PROSITE documentation PDOC52087

Lipin/Ned1/Smp2 (LNS2) domain profile

Phosphatidic acid (PA) is a truly versatile lipid, with parallel activities as a vital metabolic intermediate, a second messenger, and a determinant of unique membrane properties. PA serves as a precursor for lipid species such as diacylglycerol (DAG), lysophosphatidic acid, and CDP-DAG, each of which is used in its own signaling and metabolic pathways. The lipin/Ned1/Smp2 (LNS2) domain of 180 amino acids, originally characterized as the Mg(2+)-dependent catalytic domain of PA phosphatases (lipins), is catalytically inactive in Nir proteins and RdgBα that exhibit substitutions for a critical catalytic aspartate residue and another Mg(2+)-coordinating residue. Nevertheless, the LNS2 domain retains the ability to bind PA, with two conserved lysine residues shown to be essential for this interaction. The Nir/RdgBα LNS2 domain anchors the protein to the plasma membrane (PM) through PA binding [1,2,3,4].

The LNS2 domain belongs to the superfamily of haloacid dehalogenase-like (HAD-like) phosphatase proteins. The LNS2 domain adopts an α/β structure that is organized into a typical α/β sandwich resembling a Rossmann fold. The central β-sheet is flanked by α-helices (see <PDB:6TZY>). Catalytically active LNS2 domain harbor a conserved catalytic motif DxDxT, where the first Asp coordinates a Mg(2+) ion that increases its nucleophilicity, and the second Asp participates in acid/base catalysis. The Mg(2+) ion is coordinated by the sidechain of the first Asp residue of the DxDxT motif, as well as by the sidechain of an Asn and the mainchain carbonyl oxygen of the second Asp [4,5,6].

Protein families known to contain a LNS2 domain are listed below:

• Lipin/Pah phosphatidic acid phosphatases (PAPs) are Mg(2+)-dependent enzymes that catalyze the dephosphorylation of PA to produce diacylglycerol. Lipin/Pah PAPs regulate energy storage, energy mobilization, adipogenesis, phospholipid synthesis, autophagy, chylomicron secretion, and fatty acid synthesis. The architecture of lipin/Pah PAPs varies, but all PAPs contain two highly conserved N-Lip and C-Lip regions that combine to form two domains: an immunoglobulin-like (Ig-like) domain and a catalytic LNS2 domain. Lipin/Pah are evolutionarily conserved from yeast to humans. There are three lipin paralogs with multiple splicing variants in humans and mice, one PA phosphohydrolase (Pah, previously known as Smp2) in Saccharomyces cerevisiae, and two Pah enzymes (Pah1 and Pah2) in the ciliate Tetrahymena thermophila [5,6].
• Class IIA phosphatidylinositol transfer proteins (PITPs), the PITPNM/Nir/ RdgB subfamily, regulate basal levels of phosphatidylinositol (4,5)- bisphosphate (PI(4,5)P(2)) at the plasma membrane. The official name is PITPNM; the nomenclature "RdgB" originates from the prototypical Drosophila PITP associated with retinal degeneration, whereas "Nir" nomenclature refers to their initial identification as PYK2 N-terminal domain- interacting receptors. In mammals, there are two Nir proteins (Nir2 and Nir3), whilst Drosophila expresses a single protein. Class IIA proteins (e.g. Nir2, Nir3 and RdgBα) are multidomain proteins which share a common domain architecture comprising an N-terminal PITP domain (see <PDOC52086>), a FFAT motif, a DDHD (see <PDOC51043>) and a C-terminal LNS2 domain. The PITPNM LNS2 domains exhibit substitutions for a critical catalytic aspartate residue and therefore lack PAP-activity [2,3,4].
• Nir1 (encoded by Pitpnm3) is structurally related to Class IIA proteins but lacks the PITP domain. It acts as a scaffold that facilitates Nir2 recruitment to endoplasmic reticulum (ER)-PM contact sites [1].

The profile we developed covers the entire LNS2 domain.