3MAF

Crystal structure of StSPL (asymmetric form)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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:  
    3MAD, 3MAF, 3MBB, 3MAU, 3MC6

  • 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-coupled receptors of the lysophospholipid receptor family, and inside the cell, as a second messenger ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
sphingosine-1-phosphate lyaseA518Symbiobacterium thermophilumMutation(s): 0 
Gene Names: STH1274
EC: 4.1.2.27
UniProt
Find proteins for Q67PY4 (Symbiobacterium thermophilum (strain T / IAM 14863))
Explore Q67PY4 
Go to UniProtKB:  Q67PY4
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
sphingosine-1-phosphate lyaseB518Symbiobacterium thermophilumMutation(s): 0 
Gene Names: STH1274
EC: 4.1.2.27
UniProt
Find proteins for Q67PY4 (Symbiobacterium thermophilum (strain T / IAM 14863))
Explore Q67PY4 
Go to UniProtKB:  Q67PY4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
 D [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
 C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP		AL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.19α = 90
b = 84.9β = 90
c = 131.32γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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