Stearoyl-CoA desaturase (SCD) is conserved in all eukaryotes and introduces the first double bond into saturated fatty acyl-CoAs1,2,3,4. Because the monounsaturated products of SCD are key precursors of membrane phospholipids, cholesterol esters and triglycerides, SCD is pivotal in fatty acid metabolism. Humans have two SCD homologues (SCD1 and SCD5), while mice have four (SCD1–SCD4). SCD1-deficient mice do not become obese or diabetic when fed a high-fat diet because of improved lipid metabolic profiles and insulin sensitivity5,6. Thus, SCD1 is a pharmacological target in the treatment of obesity, diabetes and other metabolic diseases7. SCD1 is an integral membrane protein located in the endoplasmic reticulum, and catalyses the formation of a cis-double bond between the ninth and tenth carbons of stearoyl- or palmitoyl-CoA8,9. The reaction requires molecular oxygen, which is activated by a di-iron centre, and cytochrome b5, which regenerates the di-iron centre10. To understand better the structural basis of these characteristics of SCD function, here we crystallize and solve the structure of mouse SCD1 bound to stearoyl-CoA at 2.6 Å resolution. The structure shows a novel fold comprising four transmembrane helices capped by a cytosolic domain, and a plausible pathway for lateral substrate access and product egress. The acyl chain of the bound stearoyl-CoA is enclosed in a tunnel buried in the cytosolic domain, and the geometry of the tunnel and the conformation of the bound acyl chain provide a structural basis for the regioselectivity and stereospecificity of the desaturation reaction. The dimetal centre is coordinated by a unique spacial arrangement of nine conserved histidine residues that implies a potentially novel mechanism for oxygen activation. The structure also illustrates a possible route for electron transfer from cytochrome b5 to the di-iron centre.
This is a preview of subscription content, access via your institution
Open Access articles citing this article.
Nature Communications Open Access 27 May 2022
Essential role of a conserved aspartate for the enzymatic activity of plasmanylethanolamine desaturase
Cellular and Molecular Life Sciences Open Access 28 March 2022
Journal of Experimental & Clinical Cancer Research Open Access 24 August 2021
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
Goren, M. A. & Fox, B. G. Wheat germ cell-free translation, purification, and assembly of a functional human stearoyl-CoA desaturase complex. Protein Expr. Purif. 62, 171–178 (2008)
Paton, C. M. & Ntambi, J. M. Biochemical and physiological function of stearoyl-CoA desaturase. Am. J. Physiol. Endocrinol. Metab. 297, E28–E37 (2009)
Sperling, P., Ternes, P., Zank, T. K. & Heinz, E. The evolution of desaturases. Prostaglandins Leukot. Essent. Fatty Acids 68, 73–95 (2003)
Strittmatter, P. et al. Purification and properties of rat liver microsomal stearyl coenzyme A desaturase. Proc. Natl Acad. Sci. USA 71, 4565–4569 (1974)
Gutiérrez-Juárez, R. et al. Critical role of stearoyl-CoA desaturase-1 (SCD1) in the onset of diet-induced hepatic insulin resistance. J. Clin. Invest. 116, 1686–1695 (2006)
Ntambi, J. M. et al. Loss of stearoyl-CoA desaturase-1 function protects mice against adiposity. Proc. Natl Acad. Sci. USA 99, 11482–11486 (2002)
Zhang, Z., Dales, N. A. & Winther, M. D. Opportunities and challenges in developing stearoyl-coenzyme A desaturase-1 inhibitors as novel therapeutics for human disease. J. Med. Chem. 57, 5039–5056 (2014)
Bloch, K. Enzymatic synthesis of monounsaturated fatty acids. Acc. Chem. Res. 2, 193–202 (1969)
Enoch, H. G., Catala, A. & Strittmatter, P. Mechanism of rat liver microsomal stearyl-CoA desaturase. Studies of the substrate specificity, enzyme-substrate interactions, and the function of lipid. J. Biol. Chem. 251, 5095–5103 (1976)
Behrouzian, B. & Buist, P. H. Fatty acid desaturation: variations on an oxidative theme. Curr. Opin. Chem. Biol. 6, 577–582 (2002)
Pebay-Peyroula, E., Rummel, G., Rosenbusch, J. P. & Landau, E. M. X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science 277, 1676–1681 (1997)
Man, W. C., Miyazaki, M., Chu, K. & Ntambi, J. M. Membrane topology of mouse stearoyl-CoA desaturase 1. J. Biol. Chem. 281, 1251–1260 (2006)
Lou, Y. & Shanklin, J. Evidence that the yeast desaturase Ole1p exists as a dimer in vivo . J. Biol. Chem. 285, 19384–19390 (2010)
Meesapyodsuk, D. & Qiu, X. Structure determinants for the substrate specificity of acyl-CoA Δ9 desaturases from a marine copepod. ACS Chem. Biol. 9, 922–934 (2014)
Dallerac, R. et al. A Δ9 desaturase gene with a different substrate specificity is responsible for the cuticular diene hydrocarbon polymorphism in Drosophila melanogaster . Proc. Natl Acad. Sci. USA 97, 9449–9454 (2000)
Miyazaki, M., Bruggink, S. M. & Ntambi, J. M. Identification of mouse palmitoyl-coenzyme A Δ9-desaturase. J. Lipid Res. 47, 700–704 (2006)
Shanklin, J., Whittle, E. & Fox, B. G. Eight histidine residues are catalytically essential in a membrane-associated iron enzyme, stearoyl-CoA desaturase, and are conserved in alkane hydroxylase and xylene monooxygenase. Biochemistry 33, 12787–12794 (1994)
Shanklin, J., Achim, C., Schmidt, H., Fox, B. G. & Munck, E. Mossbauer studies of alkane omega-hydroxylase: evidence for a diiron cluster in an integral-membrane enzyme. Proc. Natl Acad. Sci. USA 94, 2981–2986 (1997)
Högbom, M., Huque, Y., Sjoberg, B. M. & Nordlund, P. Crystal structure of the di-iron/radical protein of ribonucleotide reductase from Corynebacterium ammoniagenes. Biochemistry 41, 1381–1389 (2002)
Lindqvist, Y., Huang, W., Schneider, G. & Shanklin, J. Crystal structure of delta9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins. EMBO J. 15, 4081–4092 (1996)
Sazinsky, M. H. & Lippard, S. J. Correlating structure with function in bacterial multicomponent monooxygenases and related diiron proteins. Acc. Chem. Res. 39, 558–566 (2006)
Broadwater, J. A., Ai, J., Loehr, T. M., Sanders-Loehr, J. & Fox, B. G. Peroxodiferric intermediate of stearoyl-acyl carrier protein Δ9 desaturase: oxidase reactivity during single turnover and implications for the mechanism of desaturation. Biochemistry 37, 14664–14671 (1998)
Moënne-Loccoz, P., Baldwin, J., Ley, B. A., Loehr, T. M. & Bollinger, J. M., Jr O2 activation by non-heme diiron proteins: identification of a symmetric μ-1,2-peroxide in a mutant of ribonucleotide reductase. Biochemistry 37, 14659–14663 (1998)
Banerjee, R., Proshlyakov, Y., Lipscomb, J. D. & Proshlyakov, D. A. Structure of the key species in the enzymatic oxidation of methane to methanol. Nature 518, 431–434 (2015)
Behrouzian, B. et al. Mechanism of fatty acid desaturation in the green alga Chlorella vulgaris . Eur. J. Biochem. 268, 3545–3549 (2001)
Buist, P. H., Behrouzian, B., Kostas, A. A., Dawson, B. & Black, B. Fluorinated fatty acids: new mechanistic probes for desaturases. Chem. Commun. 23, 2671–2672 (1996)
Light, R. J., Lennarz, W. J. & Bloch, K. The metabolism of hydroxystearic acids in yeast. J. Biol. Chem. 237, 1793–1800 (1962)
Dailey, H. A. & Strittmatter, P. Characterization of the interaction of amphipathic cytochrome b5 with stearyl coenzyme A desaturase and NADPH:cytochrome P-450 reductase. J. Biol. Chem. 255, 5184–5189 (1980)
Page, C. C., Moser, C. C., Chen, X. & Dutton, P. L. Natural engineering principles of electron tunnelling in biological oxidation-reduction. Nature 402, 47–52 (1999)
Mitchell, A. et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43, D213–D221 (2015)
Jaakola, V. P. et al. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322, 1211–1217 (2008)
Ujwal, R. & Bowie, J. U. Crystallizing membrane proteins using lipidic bicelles. Methods 55, 337–341 (2011)
Caffrey, M. & Cherezov, V. Crystallizing membrane proteins using lipidic mesophases. Nature Protocols 4, 706–731 (2009)
Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)
Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. D 69, 1204–1214 (2013)
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data. Methods Enzymol. 276, 307–326 (1997)
Sheldrick, G. M. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D 66, 479–485 (2010)
Vagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D 66, 22–25 (2010)
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)
Wang, J. W. et al. SAD phasing by combination of direct methods with the SOLVE/RESOLVE procedure. Acta Crystallogr. D 60, 1244–1253 (2004)
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)
Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D 68, 352–367 (2012)
Painter, J. & Merritt, E. A. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr. D 62, 439–450 (2006)
Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–W383 (2007)
Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004)
Arnesano, F., Banci, L., Bertini, I., Felli, I. C. & Koulougliotis, D. Solution structure of the B form of oxidized rat microsomal cytochrome b 5 and backbone dynamics via 15N rotating-frame NMR-relaxation measurements. Biological implications. Eur. J. Biochem. 260, 347–354 (1999)
West, R. W., Jr, Yocum, R. R. & Ptashne, M. Saccharomyces cerevisiae GAL1–GAL10 divergent promoter region: location and function of the upstream activating sequence UASG. Mol. Cell. Biol. 4, 2467–2478 (1984)
Stukey, J. E., McDonough, V. M. & Martin, C. E. Isolation and characterization of OLE1, a gene affecting fatty acid desaturation from Saccharomyces cerevisiae . J. Biol. Chem. 264, 16537–16544 (1989)
Gomez, F. E. et al. Molecular differences caused by differentiation of 3T3–L1 preadipocytes in the presence of either dehydroepiandrosterone (DHEA) or 7-oxo-DHEA. Biochemistry 41, 5473–5482 (2002)
This work was supported by the US National Institutes of Health (R01DK088057, R01GM098878, R01HL086392, U54GM095315, U54GM094584 and R01GM050853), the American Heart Association (12EIA8850017), and the Cancer Prevention and Research Institute of Texas (R12MZ). Final data were collected at Northeastern Collaborative Access Team (NE-CAT) beamlines, which are supported by a grant from the National Institute of General Medical Sciences (P41GM103403). Crystals were screened at beamline 17-ID at the Advanced Photon Source, beamlines 8.2.2 and 5.0.2 at Berkeley Center for Structural Biology at the Lawrence Berkeley Laboratory.
The authors declare no competing financial interests.
Extended data figures and tables
The N terminus of mouse SCD1 is not shown. For all the other sequences, only the region aligning to mouse SCD1 is included. Secondary structure elements from the mouse SCD1 crystal structure are labelled. Residues discussed in the text are highlighted in red (histidines in the primary coordination sphere of the dimetal unit), purple (carboxylates in the secondary coordination sphere of the dimetal unit), blue (acyl-chain binding site), yellow (CoA-binding site), green (residues that may determine the length of bound acyl chains), black (mutations that change the substrate specificity in mouse SCD3) and grey (Arg249 in the transmembrane region). The accession numbers for sequences included in the alignment are: mouse SCD1 (GI: 31543675), mouse SCD3 (GI: 13277368), human SCD1 (GI: 53759151), zebrafish SCD1 (GI: 28394115), D. melanogaster desat2 (GI: 24646295), C. hyperboreus ChDes9-1 (GI: 589834955), C. elegans FAT5 (GI: 544604099), delta-9 desaturase from Synechocystis sp. PCC 6803 (GI: 339274799), delta-9 desaturase from A. thaliana (GI: 18402641), and yeast OLE1 (GI: 1322552).
The conserved arginine residue Arg249, located on TM4 within the transmembrane region of the protein, forms a hydrogen bond with the carbonyl oxygen of Cys222 on TM3. This interaction may help stabilize the kink in TM3 caused by Pro226 on the following turn.
Four views of the cytoplasmic domain. The proposed amphipathic helices are coloured blue, while the other helices forming the cytoplasmic domain are green.
Cross-sections of the crystal lattice for the P212121 mouse SCD1 lipidic cubic phase crystals, viewed from two perpendicular directions. One asymmetric unit is coloured blue. Within an individual asymmetric unit, interactions between the two chains are mediated by residues from a C-terminal cloning artefact. All interactions with chains in neighbouring asymmetric units involve antiparallel orientations of the interacting monomers and have small interface areas.
a, Stearoyl-CoA bound to SCD1 is superposed with the weighted 2Fo − Fc electron density contoured at 1.5σ (left) or Fo − Fc electron density calculated with the substrate molecule omitted and contoured at 2.3σ (right). b, Stereoview of the dimetal centre and coordinating histidines, shown with the weighted 2Fo − Fc density contoured at 2σ. c–e, The dimetal centre superposed with the anomalous difference map, contoured at 5σ (c), the Fo − Fc density calculated with the zinc atoms omitted, contoured at 3σ (d), and the Fo − Fc density calculated with the ordered water molecule between M1 and Asn261 omitted, contoured at 3σ (e).
a, b, Analysis of two separate yeast expression trials after introduction of mutations to mouse SCD3 to impart catalytic specificity of mouse SCD1. Contents of lanes are as indicated in the gel. The position of SCD is indicated by a black star. Additional bands are other proteins detected by the polyclonal antibody. Dotted line in a shows the portion of the complete gel image included in Fig. 2f; dotted line in b shows the corresponding expression trials from the second experiment. a, Expression trial 1, with gel artefacts in lanes 2 and 3. b, Expression trial 2, with gel artefacts in lanes 4, 6 and 7.
a, Stereoview of residues forming both the first and second coordination shell around the dimetal centre in mouse SCD1. b, Stereoview of the coordination of the dimetal centre in the stearoyl-acyl carrier protein desaturase from the castor bean (PDB accession 1AFR).
The surface of the substrate tunnel housing the acyl chain is shown, with the structural elements AH1, H2 and TM4, and the hydrogen-bonded residues Thr257 and Gln143 highlighted in the inset. The proximity of these two residues creates the kinked shape of the substrate tunnel, and their separation would result in a larger opening capable of releasing the product into the bilayer.
Two perpendicular views of mouse SCD1, from within the plane of the membrane and from the cytoplasmic side, showing the interaction between the N terminus (red ribbon) and the cytosolic domain (beige surface). The dashed yellow circles indicate the approximate location of the metal atoms.
About this article
Cite this article
Bai, Y., McCoy, J., Levin, E. et al. X-ray structure of a mammalian stearoyl-CoA desaturase. Nature 524, 252–256 (2015). https://doi.org/10.1038/nature14549
This article is cited by
Nature Reviews Drug Discovery (2022)
Journal of Physiology and Biochemistry (2022)
Applied Microbiology and Biotechnology (2022)
Essential role of a conserved aspartate for the enzymatic activity of plasmanylethanolamine desaturase
Cellular and Molecular Life Sciences (2022)
Fatty acid desaturases (FADs) modulate multiple lipid metabolism pathways to improve plant resistance
Molecular Biology Reports (2022)