Sugimoto, H. et al. Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase. Proc. Natl Acad. Sci. USA 103, 2611-2616

Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 03/2006; 103(8):2611-6. DOI: 10.1073/pnas.0508996103
Source: PubMed


Human indoleamine 2,3-dioxygenase (IDO) catalyzes the cleavage of the pyrrol ring of L-Trp and incorporates both atoms of a molecule of oxygen (O2). Here we report on the x-ray crystal structure of human IDO, complexed with the ligand inhibitor 4-phenylimidazole and cyanide. The overall structure of IDO shows two alpha-helical domains with the heme between them. A264 of the flexible loop in the heme distal side is in close proximity to the iron. A mutant analysis shows that none of the polar amino acid residues in the distal heme pocket are essential for activity, suggesting that, unlike the heme-containing monooxygenases (i.e., peroxidase and cytochrome P450), no protein group of IDO is essential in dioxygen activation or proton abstraction. These characteristics of the IDO structure provide support for a reaction mechanism involving the abstraction of a proton from the substrate by iron-bound dioxygen. Inactive mutants (F226A, F227A, and R231A) retain substrate-binding affinity, and an electron density map reveals that 2-(N-cyclohexylamino)ethane sulfonic acid is bound to these residues, mimicking the substrate. These findings suggest that strict shape complementarities between the indole ring of the substrate and the protein side chains are required, not for binding, but, rather, to permit the interaction between the substrate and iron-bound dioxygen in the first step of the reaction. This study provides the structural basis for a heme-containing dioxygenase mechanism, a missing piece in our understanding of heme chemistry.

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    • "Indoleamine 2,3-dioxygenase (IDO) has emerged as a pivotal modulator/regulator of the immune response [13], [28], [34]. IDO is a heme-containing cytosolic enzyme that is the rate limiting catalyst to the metabolism of the essential amino acid tryptophan within the kynurenine pathway [15], [16]. These genes contain interferon (IFN) response elements and therefore, IFNs are powerful inducers of IDO expression [23]. "
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    PLoS ONE 04/2014; 9(4):e95720. DOI:10.1371/journal.pone.0095720 · 3.23 Impact Factor
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    • "For synthesis of peptides we selected epitopes that are surface‐ oriented and hydrophilic [Sugimoto et al., 2006]. We determined three regions on the IDO1 protein sequence that had good hydrophilicity as predicted by the Lasergene software (DNAStar, WI). "
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    Journal of Cellular Biochemistry 02/2014; 115(2). DOI:10.1002/jcb.24674 · 3.26 Impact Factor
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    • "With both helices running parallel, structural changes are potentially transmitted to the heme and/or the gating residues via these rigid structures. (B) Crystal structure of wild type rhIDO-1 showing the proximity between C85 and C129 (5.7 angstroms) and the heme active site (PDB: 2D0T, [16] "
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    ABSTRACT: The hemoprotein indoleamine 2,3-dioxygenase-1 (IDO1) is the first and rate-limiting enzyme in mammalian tryptophan metabolism. Interest in IDO1 continues to grow, due to the ever expanding influence IDO1 plays in the immune response. This study examined the contribution of all individual cysteine residues towards the overall catalytic properties and stability of recombinant human IDO1 via mutagenesis studies using a range of biochemical and spectroscopic techniques, including in vitro kinetic assessment, secondary structure identification via circular dichroism spectroscopy and thermal stability assessment. Upon mutation of cysteine residues we observed changes in secondary structure (principally, shifting from α-helix/β-sheet features to random coil structures) that produced out of plane heme torsion and puckering, changes to thermal stability (including gains in stability for one mutant protein) and differences in enzymatic activity (such as, increased ability to convert non-natural substrates, e.g. D-tryptophan) from wild type IDO1 enzyme.
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