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PDBsum entry 1glf

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1glf
Jmol
Contents
Protein chains
498 a.a. *
Ligands
PO4 ×2
ADP ×4
GOL ×4
Waters ×200
* Residue conservation analysis
PDB id:
1glf
Name: Transferase
Title: Crystal structures of escherichia coli glycerol kinase and t a65t in an inactive tetramer: conformational changes and im for allosteric regulation
Structure: Protein (glycerol kinase). Chain: o, y, z, x. Engineered: yes. Other_details: glycerol adenosine diphosphate orthophosphat
Source: Escherichia coli. Organism_taxid: 562. Gene: glpk. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.62Å     R-factor:   0.146    
Authors: M.D.Feese,H.R.Faber,C.E.Bystrom,D.W.Pettigrew,S.J.Remington
Key ref:
M.D.Feese et al. (1998). Glycerol kinase from Escherichia coli and an Ala65-->Thr mutant: the crystal structures reveal conformational changes with implications for allosteric regulation. Structure, 6, 1407-1418. PubMed id: 9817843 DOI: 10.1016/S0969-2126(98)00140-3
Date:
30-Aug-98     Release date:   16-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A6F3  (GLPK_ECOLI) -  Glycerol kinase
Seq:
Struc:
502 a.a.
498 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
Bound ligand (Het Group name = ADP)
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!
  Cellular component     cytosol   1 term 
  Biological process     metabolic process   7 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(98)00140-3 Structure 6:1407-1418 (1998)
PubMed id: 9817843  
 
 
Glycerol kinase from Escherichia coli and an Ala65-->Thr mutant: the crystal structures reveal conformational changes with implications for allosteric regulation.
M.D.Feese, H.R.Faber, C.E.Bystrom, D.W.Pettigrew, S.J.Remington.
 
  ABSTRACT  
 
BACKGROUND: Glycerol kinase (GK) from Escherichia coli is a velocity-modulated (V system) enzyme that has three allosteric effectors with independent mechanisms: fructose-1,6-bisphosphate (FBP); the phosphocarrier protein IIAGlc; and adenosine nucleotides. The enzyme exists in solution as functional dimers that associate reversibly to form tetramers. GK is a member of a superfamily of ATPases that share a common ATPase domain and are thought to undergo a large conformational change as an intrinsic step in their catalytic cycle. Members of this family include actin, hexokinase and the heat shock protein hsc70. RESULTS: We report here the crystal structures of GK and a mutant of GK (Ala65-->Thr) in complex with glycerol and ADP. Crystals of both enzymes contain the same 222 symmetric tetramer. The functional dimer is identical to that described previously for the IIAGlc-GK complex structure. The tetramer interface is significantly different, however, with a relative 22.3 degrees rotation and 6.34 A translation of one functional dimer. The overall monomer structure is unchanged except for two regions: the IIAGlc-binding site undergoes a structural rearrangement and residues 230-236 become ordered and bind orthophosphate at the tetramer interface. We also report the structure of a second mutant of GK (IIe474-->Asp) in complex with IIAGlc; this complex crystallized isomorphously to the wild type IIAGlc-GK complex. Site-directed mutants of GK with substitutions at the IIAGlc-binding site show significantly altered kinetic and regulatory properties, suggesting that the conformation of the binding site is linked to the regulation of activity. CONCLUSIONS: We conclude that the new tetramer structure presented here is an inactive form of the physiologically relevant tetramer. The structure and location of the orthophosphate-binding site is consistent with it being part of the FBP-binding site. Mutational analysis and the structure of the IIAGlc-GK(IIe474-->Asp) complex suggest the conformational transition of the IIAGlc-binding site to be an essential aspect of IIAGlc regulation.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Stereoview of one loop of the orthophosphate-binding site of the GK tetramer II. The bound orthophosphate molecule is shown with open bonds. Apparent hydrogen bonds between the bound orthophosphate and the protein and one bound water molecular are shown as thin lines with labels showing the interatomic distances (in ).
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 1407-1418) copyright 1998.  
  Figure was selected by the author.  

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.  
18560157 M.Sugahara, Y.Asada, Y.Morikawa, Y.Kageyama, and N.Kunishima (2008).
Nucleant-mediated protein crystallization with the application of microporous synthetic zeolites.
  Acta Crystallogr D Biol Crystallogr, 64, 686-695.
PDB codes: 1wmm 2dpn 2hd9 2zbn
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
17999468 A.Gorrell, and J.G.Ferry (2007).
Investigation of the Methanosarcina thermophila acetate kinase mechanism by fluorescence quenching.
  Biochemistry, 46, 14170-14176.  
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.  
12636049 C.Hellerud, A.Burlina, C.Gabelli, J.R.Ellis, P.G.Nyholm, and S.Lindstedt (2003).
Glycerol metabolism and the determination of triglycerides--clinical, biochemical and molecular findings in six subjects.
  Clin Chem Lab Med, 41, 46-55.  
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.  
12829458 T.Schlick (2003).
Engineering teams up with computer-simulation and visualization tools to probe biomolecular mechanisms.
  Biophys J, 85, 1-4.  
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.  
11080166 A.Hofmann, A.Zdanov, P.Genschik, S.Ruvinov, W.Filipowicz, and A.Wlodawer (2000).
Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction.
  EMBO J, 19, 6207-6217.
PDB code: 1fsi
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.  
10734184 W.G.Krebs, and M.Gerstein (2000).
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.
  Nucleic Acids Res, 28, 1665-1675.  
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.