5DLV

Crystal structure of Autotaxin (ENPP2) with tauroursodeoxycholic acid (TUDCA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Steroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling.

Keune, W.J.Hausmann, J.Bolier, R.Tolenaars, D.Kremer, A.Heidebrecht, T.Joosten, R.P.Sunkara, M.Morris, A.J.Matas-Rico, E.Moolenaar, W.H.Oude Elferink, R.P.Perrakis, A.

(2016) Nat Commun 7: 11248-11248

  • DOI: 10.1038/ncomms11248
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Autotaxin (ATX) generates the lipid mediator lysophosphatidic acid (LPA). ATX-LPA signalling is involved in multiple biological and pathophysiological processes, including vasculogenesis, fibrosis, cholestatic pruritus and tumour progression. ATX has ...

    Autotaxin (ATX) generates the lipid mediator lysophosphatidic acid (LPA). ATX-LPA signalling is involved in multiple biological and pathophysiological processes, including vasculogenesis, fibrosis, cholestatic pruritus and tumour progression. ATX has a tripartite active site, combining a hydrophilic groove, a hydrophobic lipid-binding pocket and a tunnel of unclear function. We present crystal structures of rat ATX bound to 7α-hydroxycholesterol and the bile salt tauroursodeoxycholate (TUDCA), showing how the tunnel selectively binds steroids. A structure of ATX simultaneously harbouring TUDCA in the tunnel and LPA in the pocket, together with kinetic analysis, reveals that bile salts act as partial non-competitive inhibitors of ATX, thereby attenuating LPA receptor activation. This unexpected interplay between ATX-LPA signalling and select steroids, notably natural bile salts, provides a molecular basis for the emerging association of ATX with disorders associated with increased circulating levels of bile salts. Furthermore, our findings suggest potential clinical implications in the use of steroid drugs.


    Organizational Affiliation

    Division of Biochemistry, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
A, B
827Rattus norvegicusMutation(s): 2 
Gene Names: Enpp2 (Atx, Npps2)
EC: 3.1.4.39
Find proteins for Q64610 (Rattus norvegicus)
Go to UniProtKB:  Q64610
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5D5
Query on 5D5

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A, B
2-{[(3alpha,5beta,7alpha,8alpha,14beta,17alpha)-3,7-dihydroxy-24-oxocholan-24-yl]amino}ethanesulfonic acid
C26 H45 N O6 S
BHTRKEVKTKCXOH-LBSADWJPSA-N
 Ligand Interaction
PO4
Query on PO4

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A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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

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

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A, B
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
IOD
Query on IOD

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A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

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A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 62.880α = 83.84
b = 77.832β = 79.29
c = 92.437γ = 77.08
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NWONetherlands700.10.354
NWONetherlands723.013.003

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references
  • Version 1.2: 2018-02-14
    Type: Database references