3NKP

Crystal structure of mouse autotaxin in complex with 18:1-LPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.751 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1038/nsmb.1998
  • Primary Citation of Related Structures:  

  • 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. H ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
A
831Mus musculusGene Names: Enpp2 (Npps2, Pdnp2)
EC: 3.1.4.39
Find proteins for Q9R1E6 (Mus musculus)
Go to UniProtKB:  Q9R1E6
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

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A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
EDO
Query on EDO

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A
ethane-1,2-diol
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NKP
Query on NKP

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A
(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate
18:1 LPA, oleoyl lysophosphatidic acid
C21 H41 O7 P
WRGQSWVCFNIUNZ-SQUSKLHYSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.751 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.523α = 90.00
b = 94.518β = 94.55
c = 75.503γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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