Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 100222.73 
• Atom Count: 6524 
• Residue Count: 831 
• Unique protein chains: 1

3NKN

Crystal structure of mouse autotaxin in complex with 14:0-LPA

• DOI: 10.2210/pdb3NKN/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Homo sapiens


• Deposited: 2010-06-20 Released: 2011-01-19 
• Deposition Author(s): Nishimasu, H., Ishitani, R., Mihara, E., Takagi, J., Aoki, J., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.234 
• R-Value Work: 0.184 

Literature

Crystal structure of autotaxin and insight into GPCR activation by lipid mediators

Nishimasu, H., Okudaira, S., Hama, K., Mihara, E., Dohmae, N., Inoue, A., Ishitani, R., Takagi, J., Aoki, J., Nureki, O.

(2011) Nat.Struct.Mol.Biol. 18: 205-212

• PubMed: 21240269 
• DOI: 10.1038/nsmb.1998
• Primary Citation of Related Structures:  
  3NKR, 3NKQ, 3NKP, 3NKO, 3NKM


• PubMed Abstract: 
  

Autotaxin (ATX, also known as Enpp2) is a secreted lysophospholipase D that hydrolyzes lysophosphatidylcholine to generate lysophosphatidic acid (LPA), a lipid mediator that activates G protein-coupled receptors to evoke various cellular responses. Here, we report the crystal structures of mouse ATX alone and in complex with LPAs with different acyl-chain lengths and saturations. These structures reveal that the multidomain architecture helps to maintain the structural rigidity of the lipid-binding pocket, which accommodates the respective LPA molecules in distinct conformations. They indicate that a loop region in the catalytic domain is a major determinant for the substrate specificity of the Enpp family enzymes. Furthermore, along with biochemical and biological data, these structures suggest that the produced LPAs are delivered from the active site to cognate G protein-coupled receptors through a hydrophobic channel.

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Organizational Affiliation: 

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2	A	831	Mus musculus	Mutation(s): 0  Gene Names: Enpp2 (Npps2, Pdnp2) EC: 3.1.4.39
Find proteins for Q9R1E6 (Mus musculus) Go to UniProtKB:  Q9R1E6

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
SCN	A	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NKN	A	(2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate 14:0 LPA, myristoyl lysophosphatidic acid C17 H35 O7 P FAZBDRGXCKPVJU-MRXNPFEDSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.234 
• R-Value Work: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 61.580	α = 90.00
b = 94.617	β = 94.86
c = 75.372	γ = 90.00

Software Package:

Software Name	Purpose
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-20 
• Released Date: 2011-01-19 
• Deposition Author(s): Nishimasu, H., Ishitani, R., Mihara, E., Takagi, J., Aoki, J., Nureki, O.

Revision History 

• Version 1.0: 2011-01-19
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2014-02-19
  Type: Database references
• Version 1.3: 2017-11-08
  Type: Refinement description