Skip to main content
NCBI home page
NIHPA Author Manuscripts logoLink to NIHPA Author Manuscripts
. Author manuscript; available in PMC: 2025 Jan 1.
Published in final edited form as: Adv Biol Regul. 2023 Dec 17;91:101010. doi: 10.1016/j.jbior.2023.101010

Three kingdoms and one ceramide to rule them all. A comparison of the structural basis of ceramide-dependent regulation of sphingolipid biosynthesis in animals, plants, and fungi

Mohammed AL Mughram 1,2, Glen E Kellogg 1, Binks W Wattenberg 3,*
PMCID: PMC10922298  NIHMSID: NIHMS1954133  PMID: 38135565

Abstract

Sphingolipids are a diverse class of lipids with essential functions as determinants of membrane physical properties and as intra- and intercellular signaling agents. Disruption of the normal biochemical processes that establish the levels of individual sphingolipids is associated with a variety of human diseases including cancer, cardiovascular disease, metabolic disease, skin diseases, and lysosomal storage diseases. A unique aspect of this metabolic network is that there is a single enzymatic step that initiates the biosynthetic pathway for all sphingolipids. This step is catalyzed by the enzyme serine palmitoyltranserase (SPT). Under most circumstances SPT condenses serine and the 16-carbon acyl-CoA, palmitoyl-CoA to produce the precursor of all sphingolipids. SPT, a four-subunit protein complex, is subject to classic feedback regulation: when cellular sphingolipids are elevated, SPT activity is inhibited. Ceramide is the sphingolipid sensed by this system and it regulates SPT by directly binding to the complex. The ceramide binding site in the SPT complex, and how ceramide binding results in SPT inhibition, has now been determined in vertebrates, plants, and yeast using molecular modeling and cryo-electron microscopy. Here we discuss the similarities and differences revealed by these resolved structures and the surprising result that ceramide binds at almost identical positions in the SPT complex of these divergent organisms, but accomplishes SPT regulation in very different ways.

Introduction

Sphingolipids are a large and diverse group of lipids that serve a variety of functions in cells and tissues and are implicated, when dysregulated, in pathological conditions (Hannun and Obeid, 2018). But they all start in the same place with the initiating and rate limiting enzyme serine palmitoyltransferase (SPT) (Figure 1). Once the precursor of the sphingosine backbone (3-ketodihydrosphingosine) is produced by SPT, subsequent enzymatic conversions produce ceramide, sphingomyelin, the array of glycosylceramides, and, by both de novo synthesis and hydrolysis of ceramide, sphingoid bases (Figure 1). Although these conversions can cycle the sphingoid backbone throughout the sphingolipid metabolic network, once the sphingoid backbone is produced by SPT there is only one way to eliminate it completely, through the action of sphingosine-1-phosphate (S1P) lyase (Aguilar and Saba, 2012). In this sense, sphingolipid metabolism is a closed system and the input, mediated by SPT, and the output, mediated by S1P lyase are essential regulators of the total sphingolipid pool. But how is this regulation achieved? Here, we review how recent work, and a previously unreported model, has revealed that sphingolipid directly binds to, and regulates, the SPT complex in the animal, plant, and fungal kingdoms.

Figure 1. The sphingolipid biosynthetic and metabolic pathways.

Figure 1.

Open in a new tab

The Orm/ORMDLs-Regulatory subunits of the SPT complex

Like any well-behaved biosynthetic pathway, the initiating and rate-limiting step, SPT, is homeostatically controlled. It has been known for decades that when sphingolipid levels in cells rise, activity of SPT is diminished (Mandon et al., 1991). An understanding of the mechanistic basis of the homeostatic regulation of SPT was accelerated by the simultaneous identification by two yeast groups of small, membrane-bound proteins of the endoplasmic reticulum (ER), the Orms (of which there are two isoforms, 1 and 2), that were required for that regulation (Breslow et al., 2010; Han et al., 2010). Our group as well as others demonstrated that the mammalian homologues of the Orms, termed the ORMDLs (of which there are three isoforms, 1-3), performed the same regulatory function (Breslow et al., 2010; Siow and Wattenberg, 2012) (reviewed in (Davis et al., 2018)). Previous studies of SPT had established that it consists of three subunits. SPTLC1 in mammals (LCB1 in yeast and plants) is required for stability of the protein and contributes to the active site (reviewed in (Lowther et al., 2012)) . SPTLC2 (LCB2 in yeast in plants) contains the catalytic site and binds the required co-factor pyridoxyl 5’ phosphate. The so-called small subunit, SPTss (of which there are two isoforms, a and b) in mammals and plants, Tsc3 in yeast, determines the acyl-CoA substrate specificity of the enzyme and helps to bind the complex to the ER membrane (Harmon et al., 2013). Subsequently, the discovery of the Orms/ORMDLs prompted their identity as a fourth subunit. This was initially established by co-immunprecipitation (Siow et al., 2015), and later by purification of the SPT complex and determination of the three-dimensional structure by cryo-electron microscopy (reviewed in (Wattenberg, 2021)).

Structure of the mammalian SPT/ORMDL complex

The mammalian structure was first reported in 2021 by two groups, one led by Xin Gong at the Southern Institute for Science and Technology at in Shenzhen, China, (Li et al., 2021) and the other led by Chia-Hsueh Lee at St. Jude in Memphis, USA (Wang et al., 2021). The structures are nearly identical with one difference involving the amino terminus of ORMDL, discussed below, which has since been explained. These elegant structures have been recently reviewed (Wattenberg, 2021), and so will only be discussed here briefly. The mammalian complex is a symmetrical dimer, with each monomer composed of all four subunits (Figure 2). Interestingly, the dimer is bridged by an amino-terminal transmembrane helix contributed by SPTLC1 that crosses from one monomer to the other. The complex is anchored in the ER membrane by that helix, by a transmembrane helix and amphipathic helix contributed by ssSPTa, an amphipathic helix contributed by SPTLC2, and by the four transmembrane helices of ORMDL3 (the isoform used in these preparations). The active site is a cavity contributed by SPTLC1 and −2 that accommodates the substrates and positions the pyridoxyl 5’ phosphate for catalysis. The Arabadopsis and yeast structures are very similar to the mammalian structure. The notable exception is that in yeast the amino-terminal alpha helix of LCB2 does not cross the dimer, as in the human and Arabidopsis structures, but instead occupies the same site interacting with Orm but in the monomer. This apparently weakens the dimer sufficiently such that the yeast SPT is predominantly in the monomeric form (Schäfer et al., 2023).

Figure 2. Structure of the human SPTLC1/SPTLC2/SPTssa/ORMDL 3 complex (from (Wang et al., 2021).

Figure 2.

Open in a new tab

PDB 7K0M).

Direct sensing of ceramide by the SPT/ORMDL complex to achieve homeostatic regulation of sphingolipid biosynthesis.

In yeast the Orm-mediated regulation of SPT is accomplished, at least in part, by phosphorylation of serines residing in the amino terminus of Orm. At low sphingolipid levels phosphorylation of Orm by the kinase Ypk1 relieves SPT of Orm inhibition (Roelants et al., 2011). However, in mammalian cells and plants the ORMDLs/Orms lack the amino-terminal segments containing those phosphorylation sites. This suggest that in the multi-cellular organisms, sphingolipid sensing requires a different mechanism to provide homeostatic regulation of SPT by the ORMDL/Orm proteins.

If the ORMDLs/Orms do not respond to changes in cellular sphingolipid levels by altering the phosphorylation status of the proteins, how do they sense these levels, and how does that translate into regulation of SPT activity? It is possible, for example, that protein levels of the ORMDLs are regulated by gene expression, regulated protein turnover, or regulated mRNA translation. Indeed, there is evidence that ORMDL turnover is regulated to some extent under specific conditions (Sasset et al., 2021; Wang et al., 2015). However, this does not seem to be a general mechanism for the sphingolipid-dependent regulation of SPT activity. Levels of ORMDL protein are unchanged when SPT is inhibited by elevated sphingolipid levels (Siow et al., 2015).

A significant advance in unraveling this mystery was the observation that the sphingolipid and ORMDL-dependent inhibition of SPT could be recapitulated with isolated membranes (Davis et al., 2019). Several key observations emerged from that biochemical system. 1) Regulation does not require soluble cytosolic components or ATP. This essentially rules out that regulation is achieved by post-translational modifications, changes in gene expression, mRNA translation, or protein turnover. All of these processes require ATP, cytosolic proteins, or both. 2) Ceramide is the sphingolipid that is sensed by this system. 3) Yeast membranes also respond to ceramide in an Orm-dependent manner. 4) Only the native stereoisomer of ceramide can trigger SPT inhibition. The stereospecificity of the ceramide response is especially revealing. Stereospecificity is the hallmark of a specific binding site for a ligand. This observation strongly suggested that ceramide bound to the SPT/ORMDL complex triggers inhibition. Three recent publications confirm this concept by determining that there is a ceramide binding site in the SPT complex and demonstrate that this binding is responsible for Orm/ORMDL regulation of SPT.

Methods

Computational docking of ceramide.

The structure of the ceramide substrate was pre-built and energy minimized in Sybyl-X 2.11 (Tripos, St. Louis, MO). The structure of the SPT-ORMDL3 complex was obtained from the PDB (ID: 7K0O), and imported into Sybyl, where hydrogens were added and charges were computed (Gasteiger-Hückel method), and subjected to a hydrogen-only minimization for 10000 steps. A series of docking experiments were carried out using GOLD (Verdonk et al., 2003) to identify and optimize ceramide bound in its favorable binding site. Optimal poses and binding scores were obtained based on the assumption that the binding binding site would be found within a 15 Å radius of Asn13 of ORMDL3. Ceramide binding was evaluated and ranked based on GOLD’s chemPLP and HINT (Sarkar and Kellogg, 2010) scores.

Ceramide binding to the SPT/ORMDL/Orm complex. Modeling and resolution in the determined structures.

A computationally-based model of ceramide binding to the SPT/ORMDL complex.

Subsequent to publication of the SPT/ORMDL structures our group used a molecular docking approach to identify potential ceramide binding sites and poses in the SPT complex structure (pdb: 7K0O(Wang et al., 2021)). This effort utilized the docking algorithm GOLD (Verdonk 2003) and rescoring by HINT(Sarkar and Kellogg, 2010) (details provided in Methods). This yielded a binding site that nestled ceramide between ORMDL transmembrane helices 1 and 2 of ORMDL as well as contacting SPTLC2 (Figure 3). This structure predicts a potentially important hydrogen bond between asparagine 12 (Asn12) of ORMDL and the 1’ hydroxyl of ceramide. An additional hydrogen bond between the N-acyl carbonyl and tyrosine 122 (Y122) of SPTLC2 is also predicted. The sphingoid base and N-acyl chain of ceramide make potential hydrophobic contacts with the transmembrane helices of ORMDL.

Figure 3. Position of ceramide bound to the SPT/ORMDL/ORM complex.

Figure 3.

Open in a new tab

Red spheres represent ceramide bound to the complex. A. Computational docking of ceramide. C8 ceramide was computationally docked into the human SPTLC1/SPTLC2/SPTssa/ORMDL3 complex as described above based on PDB 7K0O,(Wang et al., 2021). Residues 78-98 of SPTLC2 have been removed for clarity. B. Human SPTLC1/SPTLC2/SPTssa/ORMDL3 complex with ceramide resolved by cryo-electron microscopy. C6 ceramide resolved in the structure. (PDB 7YIU, (Xie et al., 2023). Residues 75-98 of SPTLC2 have been removed for clarity. C. Arabidopsis LCB1/LCB2a/SPTssa/ORM1 with ceramide resolved by cryo-electron microscopy. C24 ceramide resolved in the structure. (PDB 7YJM (Liu et al., 2023). Residues 16-36 of LCB2a have been removed for clarity. D. Yeast LCB1/LCB2/Tsc3/Orm1 with ceramide resolved by cryo-electron microscopy (PDB 8C80, (Schäfer et al., 2023)). C26 ceramide is resolved in the structure. Residues 70-90 of LCB2 have been removed for clarity

New cryo-electron microscopy-determined structures of the SPT complex from three diverse organisms resolve bound ceramide in nearly identical positions to each other and to the computationally predicted binding site.

In the last year three manuscripts reported ceramide resolved in the human SPT/ORMDL complex(Xie et al., 2023), the yeast SPT/Orm/Sac1 complex (Sac1 is a phosphatidyl inositol-4-phosphate phosphatase)(Schäfer et al., 2023), and the Arabidopsis SPT/Orm complex (Liu et al., 2023). All three groups used lipidomic analysis to determine that the purified proteins all contain bound ceramide. They then went on to resolve ceramide in those structures. A comparison of the three binding sites to each other and to the computational model is shown in Figure 3. All of these structures position ceramide at the same site, nestled next to transmembrane helices 1 and 2 of ORMDL/Orm and SPTLC2/LCB2. This positioning predicts specific hydrogen bonding interactions between ceramide and ORMDL/Orm in each of these structures, outlined below. Importantly the functional importance of each of these interactions was tested experimentally in both the purified protein preparations and in the context of cells and ER membranes and each of these interactions was confirmed to contribute to the ability of ceramide to regulate SPT activity.

Hydrogen bonds between ceramide and ORMDL/Orm

The hydrogen bond between ORMDL Asn12 to the 1’hydroxyl of ceramide predicted by our model is also predicted in the resolved human structure and to an equivalent asparagine (Asn17) in the Arabidopis Orm structure. While the equivalent asparagine in the yeast Orm1 (Asn76) is conserved between species in the protein sequence, in the solved yeast cryo-EM structure the 1’ hydroxyl of ceramide is too far from Asn76 (5.2 Å) to form a strong hydrogen bond. There are additional differences in predicted hydrogen bonds to ORMDL/Orm between these structures. There is a predicted hydrogen bond between the 3’ hydroxyl of ceramide to phenylalanine 63 of ORMDL in the human structure. This is not predicted in the Arabidopis Orm structure, but is replaced by a hydrogen bond to serine 63 of Orm1.

Hydrogen bonds between ceramide and SPTLC2/LCB2

All of these structures predicted hydrogen bonds between the polar headgroup of ceramide and SPTLC2/LCB2. There is a predicted hydrogen bond between the amide carbonyl of ceramide and analogous tyrosines in the structures of all three species (Y122 of human SPTLC2, Y55 of Arabidopis LCB2, and Y110 of yeast LCB2.)

While the site of ceramide binding and the positioning of the ceramide headgroup is nearly identical in the four structures, there is some variation between the structures in the positioning of the hydrophobic tail of the sphingoid base and the N-acylated fatty acid. It should be noted that both the ceramide sphingoid backbone and the fatty acid component in these structures vary somewhat. The ceramide in the computational model is sphingosine N-acylated to an 8-carbon fatty-acid, in the human cryo EM structure sphingosine N-acylated to a 6-carbon fatty-acid but also resolves an endogenous ceramide with a longer acyl chain, in the Arabidopis phytosphingosine N-acylated to a 24-carbon fatty-acid, and in the yeast structure phytosphingosine N-acylated to a 26-carbon fatty-acid.

The orientation of the hydrophobic aspects of ceramide is very similar when comparing the resolved human and Arabidopis structures. In those structures the sphingoid backbone is angled away from the ORMDL/Orm transmembrane helices and the N-acylated fatty acid is oriented towards those helices. Our docked structure differs in that the sphingoid backbone appears to have hydrophobic interactions with the ORMDL transmembrane helices 1 and 2, while the N-acylated fatty acid maintains a similar orientation to that in resolved human and Arabidopis structures. The differences between the computationally docked ceramide and the pose of ceramide in the cryo-EM structure may be due to how each were prepared. The computationally docked structure did not include either detergent or phospholipid, while the preparation used for the cryo-EM structures utilized the detergent glycol-diosgenin (GDN). Ultimately, determining the exact pose of the ceramide will require inclusion of the ER bilayer lipids in both computational and cryo-EM derived structures. The orientation of the hydrophobic elements of ceramide in the yeast complex is somewhat different. The sphingoid backbone interacts with helices 1 and 2 of Orm, much like our docked structure of the human ORMDL, but the N-acyl fatty acid, which is longer than those resolved in the human and Arabidopis structures, crosses over helix 2 of Orm and appears to project into the surrounding phospholipid bilayer. Importantly, while the details differ, all of the structures suggest that there are important hydrophobic interactions between ceramide and transmembrane helices 1 and 2 of ORMDL/Orm. It is likely that this interaction is important for ceramide binding.

The inhibitory mode of ORMDL/Orms

The mammalian SPT complex: Ceramide binding stabilizes the amino-terminus of ORMDL in the SPT substrate binding pocket.

The initial structure of the SPT/ORMDL published by Lee and colleagues (Wang et al., 2021) and the subsequent structure of the complex with ceramide bound by Gong’s lab (Xie et al., 2023) both position the amino terminus of ORMDL in the substrate binding pocket of SPT (Figure 4 Panel A). (The construct used in the initial structure by Gong and colleagues lacked some amino-terminal residues in ORMDL and so the amino terminus was not resolved. The more recent structures by this group used a construct with a full-length amino terminus). This immediately suggests that ceramide binding to the ORMDL/SPT complex results in a conformational change that stabilizes the ORMDL amino terminus in the substrate binding pocket, thus inhibiting the enzyme. This model is substantiated by the ceramide-free structures solved by Gong and colleagues, utilizing the ceramide binding mutations discussed above (Xie et al., 2023). In the absence of ceramide binding, the amino-terminus of ORMDL is unresolved and not positioned in the SPT substrate binding pocket. The details of how ceramide binding accomplishes stabilization of the ORMDL amino-terminus in the substrate binding pocket remain to be elucidated. There are subtle shifts in the ORMDL structure, but a full accounting of how this results in stabilization of the amino-terminus remains unclear.

Figure 4. Position of the amino-termini of ORMDL/ORM in the SPT/ORMDL/ORM complexes.

Figure 4.

Open in a new tab

The amino-termini of ORMDL/ORM are represented as pink spheres in the illustrated complexes. A. Human SPTLC1/SPTLC2/SPTssa/ORMDL3 complex(Xie et al., 2023). Residues 78-98 of SPTLC2 have been removed for clarity. B. Arabidopsis LCB1/LCB2a/SPTssa/ORM1 (Liu et al., 2023). Residues 16-36 of LCB2 have been removed for clarity. C. Yeast LCB1/LCB2/Tsc3/Orm1complex (Schäfer et al., 2023). Residues 70-90 of LCB2 have been removed for clarity. Based on structures listed in Figure 3.

The Arabidopsis SPT complex: Ceramide binding stabilizes a hybrid beta sheet structure, positioning residues in the ORM amino-terminus that would interfere with substrate binding.

In contrast to the mammalian ORMDL, ceramide binding does not stabilize the amino-terminus of ORM directly into the substrate binding pocket (Figure 4, Panel B). Instead, ceramide binding induces the formation of a beta sheet that is comprised of residues in the amino termini of both ORM (residues 5-8) and LCB2 (residues 1-5). The induced beta sheet lies just below the substrate binding pocket. The formation of this beta sheet positions two ORM residues, Met14 and Asn15 at a position that would clash with bound acyl-CoA in the active site. Thus, while in the Arabidopsis SPT complex ceramide binds at a site almost identical to the mammalian complex, the molecular details of how that binding results in SPT inhibition are somewhat different. This suggests that ceramide regulation of SPT activity is important for both organisms, but that there is flexibility in how that regulation is achieved.

The yeast SPT complex: Ceramide binding blocks entry into the substrate binding site through interaction with a substrate gate.

A substantial difference between the Orms of yeast and the mammalian and Arabidopsis homologues is that the amino termini of the yeast Orms is extended by over 60 amino acids relative to the homologous sequences. That amino-terminal extension contains the regulatory phosphorylation sites (Roelants et al., 2011). This amino-terminal extension is not localized near the substrate binding pocket, but instead is directed away from that pocket to form an interaction with LCB2 (Figure 4 Panel C.) Therefore, a mechanism that mediates the ceramide-dependent inhibition of SPT must operate in the yeast SPT/Orm complex. In the yeast structure, the ceramide headgroup is positioned near a substrate site gating loop (termed the PATP loop) the entrance of the substrate binding pocket. Frohlich and colleagues suggest that ceramide binding forces the PATP loop into the entrance of the substrate binding pocket to achieve inhibition of SPT activity (Schäfer et al., 2023). While it is clear that phosphorylation of critical serines in the amino terminus of the yeast Orm relieves SPT inhibition, the structural basis for this effect is not yet clear.

Summary and Future Directions

The beautiful structural studies of the SPT complex in three quite distinct organisms have revealed an intricate, but highly conserved protein complex. This conservation reinforces the notion that SPT function and regulation is an essential metabolic linchpin. All three SPT complexes are regulated by ceramide binding and all three bind ceramide in essentially the same position. Yet, strikingly, each uses a different molecular mechanism to achieve ceramide-dependent inhibition of SPT. The homeostatic regulation of SPT by ceramide clearly has a strong evolutionary benefit. Why different organisms use different structural features to accomplish that regulation is a fascinating mystery. One possibility is that there are additional regulatory systems that impinge on this complex. It is known, for example, that, as cited above, protein turnover of ORMDL can impact on SPT regulation (Sasset et al., 2022; Wang et al., 2015). There is also the potential for allosteric protein modulators of the complex that have yet to be identified. The detailed structural changes that ceramide binding imparts to the SPT complex to establish the inhibitory state are not easily recognizable from the static Cryo-EM structures. It is likely that extensive molecular dynamic modeling will be required to approach how ceramide controls SPT activity. This understanding could well have therapeutic impact. There are clinical settings in which inhibition of SPT may be advantageous, for example in sphingolipid storage diseases. On the flip side, enhancing SPT activity may have application in cancer therapy, by promoting the production of cytotoxic sphingolipids, or in diseases of the skin, in which depletion of ceramide accompanies the loss of skin barrier function (Holleran et al., 2006). These three studies illustrate the power and importance of structural determination and how lipid binding can be an intrinsic aspect of enzymatic regulation. We can look forward with pleasure to both biochemical, computational, and structural investigations of this and other lipid metabolic enzymes.

Acknowledgements:

Preparation of this manuscript was supported by the NIH National Institute of Neurological Disorders and Stroke.

Footnotes

Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

The authors have no conflict of interests to declare.

References

  1. Aguilar A, and Saba JD. 2012. Truth and consequences of sphingosine-1-phosphate lyase. Adv. Biol. Regul 52:17–30. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Breslow DK, Collins SR, Bodenmiller B, Aebersold R, Simons K, Shevchenko A, Ejsing CS, and Weissman JS. 2010. Orm family proteins mediate sphingolipid homeostasis. Nature. 463:1048–1053. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Davis D, Kannan M, and Wattenberg B. 2018. Orm/ORMDL proteins: Gate guardians and master regulators. Advances in biological regulation. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Davis DL, Gable K, Suemitsu J, Dunn TM, and Wattenberg BW. 2019. The ORMDL/Orm-serine palmitoyltransferase (SPT) complex is directly regulated by ceramide: Reconstitution of SPT regulation in isolated membranes. J Biol Chem. 294:5146–5156. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Han S, Lone MA, Schneiter R, and Chang A. 2010. Orm1 and Orm2 are conserved endoplasmic reticulum membrane proteins regulating lipid homeostasis and protein quality control. Proc. Natl. Acad. Sci. U. S. A 107:5851–5856. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hannun YA, and Obeid LM. 2018. Sphingolipids and their metabolism in physiology and disease. Nature reviews. Molecular cell biology 19:175–191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Harmon JM, Bacikova D, Gable K, Gupta SD, Han G, Sengupta N, Somashekarappa N, and Dunn TM. 2013. Topological and Functional Characterization of the ssSPTs, Small Activating Subunits of Serine Palmitoyltransferase. J. Biol. Chem [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Holleran WM, Takagi Y, and Uchida Y. 2006. Epidermal sphingolipids: metabolism, function, and roles in skin disorders. FEBS Lett. 580:5456–5466. [DOI] [PubMed] [Google Scholar]
  9. Li S, Xie T, Liu P, Wang L, and Gong X. 2021. Structural insights into the assembly and substrate selectivity of human SPT–ORMDL3 complex. Nature Structural & Molecular Biology. [DOI] [PubMed] [Google Scholar]
  10. Liu P, Xie T, Wu X, Han G, Gupta SD, Zhang Z, Yue J, Dong F, Gable K, Niranjanakumari S, Li W, Wang L, Liu W, Yao R, Cahoon EB, Dunn TM, and Gong X. 2023. Mechanism of sphingolipid homeostasis revealed by structural analysis of Arabidopsis SPT-ORM1 complex. Science advances. 9:eadg0728. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lowther J, Naismith JH, Dunn TM, and Campopiano DJ. 2012. Structural, mechanistic and regulatory studies of serine palmitoyltransferase. Biochem. Soc. Trans 40:547–554. [DOI] [PubMed] [Google Scholar]
  12. Mandon EC, van Echten G, Birk R, Schmidt RR, and Sandhoff K. 1991. Sphingolipid biosynthesis in cultured neurons. Down-regulation of serine palmitoyltransferase by sphingoid bases. European journal of biochemistry. 198:667–674. [DOI] [PubMed] [Google Scholar]
  13. Roelants FM, Breslow DK, Muir A, Weissman JS, and Thorner J. 2011. Protein kinase Ypk1 phosphorylates regulatory proteins Orm1 and Orm2 to control sphingolipid homeostasis in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A 108:19222–19227. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Sarkar A, and Kellogg GE. 2010. Hydrophobicity--shake flasks, protein folding and drug discovery. Current topics in medicinal chemistry. 10:67–83. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Sasset L, Chowdhury KH, Manzo OL, Rubinelli L, Konrad C, Maschek JA, Manfredi G, Holland WL, and Di Lorenzo A. 2021. S1P controls endothelial sphingolipid homeostasis via ORMDL. bioRxiv:2021.2010.2022.465503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Sasset L, Chowdhury KH, Manzo OL, Rubinelli L, Konrad C, Maschek JA, Manfredi G, Holland WL, and Di Lorenzo A. 2022. Sphingosine-1-phosphate controls endothelial sphingolipid homeostasis via ORMDL. EMBO reports:e54689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Schäfer J-H, Körner C, Esch BM, Limar S, Parey K, Walter S, Januliene D, Moeller A, and Fröhlich F. 2023. Structure of the ceramide-bound SPOTS complex. Nature communications. 14:6196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Siow D, Sunkara M, Dunn TM, Morris AJ, and Wattenberg B. 2015. ORMDL/serine palmitoyltransferase stoichiometry determines effects of ORMDL3 expression on sphingolipid biosynthesis. J Lipid Res. 56:898–908. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Siow DL, and Wattenberg BW. 2012. Mammalian ORMDL Proteins Mediate the Feedback Response in Ceramide Biosynthesis. J. Biol. Chem 287:40198–40204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, and Taylor RD. 2003. Improved protein-ligand docking using GOLD. Proteins. 52:609–623. [DOI] [PubMed] [Google Scholar]
  21. Wang S, Robinet P, Smith JD, and Gulshan K. 2015. ORMDL orosomucoid-like proteins are degraded by free-cholesterol-loading-induced autophagy. Proceedings of the National Academy of Sciences of the United States of America. 112:3728–3733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Wang Y, Niu Y, Zhang Z, Gable K, Gupta SD, Somashekarappa N, Han G, Zhao H, Myasnikov AG, Kalathur RC, Dunn TM, and Lee C-H. 2021. Structural insights into the regulation of human serine palmitoyltransferase complexes. Nature Structural & Molecular Biology. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Wattenberg BW 2021. Kicking off sphingolipid biosynthesis: structures of the serine palmitoyltransferase complex. Nature Structural & Molecular Biology. [DOI] [PubMed] [Google Scholar]
  24. Xie T, Liu P, Wu X, Dong F, Zhang Z, Yue J, Mahawar U, Farooq F, Vohra H, Fang Q, Liu W, Wattenberg BW, and Gong X. 2023. Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis. Nature communications. 14:3475. [DOI] [PMC free article] [PubMed] [Google Scholar]

RESOURCES