Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

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

 2XR9

Crystal structure of Autotaxin (ENPP2)

• PDB DOI: 10.2210/pdb2XR9/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2010-09-13 Released: 2011-01-19 
• Deposition Author(s): Kamtekar, S., Hausmann, J., Day, J.E., Christodoulou, E., Perrakis, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.221 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

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

• PubMed: 21240271 
• DOI: 10.1038/nsmb.1980
• Primary Citation of 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.

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Related Citations: 

• Mammalian Cell Expression, Purification, Crystallization and Microcrystal Data Collection of Autotaxin/Enpp2, a Secreted Mammalian Glycoprotein.
  Hausmann, J., Christodoulou, E., Kasiem, M., De Marco, V., van Meeteren, L.A., Moolenaar, W.H., Axford, D., Owen, R.L., Evans, G., Perrakis, A.
  (2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1130

• Crystallization and Preliminary X-Ray Diffraction Analysis of Rat Autotaxin.
  Day, J.E., Hall, T., Pegg, L.E., Benson, T.E., Hausmann, J., Kamtekar, S.
  (2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1127

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2	A	827	Rattus norvegicus	Mutation(s): 1  Gene Names: Enpp2, Atx, Npps2 EC: 3.1.4.39
UniProt
Find proteins for Q64610 (Rattus norvegicus) Explore Q64610  Go to UniProtKB:  Q64610

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	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	J [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SCN	C [auth A], D [auth A], E [auth A], F [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA	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 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.808	α = 98.78
b = 63.289	β = 106.22
c = 70.471	γ = 99.77

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Kamtekar, S., Hausmann, J., Day, J.E., Christodoulou, E., Perrakis, A.

Revision History  

• 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