To see full content of that page you need the activeISee plugin.
Get the latest version from here.

Structure of IDP00743

1.9 ANGSTROM CRYSTAL STRUCTURE OF GLYCEROL KINASE (GLPK) FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH GLYCEROL

Edit deposit information
CSGID target
IDP00743 
PDB Id
3G25 (NCBI MMDB
Authors
G.Minasov,T.Skarina,O.Onopriyenko,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Jan 30, 2009 
Release Date
Feb 17, 2009 

Annotation

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 

Ligands

Ligand code Name Ligand type
NA Sodium ion crystallization
PO4 PHOSPHATE ION crystallization
MSE modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=63.75Å, b=193.74Å, c=91.67Å
α=90.00, β=103.60, γ=90.00 
Solvent content
49.5  
Matthews coefficient
2.44  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
44.81-1.90Å (1.95-1.90Å)  
Rall(%)
19.5 
Rwork(%)
19.3 (23.5) 
Rfree(%)
24.6 (28.2) 
Num. observed reflections
168209 (12247) 
Num. Rfree reflections
8410 (599) 
Completeness(%)
99.8 (98.5) 

Model parameters

Num Atoms
16095  
Num Waters
1174  
Num Hetatoms
1761  
Model mean isotropic B factor
15.060Å2  
RMSD bond length
0.014Å  
RMSD bond angle
1.679°  
Filename uploaded
rcsb051327.pdb (uploaded on Feb 13, 2009 2:57 PM)  
Inserted
Mar 27, 2009