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X-ray structure of a mammalian stearoyl-CoA desaturase

Abstract

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.

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Figure 1: Structure and topology of mouse SCD1.
Figure 2: Architecture of the acyl-CoA binding site.
Figure 3: The dimetal centre.
Figure 4: Proposed interactions between cytb5 and SCD1.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited with the Protein Data Bank under accession number 4YMK.

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Acknowledgements

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.

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Authors and Affiliations

Authors

Contributions

M.Z., B.G.F. and Y.B. conceived the project. Y.B., J.G.M. and E.J.L. expressed, purified and crystallized mouse SCD1, and solved and refined the structure. P.S. and B.G.F. designed and performed mutagenesis and yeast complementation experiments. K.R.R. advised on data collection and structure determination. All authors analysed data and wrote the manuscript.

Corresponding authors

Correspondence to Brian G. Fox or Ming Zhou.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Sequence alignment of mouse SCD1 with other integral membrane desaturases.

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).

Extended Data Figure 2 Structural role of Arg249.

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.

Extended Data Figure 3 Structure of the SCD1 cytoplasmic domain.

Four views of the cytoplasmic domain. The proposed amphipathic helices are coloured blue, while the other helices forming the cytoplasmic domain are green.

Extended Data Figure 4 The mouse SCD1 crystal lattice.

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.

Extended Data Figure 5 Electron density maps for acyl-CoA and the dimetal centre.

a, Stearoyl-CoA bound to SCD1 is superposed with the weighted 2FoFc electron density contoured at 1.5σ (left) or FoFc 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 2FoFc density contoured at 2σ. ce, The dimetal centre superposed with the anomalous difference map, contoured at 5σ (c), the FoFc density calculated with the zinc atoms omitted, contoured at 3σ (d), and the FoFc density calculated with the ordered water molecule between M1 and Asn261 omitted, contoured at 3σ (e).

Extended Data Figure 6 Western blot analysis of SCD expression.

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.

Extended Data Figure 7 Coordination in diiron-containing desaturases.

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).

Extended Data Figure 8 The Thr257–Gln143 hydrogen bond blocks product egress.

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.

Extended Data Figure 9 The SCD1 N terminus.

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.

Extended Data Table 1 Crystallographic and structure refinement statistics

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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

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