Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling

Abstract

Enpp1 is a membrane-bound glycoprotein that regulates bone mineralization by hydrolyzing extracellular nucleotide triphosphates to produce pyrophosphate. Enpp1 dysfunction causes human diseases characterized by ectopic calcification. Enpp1 also inhibits insulin signaling, and an Enpp1 polymorphism is associated with insulin resistance. However, the precise mechanism by which Enpp1 functions in these cellular processes remains elusive. Here, we report the crystal structures of the extracellular region of mouse Enpp1 in complex with four different nucleotide monophosphates, at resolutions of 2.7-3.2 Å. The nucleotides are accommodated in a pocket formed by an insertion loop in the catalytic domain, explaining the preference of Enpp1 for an ATP substrate. Structural mapping of disease-associated mutations indicated the functional importance of the interdomain interactions. A structural comparison of Enpp1 with Enpp2, a lysophospholipase D, revealed marked differences in the domain arrangements and active-site architectures. Notably, the Enpp1 mutant lacking the insertion loop lost the nucleotide-hydrolyzing activity but instead gained the lysophospholipid-hydrolyzing activity of Enpp2. Our findings provide structural insights into how the Enpp family proteins evolved to exert their diverse cellular functions. molecular evolution | X-ray crystallography

Autotaxin: structure-function and signaling

“…( 78,79 ). Bottom row, structures of nucleotides bound to ENPP1 ( 66 ). The structures shown are available in the PDB.…”

“…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.…”

Molecular Basis of Purinergic Signal Metabolism by Ectonucleotide Pyrophosphatase/Phosphodiesterases 4 and 1 and Implications in Stroke*

“…2). Human NPP4 shares 40% sequence identity with NPP1 throughout the catalytic domain, and the structure of mouse NPP1 has been recently determined (5,58) providing the opportunity to identify the structural origins of substrate discrimination at the atomic level. Human and mouse NPP1 are 79% identical, with sequence mapping of the human sequence onto the mouse NPP1 structure showing that all sequence differences are outside the substrate-binding and active sites.…”

Dpy-19 like 3-mediated C-mannosylation and expression levels of RPE-spondin in human tumor cell lines

“…RPESP has certain domains: An N-terminal signal peptide toward the secretory pathway, followed by a somatomedin B (SMB) domain and TSR-1. Specific proteins containing the SMB domain have been reported to bind plasminogen activator inhibitor-1 and ectonucleotide pyrophosphatase/phosphodiesterase 1 (15)(16)(17)(18); however, the physiological functions of its association remain unclear. In the TSR-1 domain, RPESP has two putative C-mannosylation sites, the W 80 and W 83 residues.…”