Abstract
Stearoyl–coenzyme A desaturase-1 (SCD1) has an important role in lipid metabolism, and SCD1 inhibitors are potential therapeutic agents for the treatment of metabolic diseases and cancers. Here we report the 3.25-Å crystal structure of human SCD1 in complex with its substrate, stearoyl–coenzyme A, which defines the new SCD1 dimetal catalytic center and reveals the determinants of substrate binding to provide insights into the catalytic mechanism of desaturation of the stearoyl moiety. The structure also provides a mechanism for localization of SCD1 in the endoplasmic reticulum: human SCD1 folds around a tight hydrophobic core formed from four long α-helices that presumably function as an anchor spanning the endoplasmic reticulum membrane. Furthermore, our results provide a framework for the rational design of pharmacological inhibitors targeting the SCD1 enzyme.
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Acknowledgements
We thank K. Wilson for critical comments. We thank the staff of the Berkeley Center for Structural Biology (BCSB) who operate ALS beamline 5.0.3 and the staff of GM/CA who operate APS beamline 23ID-D. The BCSB is supported in part by the US National Institutes of Health, US National Institute of General Medical Sciences, and GM/CA has been funded in whole or in part with federal funds from the US National Cancer Institute (Y1-CO-1020) and the US National Institute of General Medical Sciences (Y1-GM-1104). The Advanced Light Source and Advanced Photon Source are supported by the Director, Office of Science, Office of Basic Energy Sciences of the US Department of Energy, under contracts DE-AC02-05CH11231 and DE-AC02-06CH11357, respectively. Beamline 8.3.1 at the Advanced Light Source is operated by the University of California Office of the President, Multicampus Research Programs and Initiatives grant MR-15-328599 and Program for Breakthrough Biomedical Research, which is partially funded by the Sandler Foundation. Additional support comes from the US National Institutes of Health (GM105404, GM073210, GM082250 and GM094625), the US National Science Foundation (1330685), Plexxikon Inc. and the M.D. Anderson Cancer Center.
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H.W. was responsible for research strategy; B.-C.S. designed the research and constructs; B.-C.S. and I.L. performed molecular biology; K.L. and H.Z. expressed native and SeMet-labeled protein, respectively; H.Z. purified both native and SeMet-labeled protein with input from H.W.; H.W. and M.G.K. performed crystallization; G.S. and W.L. collected and processed diffraction data and conducted X-ray fluorescence and absorption spectroscopy experiments; H.W. and M.G.K. determined the phases to solve the structure; H.W. built and refined the structure; and H.W. and M.G.K. analyzed the data and wrote the paper, incorporating comments from all authors.
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Integrated supplementary information
Supplementary Figure 1 Multiple sequence alignment for SCD isoforms in humans and mice.
Key residues involved in substrate binding and iron binding are labeled as carets (^) and asterisks (*), respectively. The regions enclosed by dashed lines define three conserved His-box motifs. Sequence alignments were performed with Clustal Omega and edited in Jalview.
Supplementary Figure 2 X-ray fluorescence and X-ray absorption spectroscopy suggest that hSCD1 crystals contain zinc ions.
(a) The X-ray emission spectrum collected at 15000 eV shows two peaks at 8620 eV and 9549 eV corresponding to the Kα and Kβ X-ray emission lines of zinc; (b) The X-ray emission spectra collected at 15000 eV and 11000 eV (above the Zn K1s edge) show characteristic emission lines for zinc, while the spectrum collected at 9500 eV (below the Zn K1s edge) does not show these peaks. (c) X-ray absorption scan across the Zn K1s edge (9659 eV) shows the typical features of strong absorption.
Supplementary Figure 3 Comparison of the dimetal center in hSCD1 with those in two soluble di-iron–containing enzymes.
(a) The di-metal center in hSCD1 is buried between TM2, TM4, CH2 and CH8. The zinc coordination residues (histidines) are shown as sticks. Zincs and the water molecule are illustrated as black and blue spheres, respectively. (b) The di-iron center in caster acyl-ACP desaturase (PDB code 1AFR) is surrounded by a four-helix bundle (α3, α4, α6 and α7). The iron coordination residues (glutamic acids and histidines) are shown as sticks. (c) The di-iron center in benzoyl-CoA epoxidase BoxB (PDB code 3PM5) is also surrounded by a four-helix bundle (αB, αC, αE and αF).
Supplementary Figure 4 Comparison of ligand interfaces in stearoyl-CoA–hSCD1 and benzoyl-CoA–epoxidase BoxB structures.
(a) The stearoyl-CoA-protein interaction in hSCD1; (b) the benzoyl-CoA-protein interaction in epoxidase BoxB (PDB code 3PM5). Metals and substrates are shown as black spheres and yellow stick, respectively. Key residues involved in substrate interaction and metal coordination are shown as sticks. Hydrogen bonds and ionic interactions in the binding site are depicted as dashed lines.
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Wang, H., Klein, M., Zou, H. et al. Crystal structure of human stearoyl–coenzyme A desaturase in complex with substrate. Nat Struct Mol Biol 22, 581–585 (2015). https://doi.org/10.1038/nsmb.3049
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DOI: https://doi.org/10.1038/nsmb.3049
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