Crystal structures of Mmm1 and Mdm12–Mmm1 reveal mechanistic insight into phospholipid trafficking at ER-mitochondria contact sites

Abstract

The endoplasmic reticulum (ER)-mitochondria encounter structure (ERMES) comprises mitochondrial distribution and morphology 12 (Mdm12), maintenance of mitochondrial morphology 1 (Mmm1), Mdm34, and Mdm10 and mediates physical membrane contact sites and nonvesicular lipid trafficking between the ER and mitochondria in yeast. Herein, we report two crystal structures of the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain of Mmm1 and the Mdm12-Mmm1 complex at 2.8 Å and 3.8 Å resolution, respectively. Mmm1 adopts a dimeric SMP structure augmented with two extra structural elements at the N and C termini that are involved in tight self-association and phospholipid coordination. Mmm1 binds two phospholipids inside the hydrophobic cavity, and the phosphate ion of the distal phospholipid is specifically recognized through extensive H-bonds. A positively charged concave surface on the SMP domain not only mediates ER membrane docking but also results in preferential binding to glycerophospholipids such as phosphatidylcholine (PC), phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylserine (PS), some of which are substrates for lipid-modifying enzymes in mitochondria. The Mdm12-Mmm1 structure reveals two Mdm12s binding to the SMP domains of the Mmm1 dimer in a pairwise head-to-tail manner. Direct association of Mmm1 and Mdm12 generates a 210-Å-long continuous hydrophobic tunnel that facilitates phospholipid transport. The Mdm12-Mmm1 complex binds all glycerophospholipids except for phosphatidylethanolamine (PE) in vitro.

Ca2+ and lipid signals hold hands at endoplasmic reticulum–plasma membrane contact sites

“…; Jeong et al . ). Indeed, cells that lack all three ESyts showed a defect in removing diacylglycerol (DAG) from the PM during massive Ca 2+ ‐induced phospholipase C (PLC) activation suggesting that they can participate in DAG transfer between the PM and other membranes (Saheki et al .…”

“…The structure of the SMP domain of ESyt2 revealed a β-barrel module similar to those found in the tubular-lipid-binding (TULIP) superfamily. In its dimeric state, the SMP domain of ESyt2 forms an approximately 90Å-long cavity encompassing a hydrophobic channel that could serve as a tunnel to pass hydrophobic molecules, including lipids, through the aqueous phase that separates the two membranes in contact sites (Schauder et al 2014;Jeong et al 2017). Indeed, cells that lack all three ESyts showed a defect in removing diacylglycerol (DAG) from the PM during massive Ca 2+ -induced phospholipase C (PLC) activation suggesting that they can participate in DAG transfer between the PM and other membranes (Saheki et al 2016).…”

Atg2: A novel phospholipid transfer protein that mediates de novo autophagosome biogenesis

“…The ERMES complex comprises four subunits (Mdm12, Mdm35, Mdm10, and Mmm1) and mediates phospholipid transfer between mitochondria and the ER . Mdm12 and Mmm1, both of which possess SMP domains, form a tubular tetramer in a 2:2 manner, which produce a successive hydrophobic cleft through the four molecules although the significance of the long cleft remains to be established . These examples suggest that a long hydrophobic groove within a protein or protein complex could function as a pathway for LT.…”

“…51 Mdm12 and Mmm1, both of which possess SMP domains, form a tubular tetramer in a 2:2 manner, which produce a successive hydrophobic cleft through the four molecules although the significance of the long cleft remains to be established. 52 These examples suggest that a long hydrophobic groove within a protein or protein complex could function as a pathway for LT. It is necessary to experimentally validate whether Atg2 has a similar long hydrophobic groove and the groove, if it exists, mediates phospholipid transfer between membranes that are bridged by Atg2.…”

Determining the Lipid-Binding Specificity of SMP Domains: An ERMES Subunit as a Case Study

“…The SMP fold was first described in the crystal structure of the human Extended synaptotagmin-2 (E-SYT2) [17]. This was followed by several crystal structures of fungal Mdm12 [18–20] and Mmm1 [21] SMP domains; all revealed an elongated tube-shaped domain composed of two α helices capping an antiparallel β-barrel composed of five twisted strands (Fig. 1b).…”