Quite Interesting PDB Structures


Autotaxin: inhibiting a greasy pocket
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Medicinal significance of autotaxin

ATX hydrolyses LPC into LPA. HA155 is a designed inhibitor of ATX.
Autotaxin (ATX) is a secreted glycoprotein that has been implicated in various physiological and pathophysiological processes, including vascular and neural development, lymphocyte trafficking, fibrosis and tumour progression. ATX functions as lysophospholipase D (lysoPLD), hydrolysing lysophosphatidylcholine (LPC) into the signalling lipid lysophosphatidic acid (LPA). LPA stimulates cell migration, proliferation and survival in many cell types by binding to specific G protein-coupled receptors (GPCRs). Given its emerging role in disease, ATX is actively pursued as a drug target in both academia and industry.

3D structures of autotaxin in the PDB

ATX is a ~100 kDa protein that belongs to the ectonucleotide pyrophosphatase/phosphodiesterase (ENPP) enzyme family. ATX is unique in that it is the only member with lysoPLD activity (EC It removes the choline moiety from the LPC, which can vary both in the length and saturation of the acyl chain.
Recently, two teams of researchers have determined crystal structures of ATX. The Perrakis/Moolenaar groups solved the rat ATX structure in the apo form and in complex with an inhibitor (PDB entries 2xr9 and 2xrg). The Nureki/Aoki groups solved the structure of mouse ATX, also in the apo form and in complex with LPA products of differing length and saturation of the acyl chain (PDB entries 3nkr, 3nkp, 3nkq, 3nkm, 3nko and 3nkn).

Domain architecture

Autotaxin is highly conserved between rat and mouse, exhibiting 97% sequence identity. Consequently, the rat and mouse ATX structures (view-1) are very similar (0.7Å RMSD for 782 aligned Cα atoms). They consist of four tightly packed domains (view domain mappings for rat and mouse sequences). The two N-terminal cysteine-rich somatomedin-B-like (SMB) domains and the C-terminal nuclease-like (NUC) domain flank opposing sites of the central catalytic phosphodiesterase (PDE) domain (view-2). The nuclease domain is inactive but its presence helps maintain the structural integrity of the protein. Moreover, an extended “lasso” loop of about 50 residues, which starts at the end of the PDE domain, wraps tightly around the entire NUC domain to finally enter the PDE domain from the opposite site.

Binding pocket

ATX is known to bind to the surface of activated lymphocytes and platelets and it is tempting to speculate that this happens adjacent to the GPCR in order that the LPA may be released close to the cognate receptor. The means by which this is achieved remains unknown but SMB domains are likely implicated as these are known to be involved in protein-protein interactions and, in the case of ATX, to bind integrins.
The ATX crystal structures shed light on the structural basis of substrate recognition and catalysis. The mouse structures show how lipids of different length and saturation (LPA 14:0, 16:0, 18:1, 18:3, 22:6, named using lipid numbers) bind ATX. They reveal a hydrophobic pocket and a tunnel in the PDE domain, both adjacent to the catalytic site (view-3). This pocket is not present in other ENPP family members and thus represents a suitable target for designing ATX-specific inhibitors. The deep hydrophobic pocket is attributable to an 18-residue deletion in ATX compared with other ENPP proteins. The deletion engenders a hydrophobic void in which substrate and inhibitors bind.
Interestingly, a tunnel partly formed by the SMB1 domain is likely to be involved in the presentation of LPA to its receptors, as suggested by structures in which an additional lipid chain appears to bind to the tunnel. Possibly this is a lipid that is entering or exiting the active-site pocket.


The rat ATX structure shows how the nanomolar inhibitor HA155 mimics the lipid conformation that potently inhibits ATX. HA155 also forms a reversible covalent bond with the hydroxyl group of the catalytic threonine (residue 209) which is further stabilised by zinc ions (view-4).

Further exploration

Explore the occurrence of the following Pfam domains of autotaxin in the entire PDB: SMB, PDE, NUC. Find other members of the ENPP family by searching for similar sequences.


This QUIPS article was developed in collaboration with Anastassis Perrakis and Wouter Moolenaar and released in conjunction with their review paper about autotaxin structure and function.