Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 112.32 kDa 
• Atom Count: 6479 
• Modelled Residue Count: 836 
• Deposited Residue Count: 1036 
• Unique protein chains: 2

3MAF

Crystal structure of StSPL (asymmetric form)

• PDB DOI: 10.2210/pdb3MAF/pdb

• Classification: LYASE
• Organism(s): Symbiobacterium thermophilum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-23 Released: 2010-08-18 
• Deposition Author(s): Bourquin, F., Grutter, M.G., Capitani, G.

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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 

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

• PubMed: 20696404 
• DOI: 10.1016/j.str.2010.05.011
• Primary Citation of Related Structures:  
  3MAD, 3MAF, 3MAU, 3MBB, 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sphingosine-1-phosphate lyase	A	518	Symbiobacterium thermophilum	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
sphingosine-1-phosphate lyase	B	518	Symbiobacterium thermophilum	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

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 = 84.19	α = 90
b = 84.9	β = 90
c = 131.32	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-03-23 
• Released Date: 2010-08-18 
Deposition Author(s): Bourquin, F., Grutter, M.G., Capitani, G.

Revision History  

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