z. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
3.05Å     R-factor:   0.219    
Authors: M.Ormo,C.E.Bystrom,S.J.Remington
Key ref:
M.Ormö et al. (1998). Crystal structure of a complex of Escherichia coli glycerol kinase and an allosteric effector fructose 1,6-bisphosphate. Biochemistry, 37, 16565-16572. PubMed id: 9843423 DOI: 10.1021/bi981616s
Date:
05-Aug-98     Release date:   19-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A6F3  (GLPK_ECOLI) -  Glycerol kinase
Seq:
Struc:
502 a.a.
497 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
Bound ligand (Het Group name = GOL)
corresponds exactly
= ADP
+ sn-glycerol 3-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     metabolic process   7 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi981616s Biochemistry 37:16565-16572 (1998)
PubMed id: 9843423  
 
 
Crystal structure of a complex of Escherichia coli glycerol kinase and an allosteric effector fructose 1,6-bisphosphate.
M.Ormö, C.E.Bystrom, S.J.Remington.
 
  ABSTRACT  
 
The three-dimensional structures of Escherichia coli glycerol kinase (GK) with bound glycerol in the presence and absence of one of the allosteric regulators of its activity, fructose 1,6-bisphosphate (FBP), at 3.2 and 3.0 A, are presented. The molecule crystallized in space group P41212, and the structure was solved by molecular replacement. The models were refined with good stereochemistry to final R-factors of 21.1 and 21.9%, respectively. A tetrameric arrangement of monomers was observed which was essentially identical to the proposed inactive tetramer II previously described [Feese, M. D., Faber, H. R., Bystrom, C. E., Pettigrew, D. W., and Remington, S. J. (1998) Structure (in press)]. However, the crystal packing in this form was especially open, permitting the FBP binding site to be occupied and identified. The crystallographic data revealed a most unusual type of FBP binding site formed between two glycine-arginine loops (residues 234-236) where one-half of the binding site is donated by each monomer at the regulatory interface. The molecule of FBP binds in two mutually exclusive modes on a noncrystallographic 2-fold axis at 50% occupancy each; thus, a tetramer of GK binds two molecules of FBP. Ionic interactions between the 1- and 6-phosphates of FBP and Arg 236 were observed in addition to hydrogen bonding interactions between the backbone amide of Gly 234 and the 6-phosphate. No contacts between the protein and the furanose ring were observed. Mutagenesis of Arg 236 to alanine drastically reduced the extent of inhibition of GK by FBP and lowered, but did not eliminate, the ability of FBP to promote tetramer association. These observations are consistent with the previously characterized mechanism of FBP inhibition of GK, in which FBP acts both to promote dimer-tetramer assembly and to inactivate the tetramers.
 

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
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.  
18997863 P.M.Durand, K.Naidoo, and T.L.Coetzer (2008).
Evolutionary patterning: a novel approach to the identification of potential drug target sites in Plasmodium falciparum.
  PLoS ONE, 3, e3685.  
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
  17277457 R.Katsumi, Y.Koga, D.J.You, H.Matsumura, K.Takano, and S.Kanaya (2007).
Crystallization and preliminary X-ray diffraction study of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 126-129.  
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.  
15573397 D.La, B.Sutch, and D.R.Livesay (2005).
Predicting protein functional sites with phylogenetic motifs.
  Proteins, 58, 309-320.  
15574828 C.Honisch, A.Raghunathan, C.R.Cantor, B...Palsson, and D.van den Boom (2004).
High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12.
  Genome Res, 14, 2495-2502.  
12829462 P.Grayson, E.Tajkhorshid, and K.Schulten (2003).
Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics.
  Biophys J, 85, 36-48.  
12161559 A.C.Pawlyk, and D.W.Pettigrew (2002).
Transplanting allosteric control of enzyme activity by protein-protein interactions: coupling a regulatory site to the conserved catalytic core.
  Proc Natl Acad Sci U S A, 99, 11115-11120.  
11929549 E.Darbon, P.Servant, S.Poncet, and J.Deutscher (2002).
Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P-GlpK dephosphorylation control Bacillus subtilis glpFK expression.
  Mol Microbiol, 43, 1039-1052.  
11344141 C.K.Holtman, A.C.Pawlyk, N.D.Meadow, and D.W.Pettigrew (2001).
Reverse genetics of Escherichia coli glycerol kinase allosteric regulation and glucose control of glycerol utilization in vivo.
  J Bacteriol, 183, 3336-3344.  
11418773 H.S.Huang, T.Inoue, K.Ito, and T.Yoshimoto (2001).
Preliminary crystallographic study of Thermus aquaticus glycerol kinase.
  Acta Crystallogr D Biol Crystallogr, 57, 1030-1031.  
11353844 L.H.Weaver, K.Kwon, D.Beckett, and B.W.Matthews (2001).
Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator.
  Proc Natl Acad Sci U S A, 98, 6045-6050.
PDB code: 1hxd
10759857 I.Králová, D.J.Rigden, F.R.Opperdoes, and P.A.Michels (2000).
Glycerol kinase of Trypanosoma brucei. Cloning, molecular characterization and mutagenesis.
  Eur J Biochem, 267, 2323-2333.  
10636874 J.M.Jault, S.Fieulaine, S.Nessler, P.Gonzalo, A.Di Pietro, J.Deutscher, and A.Galinier (2000).
The HPr kinase from Bacillus subtilis is a homo-oligomeric enzyme which exhibits strong positive cooperativity for nucleotide and fructose 1,6-bisphosphate binding.
  J Biol Chem, 275, 1773-1780.  
10090737 C.E.Bystrom, D.W.Pettigrew, B.P.Branchaud, P.O'Brien, and S.J.Remington (1999).
Crystal structures of Escherichia coli glycerol kinase variant S58-->W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion.
  Biochemistry, 38, 3508-3518.
PDB codes: 1bwf 1glj 1gll
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.