3VZB image
Entry Detail
PDB ID:
3VZB
Title:
Crystal structure of Sphingosine Kinase 1
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2012-10-10
Release Date:
2013-05-08
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Sphingosine kinase 1
Chain IDs:A, B, C
Chain Length:360
Number of Molecules:3
Biological Source:Homo sapiens
Primary Citation
Molecular basis of sphingosine kinase 1 substrate recognition and catalysis.
Structure 21 798 809 (2013)
PMID: 23602659 DOI: 10.1016/j.str.2013.02.025

Abstact

Sphingosine kinase 1 (SphK1) is a lipid kinase that catalyzes the conversion of sphingosine to sphingosine-1-phosphate (S1P), which has been shown to play a role in lymphocyte trafficking, angiogenesis, and response to apoptotic stimuli. As a central enzyme in modulating the S1P levels in cells, SphK1 emerges as an important regulator for diverse cellular functions and a potential target for drug discovery. Here, we present the crystal structures of human SphK1 in the apo form and in complexes with a substrate sphingosine-like lipid, ADP, and an inhibitor at 2.0-2.3 Å resolution. The SphK1 structures reveal a two-domain architecture in which its catalytic site is located in the cleft between the two domains and a hydrophobic lipid-binding pocket is buried in the C-terminal domain. Comparative analysis of these structures with mutagenesis and kinetic studies provides insight into how SphK1 recognizes the lipid substrate and catalyzes ATP-dependent phosphorylation.

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