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Crystal structure of human stearoyl–coenzyme A desaturase in complex with substrate

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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Figure 1: Overview of the hSCD1 structure.
Figure 2: Zinc ion–binding sites in hSCD1.
Figure 3: Substrate stearoyl-CoA–binding site.

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Protein Data Bank

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References

  1. 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).

    Article  CAS  Google Scholar 

  2. 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).

    CAS  PubMed  Google Scholar 

  3. Guy, J.E., Whittle, E., Kumaran, D., Lindqvist, Y. & Shanklin, J. The crystal structure of the ivy Δ4–16:0-ACP desaturase reveals structural details of the oxidized active site and potential determinants of regioselectivity. J. Biol. Chem. 282, 19863–19871 (2007).

    Article  CAS  Google Scholar 

  4. 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).

    Article  CAS  Google Scholar 

  5. Moche, M., Shanklin, J., Ghoshal, A. & Lindqvist, Y. Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme Δ9 stearoyl-acyl carrier protein desaturase: implications for oxygen activation and catalytic intermediates. J. Biol. Chem. 278, 25072–25080 (2003).

    Article  CAS  Google Scholar 

  6. Whittle, E., Cahoon, E.B., Subrahmanyam, S. & Shanklin, J. A multifunctional acyl-acyl carrier protein desaturase from Hedera helix L. (English ivy) can synthesize 16- and 18-carbon monoene and diene products. J. Biol. Chem. 280, 28169–28176 (2005).

    Article  CAS  Google Scholar 

  7. Shanklin, J., Guy, J.E., Mishra, G. & Lindqvist, Y. Desaturases: emerging models for understanding functional diversification of diiron-containing enzymes. J. Biol. Chem. 284, 18559–18563 (2009).

    Article  CAS  Google Scholar 

  8. 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).

    Article  CAS  Google Scholar 

  9. Stefan, N. et al. Low hepatic stearoyl-CoA desaturase 1 activity is associated with fatty liver and insulin resistance in obese humans. Diabetologia 51, 648–656 (2008).

    Article  CAS  Google Scholar 

  10. Morgan-Lappe, S.E. et al. Identification of Ras-related nuclear protein, targeting protein for Xenopus kinesin-like protein 2, and stearoyl-CoA desaturase 1 as promising cancer targets from an RNAi-based screen. Cancer Res. 67, 4390–4398 (2007).

    Article  CAS  Google Scholar 

  11. Dobrzyn, A. & Ntambi, J.M. Stearoyl-CoA desaturase as a new drug target for obesity treatment. Obes. Rev. 6, 169–174 (2005).

    Article  CAS  Google Scholar 

  12. Igal, R.A. Roles of stearoylCoA desaturase-1 in the regulation of cancer cell growth, survival and tumorigenesis. Cancers (Basel) 3, 2462–2477 (2011).

    Article  CAS  Google Scholar 

  13. Attie, A.D. et al. Relationship between stearoyl-CoA desaturase activity and plasma triglycerides in human and mouse hypertriglyceridemia. J. Lipid Res. 43, 1899–1907 (2002).

    Article  CAS  Google Scholar 

  14. Hulver, M.W. et al. Elevated stearoyl-CoA desaturase-1 expression in skeletal muscle contributes to abnormal fatty acid partitioning in obese humans. Cell Metab. 2, 251–261 (2005).

    Article  CAS  Google Scholar 

  15. Liu, G. Stearoyl-CoA desaturase inhibitors: update on patented compounds. Expert. Opin. Ther. Pat. 19, 1169–1191 (2009).

    Article  CAS  Google Scholar 

  16. Powell, D.A. An overview of patented small molecule stearoyl coenzyme-A desaturase inhibitors (2009–2013). Expert. Opin. Ther. Pat. 24, 155–175 (2014).

    Article  CAS  Google Scholar 

  17. 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).

    Article  CAS  Google Scholar 

  18. 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).

    Article  CAS  Google Scholar 

  19. Rather, L.J. et al. Structure and mechanism of the diiron benzoyl-coenzyme A epoxidase BoxB. J. Biol. Chem. 286, 29241–29248 (2011).

    Article  CAS  Google Scholar 

  20. Nordlund, P., Sjöberg, B.M. & Eklund, H. Three-dimensional structure of the free radical protein of ribonucleotide reductase. Nature 345, 593–598 (1990).

    Article  CAS  Google Scholar 

  21. Heilmann, I., Mekhedov, S., King, B., Browse, J. & Shanklin, J. Identification of the Arabidopsis palmitoyl-monogalactosyldiacylglycerol delta7-desaturase gene FAD5, and effects of plastidial retargeting of Arabidopsis desaturases on the fad5 mutant phenotype. Plant Physiol. 136, 4237–4245 (2004).

    Article  CAS  Google Scholar 

  22. Matsumoto, Y. et al. Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus. Nat. Struct. Mol. Biol. 19, 238–245 (2012).

    Article  CAS  Google Scholar 

  23. Hino, T. et al. Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330, 1666–1670 (2010).

    Article  CAS  Google Scholar 

  24. Derewenda, Z.S. Rational protein crystallization by mutational surface engineering. Structure 12, 529–535 (2004).

    Article  CAS  Google Scholar 

  25. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  26. Wang, B.C. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115, 90–112 (1985).

    Article  CAS  Google Scholar 

  27. Adams, P.D. et al. Phenix: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  Google Scholar 

  28. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  Google Scholar 

  29. Chen, V.B. et al. Molprobity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).

    Article  CAS  Google Scholar 

  30. Collaborative Computing Project. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).

  31. Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).

    Article  Google Scholar 

  32. Waterhouse, A.M., Procter, J.B., Martin, D.M.A., Clamp, M. & Barton, G.J. Jalview Version 2: a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).

    Article  CAS  Google Scholar 

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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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Authors

Contributions

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.

Corresponding authors

Correspondence to Hui Wang or Michael G Klein.

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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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