2XR9 | pdb_00002xr9

Crystal structure of Autotaxin (ENPP2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.221 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2XR9

This is version 2.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5IJQ

Literature

Structural basis of substrate discrimination and integrin binding by autotaxin.

Hausmann, J.Kamtekar, S.Christodoulou, E.Day, J.E.Wu, T.Fulkerson, Z.Albers, H.M.van Meeteren, L.A.Houben, A.J.van Zeijl, L.Jansen, S.Andries, M.Hall, T.Pegg, L.E.Benson, T.E.Kasiem, M.Harlos, K.Kooi, C.W.Smyth, S.S.Ovaa, H.Bollen, M.Morris, A.J.Moolenaar, W.H.Perrakis, A.

(2011) Nat Struct Mol Biol 18: 198-204

  • DOI: https://doi.org/10.1038/nsmb.1980
  • Primary Citation Related Structures: 
    2XR9, 2XRG

  • PubMed Abstract: 

    Autotaxin (ATX, also known as ectonucleotide pyrophosphatase/phosphodiesterase-2, ENPP2) is a secreted lysophospholipase D that generates the lipid mediator lysophosphatidic acid (LPA), a mitogen and chemoattractant for many cell types. ATX-LPA signaling is involved in various pathologies including tumor progression and inflammation. However, the molecular basis of substrate recognition and catalysis by ATX and the mechanism by which it interacts with target cells are unclear. Here, we present the crystal structure of ATX, alone and in complex with a small-molecule inhibitor. We have identified a hydrophobic lipid-binding pocket and mapped key residues for catalysis and selection between nucleotide and phospholipid substrates. We have shown that ATX interacts with cell-surface integrins through its N-terminal somatomedin B-like domains, using an atypical mechanism. Our results define determinants of substrate discrimination by the ENPP family, suggest how ATX promotes localized LPA signaling and suggest new approaches for targeting ATX with small-molecule therapeutic agents.


  • Organizational Affiliation
    • Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 99.68 kDa 
  • Atom Count: 6,753 
  • Modeled Residue Count: 783 
  • Deposited Residue Count: 827 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2827Rattus norvegicusMutation(s): 1 
EC: 3.1.4.39 (PDB Primary Data), 3.1.4.4 (UniProt)
UniProt
Find proteins for Q64610 (Rattus norvegicus)
Explore Q64610 
Go to UniProtKB:  Q64610
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64610
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q64610-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD



Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
K [auth A],
KA [auth A],
L [auth A],
LA [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
PO4

Query on PO4



Download:Ideal Coordinates CCD File
J [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
SCN

Query on SCN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
I [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.221 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.808α = 98.78
b = 63.289β = 106.22
c = 70.471γ = 99.77
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Database references, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary