Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Structural basis of kynurenine 3-monooxygenase inhibition


Inhibition of kynurenine 3-monooxygenase (KMO), an enzyme in the eukaryotic tryptophan catabolic pathway (that is, kynurenine pathway), leads to amelioration of Huntington’s-disease-relevant phenotypes in yeast, fruitfly and mouse models1,2,3,4,5, as well as in a mouse model of Alzheimer’s disease3. KMO is a flavin adenine dinucleotide (FAD)-dependent monooxygenase and is located in the outer mitochondrial membrane where it converts l-kynurenine to 3-hydroxykynurenine. Perturbations in the levels of kynurenine pathway metabolites have been linked to the pathogenesis of a spectrum of brain disorders6, as well as cancer7,8 and several peripheral inflammatory conditions9. Despite the importance of KMO as a target for neurodegenerative disease, the molecular basis of KMO inhibition by available lead compounds has remained unknown. Here we report the first crystal structure of Saccharomyces cerevisiae KMO, in the free form and in complex with the tight-binding inhibitor UPF 648. UPF 648 binds close to the FAD cofactor and perturbs the local active-site structure, preventing productive binding of the substrate l-kynurenine. Functional assays and targeted mutagenesis reveal that the active-site architecture and UPF 648 binding are essentially identical in human KMO, validating the yeast KMO–UPF 648 structure as a template for structure-based drug design. This will inform the search for new KMO inhibitors that are able to cross the blood–brain barrier in targeted therapies against neurodegenerative diseases such as Huntington’s, Alzheimer’s and Parkinson’s diseases.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Inhibition of KMO by UPF 648.
Figure 2: Yeast KMO crystal structure.
Figure 3: The Saccharomyces cerevisiae KMO active site.
Figure 4: Mechanism and importance of Arg 83.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited in the Protein Data Bank ( under accession numbers 4J2W, 4J31, 4J33, 4J36 and 4J34.


  1. Giorgini, F. et al. Histone deacetylase inhibition modulates kynurenine pathway activation in yeast, microglia, and mice expressing a mutant huntingtin fragment. J. Biol. Chem. 283, 7390–7400 (2008)

    CAS  Article  Google Scholar 

  2. Giorgini, F., Guidetti, P., Nguyen, Q., Bennett, S. C. & Muchowski, P. J. A genomic screen in yeast implicates kynurenine 3-monooxygenase as a therapeutic target for Huntington disease. Nature Genet. 37, 526–531 (2005)

    CAS  Article  Google Scholar 

  3. Zwilling, D. et al. Kynurenine 3-monooxygenase inhibition in blood ameliorates neurodegeneration. Cell 145, 863–874 (2011)

    CAS  Article  Google Scholar 

  4. Campesan, S. et al. The kynurenine pathway modulates neurodegeneration in a Drosophila model of Huntington’s disease. Curr. Biol. 21, 961–966 (2011)

    CAS  Article  Google Scholar 

  5. Green, E. W. et al. Drosophila eye color mutants as therapeutic tools for Huntington disease. Fly 6, 117–120 (2012)

    CAS  Article  Google Scholar 

  6. Schwarcz, R., Bruno, J. P., Muchowski, P. J. & Wu, H.-Q. Kynurenines in the mammalian brain: when physiology meets pathology. Nature Rev. Neurosci. 13, 465–477 (2012)

    CAS  Article  Google Scholar 

  7. Platten, M., Litzenburger, U. & Wick, W. The aryl hydrocarbon receptor in tumor immunity. Oncoimmunology 1, 396–397 (2012)

    Article  Google Scholar 

  8. Liu, X., Newton, R. C., Friedman, S. M. & Scherle, P. A. Indoleamine 2,3-dioxygenase, an emerging target for anti-cancer therapy. Curr. Cancer Drug Targets 9, 938–952 (2009)

    CAS  Article  Google Scholar 

  9. Filippini, P. et al. Emerging concepts on inhibitors of indoleamine 2,3-dioxygenase in rheumatic diseases. Curr. Med. Chem. 19, 5381–5393 (2012)

    CAS  Article  Google Scholar 

  10. Stone, T. W. & Perkins, M. N. Quinolinic acid: a potent endogenous excitant at amino acid receptors in CNS. Eur. J. Pharmacol. 72, 411–412 (1981)

    CAS  Article  Google Scholar 

  11. Schwarcz, R., Whetsell, W. O., Jr & Mangano, R. M. Quinolinic acid: an endogenous metabolite that produces axon-sparing lesions in rat brain. Science 219, 316–318 (1983)

    ADS  CAS  Article  Google Scholar 

  12. Okuda, S., Nishiyama, N., Saito, H. & Katsuki, H. Hydrogen peroxide-mediated neuronal cell death induced by an endogenous neurotoxin, 3-hydroxykynurenine. Proc. Natl Acad. Sci. USA 93, 12553–12558 (1996)

    ADS  CAS  Article  Google Scholar 

  13. Copeland, C. S., Neale, S. A. & Salt, T. E. Actions of xanthurenic acid, a putative endogenous group II metabotropic glutamate receptor agonist, on sensory transmission in the thalamus. Neuropharmacology 66, 133–142 (2013)

    CAS  Article  Google Scholar 

  14. Fazio, F. et al. Cinnabarinic acid, an endogenous metabolite of the kynurenine pathway, activates type 4 metabotropic glutamate receptors. Mol. Pharmacol. 81, 643–656 (2012)

    CAS  Article  Google Scholar 

  15. Guillemin, G. J. et al. Characterization of the kynurenine pathway in human neurons. J. Neurosci. 27, 12884–12892 (2007)

    CAS  Article  Google Scholar 

  16. Guillemin, G. J., Smith, D. G., Smythe, G. A., Armati, P. J. & Brew, B. J. Expression of the kynurenine pathway enzymes in human microglia and macrophages. Adv. Exp. Med. Biol. 527, 105–112 (2003)

    CAS  Article  Google Scholar 

  17. Cozzi, A., Carpenedo, R. & Moroni, F. Kynurenine hydroxylase inhibitors reduce ischemic brain damage: studies with (m-nitrobenzoyl)-alanine (mNBA) and 3,4-dimethoxy-[-N-4-(nitrophenyl)thiazol-2yl]-benzenesulfonamide (Ro 61–8048) in models of focal or global brain ischemia. J. Cereb. Blood Flow Metab. 19, 771–777 (1999)

    CAS  Article  Google Scholar 

  18. Moroni, F. et al. Studies on the neuroprotective action of kynurenine mono-oxygenase inhibitors in post-ischemic brain damage. Adv. Exp. Med. Biol. 527, 127–136 (2003)

    CAS  Article  Google Scholar 

  19. Richter, A. & Hamann, M. The kynurenine 3-hydroxylase inhibitor Ro 61–8048 improves dystonia in a genetic model of paroxysmal dyskinesia. Eur. J. Pharmacol. 478, 47–52 (2003)

    CAS  Article  Google Scholar 

  20. Samadi, P. et al. Effect of kynurenine 3-hydroxylase inhibition on the dyskinetic and antiparkinsonian responses to levodopa in Parkinsonian monkeys. Mov. Disord. 20, 792–802 (2005)

    Article  Google Scholar 

  21. Clark, C. J. et al. Prolonged survival of a murine model of cerebral malaria by kynurenine pathway inhibition. Infect. Immun. 73, 5249–5251 (2005)

    CAS  Article  Google Scholar 

  22. Reinhart, P. H. & Kelly, J. W. Treating the periphery to ameliorate neurodegenerative diseases. Cell 145, 813–814 (2011)

    CAS  Article  Google Scholar 

  23. Sapko, M. T. et al. Endogenous kynurenate controls the vulnerability of striatal neurons to quinolinate: implications for Huntingtons’s disease. Exp. Neurol. 197, 31–40 (2006)

    CAS  Article  Google Scholar 

  24. Ceresoli-Borroni, G., Guidetti, P., Amori, L., Pellicciari, R. & Schwarcz, R. Perinatal kynurenine 3-hydroxylase inhibition in rodents: pathophysiological implications. J. Neurosci. Res. 85, 845–854 (2007)

    CAS  Article  Google Scholar 

  25. Uemura, T. & Hirai, K. l-kynurenine 3-monooxygenase from mitochondrial outer membrane of pig liver: purification, some properties, and monoclonal antibodies directed to the enzyme. J. Biochem. 123, 253–262 (1998)

    CAS  Article  Google Scholar 

  26. Palfey, B. A. & McDonald, C. A. Control of catalysis in flavin-dependent monooxygenases. Arch. Biochem. Biophys. 493, 26–36 (2010)

    CAS  Article  Google Scholar 

  27. van Berkel, W. J. H., Kamerbeek, N. M. & Fraaije, M. W. Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts. J. Biotechnol. 124, 670–689 (2006)

    CAS  Article  Google Scholar 

  28. McCulloch, K. M., Mukherjee, T., Begley, T. P. & Ealick, S. E. Structure of the PLP degradative enzyme 2-methyl-3- hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti MAFF303099 and its mechanistic implications. Biochemistry 48, 4139–4149 (2009)

    CAS  Article  Google Scholar 

  29. Ortiz-Maldonado, M., Ballou, D. P. & Massey, V. A rate-limiting conformational change of the flavin in p-hydroxybenzoate hydroxylase is necessary for ligand exchange and catalysis: studies with 8-mercapto- and 8-hydroxy-flavins. Biochemistry 40, 1091–1101 (2001)

    CAS  Article  Google Scholar 

  30. Fukui, S., Schwarcz, R., Rapoport, S. I., Takada, Y. & Smith, Q. R. Blood–brain barrier transport of kynurenines: implications for brain synthesis and metabolism. J. Neurochem. 56, 2007–2017 (1991)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  32. McCoy, A. J., Storoni, L. C. & Read, R. J. Simple algorithm for a maximum-likelihood SAD function. Acta Crystallogr. D 60, 1220–1228 (2004)

    Article  Google Scholar 

  33. Terwilliger, T. C. et al. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr. D 64, 61–69 (2008)

    CAS  Article  Google Scholar 

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

    Article  Google Scholar 

  35. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  38. Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005)

    CAS  Article  Google Scholar 

  39. Cornell, W. D. et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117, 5179–5197 (1995)

    CAS  Article  Google Scholar 

  40. Jakalian, A., Jack, D. B. & Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J. Comput. Chem. 23, 1623–1641 (2002)

    CAS  Article  Google Scholar 

Download references


We thank R. Schwarcz for supplying UPF 648. We also thank E. McKenzie for expressing human KMO. We also thank Diamond Light Source for access to MX beamlines.

Author information

Authors and Affiliations



N.S.S., F.G., D.L. and T.F.O. initiated the project, designed experiments, analysed data and wrote the manuscript; M.A. cloned purified and crystallized proteins and performed biochemical assays; C.L. crystallized proteins, collected and processed diffraction data; D.J.H. developed and analysed some of the biochemical assays; P.L. performed molecular modelling of l-KYN binding.

Corresponding author

Correspondence to Nigel S. Scrutton.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-5 and Supplementary Tables 1-3. (PDF 1183 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Amaral, M., Levy, C., Heyes, D. et al. Structural basis of kynurenine 3-monooxygenase inhibition. Nature 496, 382–385 (2013).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing