3MAU

Crystal structure of StSPL in complex with phosphoethanolamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and Function of Sphingosine-1-Phosphate Lyase, a Key Enzyme of Sphingolipid Metabolism.

Bourquin, F.Riezman, H.Capitani, G.Grutter, M.G.

(2010) Structure 18: 1054-1065

  • DOI: 10.1016/j.str.2010.05.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sphingosine-1-phosphate lyase (SPL), a key enzyme of sphingolipid metabolism, catalyzes the irreversible degradation of sphingoid base phosphates. Its main substrate sphingosine-1-phosphate (S1P) acts both extracellularly, by binding G protein-couple ...

    Sphingosine-1-phosphate lyase (SPL), a key enzyme of sphingolipid metabolism, catalyzes the irreversible degradation of sphingoid base phosphates. Its main substrate sphingosine-1-phosphate (S1P) acts both extracellularly, by binding G protein-coupled receptors of the lysophospholipid receptor family, and inside the cell, as a second messenger. There, S1P takes part in regulating various cellular processes and its levels are tightly regulated. SPL is a pivotal enzyme regulating S1P intracellular concentrations and a promising drug target for the design of immunosuppressants. We structurally and functionally characterized yeast SPL (Dpl1p) and its first prokaryotic homolog, from Symbiobacterium thermophilum. The Dpl1p structure served as a basis for a very reliable model of Homo sapiens SPL. The above results, together with in vitro and in vivo studies of SPL mutants, reveal which residues are involved in activity and substrate binding and pave the way to studies aimed at controlling the activity of this pivotal enzyme.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
sphingosine-1-phosphate lyase
A, B, C, D
514Symbiobacterium thermophilum (strain T / IAM 14863)Mutation(s): 1 
Find proteins for Q67PY4 (Symbiobacterium thermophilum (strain T / IAM 14863))
Go to UniProtKB:  Q67PY4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EXT
Query on EXT

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Download CCD File 
B, C, D
{5-hydroxy-6-methyl-4-[(E)-{[2-(phosphonooxy)ethyl]imino}methyl]pyridin-3-yl}methyl dihydrogen phosphate
C10 H16 N2 O9 P2
AKRAFIXJWODRLT-VZUCSPMQSA-N
 Ligand Interaction
PLR
Query on PLR

Download SDF File 
Download CCD File 
A
(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
4'-DEOXYPYRIDOXINE PHOSPHATE
C8 H12 N O5 P
RBCOYOYDYNXAFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.229 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 64.360α = 90.00
b = 243.450β = 90.00
c = 280.670γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata processing
PHENIXrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance