Molecular Basis for the Substrate Stereoselectivity in Tryptophan Dioxygenase
Open Access
- 14 November 2011
- journal article
- research article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 50 (50), 10910-10918
- https://doi.org/10.1021/bi201439m
Abstract
Tryptophan dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) are the only two heme proteins that catalyze the oxidation reaction of tryptophan (Trp) to N-formylkynurenine. While human IDO is able to oxidize both l- and d-Trp, human TDO (hTDO) displays major specificity for l-Trp. In this work, we aim to interrogate the molecular basis for the substrate stereoselectivity of hTDO. Our previous molecular dynamics simulation studies of Xanthomonas campestris TDO (xcTDO) showed that a hydrogen bond between T254 (T342 in hTDO) and the ammonium group of the substrate is present in the l-Trp-bound enzyme, but not in the d-Trp-bound enzyme. The fact that this is the only notable structural alteration induced by the change in the stereo structure of the substrate prompted us to produce and characterize the T342A mutant of hTDO to evaluate the structural role of T342 in controlling the substrate stereoselectivity of the enzyme. The experimental results indicate that the mutation only slightly perturbs the global structural properties of the enzyme but totally abolishes the substrate stereoselectivity. Molecular dynamics simulations of xcTDO show that T254 controls the substrate stereoselectivity of the enzyme by (i) modulating the hydrogen bonding interaction between the NH3+ group and epoxide oxygen of the ferryl–indole 2,3-epoxide intermediate of the enzyme and (ii) regulating the dynamics of two active site loops, loop250–260 and loop117–130, critical for substrate binding.This publication has 29 references indexed in Scilit:
- Complete Reaction Mechanism of Indoleamine 2,3-Dioxygenase as Revealed by QM/MM SimulationsThe Journal of Physical Chemistry B, 2011
- Substrate stereo-specificity in tryptophan dioxygenase and indoleamine 2,3-dioxygenaseProteins-Structure Function and Bioinformatics, 2010
- Evidence for a ferryl intermediate in a heme-based dioxygenaseProceedings of the National Academy of Sciences of the United States of America, 2009
- Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenaseProceedings of the National Academy of Sciences, 2007
- Crystal Structure and Mechanism of Tryptophan 2,3-Dioxygenase, a Heme Enzyme Involved in Tryptophan Catabolism and in Quinolinate Biosynthesis,Biochemistry, 2006
- Dioxygen affinity in heme proteins investigated by computer simulationJournal of Inorganic Biochemistry, 2006
- Biochemical and medical aspects of the indoleamine 2,3-dioxygenase-initiated l-tryptophan metabolismBiochemical and Biophysical Research Communications, 2005
- Heme-Containing OxygenasesChemical Reviews, 1996
- AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of moleculesComputer Physics Communications, 1995
- Molecular dynamics with coupling to an external bathThe Journal of Chemical Physics, 1984