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X-ray structure of a mammalian stearoyl-CoA desaturase

Nature volume 524, pages 252–256 (2015)Cite this article

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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.

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Protein Data Bank

Data deposits

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

References

  1. 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)

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Paton, C. M. & Ntambi, J. M. Biochemical and physiological function of stearoyl-CoA desaturase. Am. J. Physiol. Endocrinol. Metab. 297, E28–E37 (2009)

    CAS  PubMed  Google Scholar 

  3. Sperling, P., Ternes, P., Zank, T. K. & Heinz, E. The evolution of desaturases. Prostaglandins Leukot. Essent. Fatty Acids 68, 73–95 (2003)

    CAS  PubMed  Google Scholar 

  4. Strittmatter, P. et al. Purification and properties of rat liver microsomal stearyl coenzyme A desaturase. Proc. Natl Acad. Sci. USA 71, 4565–4569 (1974)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  5. 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)

    PubMed  PubMed Central  Google Scholar 

  6. 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)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  7. 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)

    CAS  PubMed  Google Scholar 

  8. Bloch, K. Enzymatic synthesis of monounsaturated fatty acids. Acc. Chem. Res. 2, 193–202 (1969)

    CAS  Google Scholar 

  9. 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 

  10. Behrouzian, B. & Buist, P. H. Fatty acid desaturation: variations on an oxidative theme. Curr. Opin. Chem. Biol. 6, 577–582 (2002)

    CAS  PubMed  Google Scholar 

  11. 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)

    CAS  PubMed  Google Scholar 

  12. 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)

    CAS  PubMed  Google Scholar 

  13. Lou, Y. & Shanklin, J. Evidence that the yeast desaturase Ole1p exists as a dimer in vivo . J. Biol. Chem. 285, 19384–19390 (2010)

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 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)

    CAS  PubMed  Google Scholar 

  15. 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)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  16. Miyazaki, M., Bruggink, S. M. & Ntambi, J. M. Identification of mouse palmitoyl-coenzyme A Δ9-desaturase. J. Lipid Res. 47, 700–704 (2006)

    CAS  PubMed  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)

    CAS  PubMed  Google Scholar 

  18. 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)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  19. 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)

    PubMed  Google Scholar 

  20. 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)

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 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)

    CAS  PubMed  Google Scholar 

  22. 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)

    CAS  PubMed  Google Scholar 

  23. 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)

    PubMed  Google Scholar 

  24. 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)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  25. Behrouzian, B. et al. Mechanism of fatty acid desaturation in the green alga Chlorella vulgaris . Eur. J. Biochem. 268, 3545–3549 (2001)

    CAS  PubMed  Google Scholar 

  26. 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)

    Google Scholar 

  27. Light, R. J., Lennarz, W. J. & Bloch, K. The metabolism of hydroxystearic acids in yeast. J. Biol. Chem. 237, 1793–1800 (1962)

    CAS  PubMed  Google Scholar 

  28. 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)

    CAS  PubMed  Google Scholar 

  29. 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)

    ADS  CAS  PubMed  Google Scholar 

  30. Mitchell, A. et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43, D213–D221 (2015)

    PubMed  Google Scholar 

  31. 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)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  32. Ujwal, R. & Bowie, J. U. Crystallizing membrane proteins using lipidic bicelles. Methods 55, 337–341 (2011)

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Caffrey, M. & Cherezov, V. Crystallizing membrane proteins using lipidic mesophases. Nature Protocols 4, 706–731 (2009)

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. D 69, 1204–1214 (2013)

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data. Methods Enzymol. 276, 307–326 (1997)

    CAS  PubMed  Google Scholar 

  37. Sheldrick, G. M. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D 66, 479–485 (2010)

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Vagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D 66, 22–25 (2010)

    CAS  PubMed  Google Scholar 

  39. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Wang, J. W. et al. SAD phasing by combination of direct methods with the SOLVE/RESOLVE procedure. Acta Crystallogr. D 60, 1244–1253 (2004)

    CAS  PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  42. Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D 68, 352–367 (2012)

    CAS  PubMed  PubMed Central  Google Scholar 

  43. 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)

    PubMed  Google Scholar 

  44. Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–W383 (2007)

    ADS  PubMed  PubMed Central  Google Scholar 

  45. Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004)

    CAS  PubMed  Google Scholar 

  46. 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)

    CAS  PubMed  Google Scholar 

  47. 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)

    CAS  PubMed  PubMed Central  Google Scholar 

  48. 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)

    CAS  PubMed  Google Scholar 

  49. 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)

    CAS  PubMed  Google Scholar 

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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

  1. Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, 77030, Texas, USA

    Yonghong Bai, Jason G. McCoy, Elena J. Levin & Ming Zhou

  2. Department of Biochemistry, University of Wisconsin–Madison, Madison, 53706, Wisconsin, USA

    Pablo Sobrado & Brian G. Fox

  3. NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, 60439, Illinois, USA

    Kanagalaghatta R. Rajashankar

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  1. Yonghong Bai
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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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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 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).

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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