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Structure of IDP00743

2.7 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with ADP and Glycerol

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CSGID target
IDP00743 
PDB Id
3GE1 (NCBI MMDB) 
Authors
G.Minasov,J.Brunzelle,T.Skarina,O.Onopriyenko,S.N.Peterson,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Feb 24, 2009 
Release Date
Mar 24, 2009 

Annotation

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Description
Glycerol kinase (GlpK) is a phosphotransferase that is involved in lipolyses, the breakdown of fat stored in fat cells and release of free fatty acids into the bloodstream. GlpK catalyzes the transfer of a phosphate from ATP to glycerol in the presence of Mg2+, thus forming glycerol 3-phosphate and ADP. GlpK has three allosteric effectors with indipendent mechanism: fructose 1,6-bisphosphate (FBP); the phosphocarrier protein IIAGlc; and adenosinemonophosphate (AMP). The product of the reaction, glycerol 3-phospate, may then be converted to dihydroxyacetone phosphate (DHAP) by the enzyme glycerol-3-phosphate dehydrogenase. DHAP can then be rearranged into glyceraldehyde 3-phosphate(GA3P) by triose phosphate isomerase(TIM), and feed into glycolysis. Another important role of the glycerol 3-phosphate is involvement in the glycerol-3-phosphate shuttle, a mechanism used to rapidly regenerate NAD+ in brain and skeletal muscle cells of mammals. The glycerol is a central component of many lipids most well-known as triglycerides, and glycerophospholipids, or phospholipids, are a major component of all cell membranes. 
Functional assignment
Glycerol Kinase 
Slides:
  • Asymmetric unit
  • Biological unit
  • B-factors distribution
  • B-factors distribution on the surface
  • Homolog superposition
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    Ligands

    Ligand code Name Ligand type
    ADP adenosine-5'-diphosphate biological
    GOL glycerol biological
    PO4 phosphate ion crystallization
    CL chloride ion crystallization
    MSE selenomethionine modified residue

    Structure information

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    Unit cell parameters

    Space Group
    P 1 21 1  
    Unit Cell

    a=63.41Å, b=193.65Å, c=91.84Å
    α=90.00, β=106.01, γ=90.00  
    Solvent content
    48.74  
    Matthews coefficient
    2.4  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    30.00-2.70Å (2.77-2.70Å)  
    Rall(%)
    19.4  
    Rwork(%)
    19.1 (32.1)  
    Rfree(%)
    25.3 (38.6)  
    Num. observed reflections
    56310 (3386)  
    Num. Rfree reflections
    2871 (193)  
    Completeness(%)
    96.8 (79.0)  

    Model parameters

    Num Atoms
    15334  
    Num Waters
    274  
    Num Hetatoms
    795  
    Model mean isotropic B factor (Å2)
    32.810  
    RMSD bond length (Å)
    0.007  
    RMSD bond angle
    1.011°  
    Filename uploaded
    rcsb051743.pdb (uploaded on Mar 18, 2009 5:21 PM)  
    Inserted
    Mar 27, 2009