Structure of NPP1, an Ectonucleotide Pyrophosphatase/Phosphodiesterase Involved in Tissue Calcification

Abstract

Ectonucleotide pyrophosphatase/phosphodiesterase-1 (NPP1) converts extracellular nucleotides into inorganic pyrophosphate, whereas its close relative NPP2/autotaxin hydrolyzes lysophospholipids. NPP1 regulates calcification in mineralization-competent tissues, and a lack of NPP1 function underlies calcification disorders. Here, we show that NPP1 forms homodimers via intramembrane disulfide bonding, but is also processed intracellularly to a secreted monomer. The structure of secreted NPP1 reveals a characteristic bimetallic active site and a nucleotide-binding groove, but it lacks the lipid-binding pocket and open tunnel present in NPP2. A loop adjacent to the nucleotide-binding site, which is disordered in NPP2, is well ordered in NPP1 and might promote nucleotide binding. Remarkably, the N-terminal somatomedin B-like domains of NPP1, unlike those in NPP2, are flexible and do not contact the catalytic domain. Our results provide a structural basis for the nucleotide pyrophosphatase activity of NPP1 and help to understand how disease-causing mutations may affect NPP1 structure and function.

Autotaxin: structure-function and signaling

“…The ATX catalytic domain is unique in that it has evolved a deep hydrophobic pocket that is not found in ENPP1 ( 65,66 ) or, to the best of our knowledge, in any other phospholipase. This pocket has an estimated volume of full inhibition of lysoPLD activity ( 75 ).…”

“…The catalytic domain of ATX and that of ENPP1, whose structure was also recently determined ( 65,66 ), is structurally similar to that of the prototypic nucleotide pyrophosphatase/phosphodiesterase (NPP) from Xanthomonas axonopodis ( Xa NPP), an evolutionary relative of alkaline phosphatases ( 67 ). The catalytic sites in ATX, ENPP1, and Xa NPP are almost identical, with the nucleophile Thr in proximity with two zinc ions, coordinated by conserved His and Asp residues.…”

Nucleotides Acting at P2Y Receptors: Connecting Structure and Function

“…Recently, the structures of 59-nucleotidase and ecto-nucleoside triphosphate diphosphohydrolase (CD39) were determined using X-ray crystallography (Heuts et al, 2012;Zimmermann et al, 2012). The structures of some of the other enzymes involved in processing purine receptor ligands, such as ecto-nucleotide pyrophosphatase/phosphodiesterase-1, have also been determined (Jansen et al, 2012). Inhibition or activation of these enzymes is an appealing means of indirectly modulating the activation of the receptors at which the nucleotides and the nucleoside adenosine act.…”

Correction: Substrate-specifying determinants of the nucleotide pyrophosphatases/phosphodiesterases NPP1 and NPP2

“…Please note that the original data cannot be located for the triple mutant (G513A/G515A/G518A) that is shown in the published Figure 6A. However, the data shown in Figure 8 and subsequently published structural data [1,2] support the conclusions that are discussed in the paper for the triple mutant. …”