Crystal structure of the tryptophan 2,3-dioxygenase from xanthomonas campestris
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
- L-tryptophan + O2 N-formyl-L-kynurenine
This enzyme belongs to the family of oxidoreductases, specifically those acting on single donors with O2 as oxidant and incorporation of two atoms of oxygen into the substrate (oxygenases). The oxygen incorporated need not be derived from O2. This family of enzymes includes tryptophan 2,3-dioxygenase (TDO, also known as tryptophan oxygenase and L-tryptophan pyrrolase) and indoleamine 2,3-dioxygenase (IDO, also known as tryptophan pyrrolase). These two enzymes are oxidoreductase enzymes that contain one noncovalently bound iron–protoporphyrin IX per monomer. These enzymes catalyze the dioxygenation of L-tryptophan (L-Trp) to N-formyl-L-kynurenine in the first and rate-limiting step of the kynurenine pathway.
The same family of enzymes also includes sIDO from Shewanella oneidensis and PrnB, the second enzyme in the pyrrolnitrin biosynthesis pathway from Pseudomonas fluorescens, although dioxygenase activity has not been demonstrated for either as yet. Recently, a new enzyme with the ability to catalyze L-tryptophan dioxygenation, INDOL1, was identified.
Tryptophan 2,3-dioxygenase was initially discovered in the 1930s and is found in both eukaryotes (human, rat, and rabbit) and prokaryotes (Xanthomonas campestris, and P. fluorescens) Expression of tryptophan 2,3-dioxygenase in mammals is normally restricted to the liver, but it has been identified in the brain and epididymis of some species, and, in some tissues, its production can be induced in response to stimuli.
Enzyme Structure 
Tryptophan 2,3-dioxygenase is a heme-containing cytosolic enzyme encoded by gene TDO2. Crystallographic studies of xcTDO (Xanthomonas campestris TDO) and rmTDO (Ralstonia metallidurans TDO) have revealed that the crystal structures of xcTDO and rmTDO are essentially identical and are intimately associated homotetrameric enzymes. They are best described as a dimer of dimers because the N terminal residues of each monomer form part of the substrate binding site in an adjacent monomer. The proteins are completely helical, and a flexible loop, involved in L-tryptophan binding, is observed just outside the active-site pocket. Interestingly, this loop appears to be substrate-binding induced, as it is observed only in crystals grown in the presence of L-tryptophan.
The only structure available with substrate bound at the active site in the catalytically active ferrous state is xcTDO. In the structure of xcTDO, the carboxy group of L-tryptophan interacts with Arg117, Tyr113 and Thr254. Amino acid residues equivalent to Arg117 and Tyr113 are found in nearly all TDO and IDO proteins. This carboxy-binding motif appears to be essential for substrate binding; arginine reorients in the presence of substrate, co-ordinating the carboxy group of L-tryptophan. The substrate ammonium group is hydrogen-bonded to the side-chain hydroxyl group of Thr254, the 7-propionate group of the heme, and a water molecule.
Enzyme Mechanism 
The initial formation of the ternary complex (1) occurs by substrate binding, followed by dioxygen binding to the ferrous protein. The ternary complex activates O2 and allows the otherwise spin-forbidden reaction to proceeed. The formation of the hydroperoxide intermediate (2) is catalyzed by the loss of the indole proton. Two mechanisms are possible: base-catalysed deprotonation or proton abstraction by bound dioxygen. However, catalysis by the ironbound dioxygen is generally proposed, as a result of experiments showing that catalytic activity is maintained upon substitution of alanine for His55 (the only basic residue in the active site of the enzyme).
The rearrangement of the hydroperoxide intermediate to form the product could occur via the dioxetane intermediate (see figure) or a Criegee intermediate. However, density functional theory calculations on the catalytic mechanism of tryptophan 2,3-dioxygenase have cast doubt on the relevance of the Criegee mechanism.
Biological Function 
Tryptophan 2,3-dioxygenase plays a central role in the physiological regulation of tryptophan flux in the human body. It catalyses the first and rate limiting step of tryptophan degradation along the kynurenine pathway and thereby regulates systemic tryptophan levels.
Disease relevance 
It has been shown that tryptophan 2,3-dioxygenase is expressed in a significant proportion of human tumors. In the same study, tryptophan 2,3-dioxygenase expression by tumors prevented their rejection by immunized mice. A tryptophan 2,3-dioxygenase inhibitor developed by the group restored the ability of these mice to reject tryptophan 2,3-dioxygenase-expressed tumors, demonstrating that tryptophan 2,3-dioxygenase inhibitors display potential in cancer therapy.
Another study showed that tryptophan 2,3-dioxygenase is potentially involved in the metabolic pathway responsible for anxiety-related behavior. Generating mice deficient for tryptophan 2,3-dioxygenase and comparing them to the wild type, the group found that the tryptophan 2,3-dioxygenase-deficient mice showed increased plasma levels not only of tryptophan, but also of serotonin and 5-HIAA in the hippocampus and midbrain. A variety of tests, such as elevated plus maze and open-field tests showed anxiolytic modulation in these knock-out mice, the findings demonstrating a direct link between tryptophan 2,3-dioxygenase and tryptophan metabolism and anxiety-related behavior under physiological conditions.
Structural studies 
- Ren S, Liu H, Licad E, Correia MA (1996). "Expression of rat liver tryptophan 2,3-dioxygenase in Escherichia coli: structural and functional characterization of the purified enzyme". Arch. Biochem. Biophys. 333 (1): 96–102. doi:10.1006/abbi.1996.0368. PMID 8806758.
- Leeds JM, Brown PJ, McGeehan GM, Brown FK, Wiseman JS (1993). "Isotope effects and alternative substrate reactivities for tryptophan 2,3-dioxygenase". J. Biol. Chem. 268 (24): 17781–6. PMID 8349662.
- Thackray SJ, Bruckmann C, Mowat CG, Forouhar F, Chapman SK, Tong L (2008). "Indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase". Handbook of Metalloproteins. doi:10.1002/0470028637.met223.
- Forouhar F, Anderson JL, Mowat CG, Vorobiev SM, Hussain A, Abashidze M, Bruckmann C, Thackray SJ, Seetharaman J, Tucker T, Xiao R, Ma LC, Zhao L, Acton TB, Montelione GT, Chapman SK, Tong L. (2007). "Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase". Proc Natl Acad Sci U S A 104 (2): 473–8. doi:10.1073/pnas.0610007104. PMID 17197414.
- De Laurentis W, Khim L, Anderson JL, Adam A, Johnson KA, Phillips RS, Chapman SK, van Pee KH, Naismith JH. (2007). "The second enzyme in pyrrolnitrin biosynthetic pathway is related to the heme-dependent dioxygenase superfamily". Biochemistry 46 (50): 12393–404. PMID 17924666.
- Ball HJ, Sanchez-Perez A, Weiser S, Austin CJ, Astelbauer F, Miu J, McQuillan JA, Stocker R, Jermiin LS, Hunt NH (2007). "Characterization of an indoleamine 2,3-dioxygenase-like protein found in humans and mice". Gene 396 (1): 203–13. PMID 17499941.
- Kotake Y.; Masayama I. Z. (1936). "Uber den Mechanismus der Kynureninbildung aus Tryptophan". Z. Physiol. Chem 243: 237–44.
- Batabyal D, Yeh SR (2007). "Human tryptophan dioxygenase: a comparison to indoleamine 2,3-dioxygenase". J. Am. Chem. Soc. 129 (50): 15690–701. PMID 18027945.
- Allegri G, Ragazzi E, Bertazzo A, Costa CV, Rocchi R. (2003). "Tryptophan metabolism along the kynurenine pathway in rats". Adv Exp Med Biol. 527: 481–96. PMID 15206766.
- Allegri G, Ragazzi E, Bertazzo A, Biasiolo M, Costa CV (2003). "Tryptophan metabolism in rabbits". Adv Exp Med Biol. 527: 473–9. PMID 15206765.
- Pilotte L, Larrieu P, Stroobant V, Colau D, Dolusic E, Frédérick R, De Plaen E, Uyttenhove C, Wouters J, Masereel B, Van den Eynde BJ (2012). "Reversal of tumoral immune resistance by inhibition of tryptophan 2,3-dioxygenase". Proc. Natl. Acad. Sci. USA. 109 (7): 2497–502. PMID 22308364.
- Zhang Y, Kang SA, Mukherjee T, Bale S, Crane BR, Begley TP, Ealick SE (2007). "Crystal structure and mechanism of tryptophan 2,3-dioxygenase, a heme enzyme involved in tryptophan catabolism and in quinolinate biosynthesis". Biochemistry 46 (1): 145–55. PMID 17198384.
- Thackray SJ, Mowat CG, Chapman SK (2008). "Exploring the mechanism of tryptophan 2,3-dioxygenase". Biochem. Soc. Trans. 36: 1120–3. PMID 19021508.
- Sono M, Roach MP, Coulter ED, Dawson JH (1996). "Heme-Containing Oxygenases". Chem. Rev. 96 (7): 2841–88. PMID 11848843.
- Chung LW, Li X, Sugimoto H, Shiro Y, Morokuma K (2008). "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-dioxygenase". J. Am. Chem. Soc. 130 (37): 12299–309. PMID 18712870.
- Kanai M, Funakoshi H, Takahashi H, Hayakawa T, Mizuno S, Matsumoto K, Nakamura T (2009). "Tryptophan 2,3-dioxygenase is a key modulator of physiological neurogenesis and anxiety-related behavior in mice". Mol. Brain 2 (8). PMID 19323847.
See also