Encyclopedia of Biophysics

2013 Edition
| Editors: Gordon C. K. Roberts

Heme Dioxygenases – Computational Studies

  • Patrick von GlehnEmail author
Reference work entry
DOI: https://doi.org/10.1007/978-3-642-16712-6_242



Heme dioxygenase enzymes catalyze the conversion of l-Tryptophan to N-Formylkynurenine via the insertion of both atoms of heme-bound molecular dioxygen at the C2 and C3 positions of the substrate (Fig.  1).
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  1. Capece L, Arrah M, Roitberg AE, Yeh SR, Marti MA, Estrin DA. Substrate stereo-specificity in tryptophan dioxygenase and indoleamine 2,3-dioxygenase. Proteins. 2010;78(14):2961–72.PubMedCentralPubMedGoogle Scholar
  2. Capece L, Lewis-Ballester A, Yeh SR, Estrin DA, Marti MA. Complete reaction mechanism of indoleamine 2,3-dioxygenase as revealed by QM/MM simulations. J Phys Chem B. 2012;116(4):1401–13.PubMedCentralPubMedGoogle Scholar
  3. Chauhan N, Thackray SJ, Rafice SA, Eaton G, Lee M, Efimov I, Basran J, Jenkins PR, Mowat CG, Chapman SK, Raven EL. Reassessment of the reaction mechanism in the heme dioxygenases. J Am Chem Soc. 2009;131(12):4186–7.PubMedGoogle Scholar
  4. Chung LW, Li X, Sugimoto H, Shiro Y, Morokuma K. Density functional theory study on a missing piece in understanding of heme chemistry: the reaction mechanism for indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenas. J Am Chem Soc. 2008;130(37):12299–309.PubMedGoogle Scholar
  5. Chung LW, Li X, Sugimoto H, Shiro Y, Morokuma K. ONIOM study on a missing piece in our understanding of heme chemistry: bacterial tryptophan 2,3-dioxygenase with dual oxidants. J Am Chem Soc. 2010;132(34):11993–12005.PubMedGoogle Scholar
  6. Guallar V, Wallrapp FH. QM/MM methods: looking inside heme proteins biochemistry. Biophys Chem. 2010;149(1–2):1–11.PubMedGoogle Scholar
  7. Jensen KP, Roos BO, Ryde U. O2-binding to heme: electronic structure and spectrum of oxyheme, studied by multiconfigurational methods. J Inorg Biochem. 2005;99(1):45–54.PubMedGoogle Scholar
  8. Lewis-Ballester A, Batabyal D, Egawa T, Lu C, Lin Y, Marti M, Capece L, Estrin DA, Yeh SR. Evidence for a ferryl intermediate in a heme-based dioxygenase. PNAS. 2009;106(41):17371–6.PubMedGoogle Scholar
  9. Röhrig UF, Awad L, Grosdidier A, Larrieu P, Stroobant V, Colau D, Cerundolo V, Simpson AJG, Vogel P, Van den Eynde BJ, Zoete V, Michielin O. Rational Design of Indoleamine 2,3-Dioxygenase Inhibitors. J Med Chem. 2010;53(3):1172–89.Google Scholar
  10. Sono M, Roach MP, Coulter ED, Dawson JH. Heme-Containing Oxygenases Chemical Reviews. 1996;96 (7):2841–88.Google Scholar
  11. Sugimoto H, Oda S, Otsuki T, Hino T, Yoshida T, Shiro Y. Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase. 2006;103(8):2611–6.Google Scholar

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© European Biophysical Societies' Association (EBSA) 2013

Authors and Affiliations

  1. 1.Centre for Computational Chemistry, School of ChemistryUniversity of BristolBristolUK