Substrate binding in human indoleamine 2,3-dioxygenase 1: A spectroscopic analysis.

Human indoleamine 2,3-dioxygenase (hIDO1) is a heme enzyme that catalyzes the oxidative cleavage of the L-tryptophan indole ring. As increased levels of hIDO1 expression in tumor cells correlate with a poor prognosis for surviving several cancer types, hIDO1 has become an appealing drug target for cancer therapy. However, detailed structural knowledge of the catalytically active complex is necessary to eb able to design de novo inhibitors selective for hIDO1. Here we have applied Fourier transform infrared (FTIR) and nanosecond time-resolved optical spectroscopy to hIDO1 variants with modified heme pocket structures to identify important amino acid residues that stabilize the substrate in the active site. A cluster of small side chain residues at positions 260-265 ensures structural flexibility of the binding site. Thr379 and Arg231 are key residues acting in concert to bind the substrate. Thr379 is the final residue of a disordered loop; the neighboring Gly380, however, is still visible in the X-ray structure of the substrate-free protein, 20Å away from the heme iron. Therefore, large-scale conformational changes are necessary to bring Thr379 close to the substrate. The use of substrate analogs further reveals that an indole-like side chain with two aromatic rings and L-stereoisomery at the Cα are required for high affinity binding.

Substrate Inhibition in Human Indoleamine 2,3-Dioxygenase.

Human indoleamine 2,3-dioxygenase (hIDO) catalyzes the oxidative cleavage of the L-tryptophan (l-Trp) pyrrole ring. Catalysis is inhibited at high substrate concentrations; mechanistic details of this observation are, however, still under debate. Using time-resolved optical spectroscopy, we have analyzed the dynamics of ternary complex formation between hIDO, l-Trp, and a diatomic ligand. The physiological ligand dioxygen (O2) was replaced by carbon monoxide to exclude enzymatic turnover. Quantitative analysis of the kinetics reveals that the ternary complex forms whenever O2 binds first, whereas an l-Trp substrate molecule arriving prior to O2 in the active site causes self-inhibition. Bound l-Trp prevents the ligand from approaching the heme iron and, therefore, impedes formation of the catalytically active ternary complex.

Ligand migration in human indoleamine-2,3 dioxygenase.

Human indoleamine 2,3-dioxygenase (hIDO), a monomeric heme enzyme, catalyzes the oxidative degradation of L-tryptophan (L-Trp) and other indoleamine derivatives. Its activity follows typical Michaelis-Menten behavior only for L-Trp concentrations up to 50 µM; a further increase in the concentration of L-Trp causes a decrease in the activity. This substrate inhibition of hIDO is a result of the binding of a second L-Trp molecule in an inhibitory substrate binding site of the enzyme. The molecular details of the reaction and the inhibition are not yet known. In the following, we summarize the present knowledge about this heme enzyme.

Ligand and substrate migration in human indoleamine 2,3-dioxygenase.

Human indoleamine 2,3-dioxygenase (hIDO), a monomeric heme enzyme, catalyzes the oxidative degradation of L-Trp and other indoleamine derivatives. Using Fourier transform infrared and optical absorption spectroscopy, we have investigated the interplay between ferrous hIDO, the ligand analog CO, and the physiological substrate L-Trp. These data provide the long sought evidence for two distinct L-Trp binding sites. Upon photodissociation from the heme iron at T > 200 K, CO escapes into the solvent. Concomitantly, L-Trp exits the active site and, depending on the l-Trp concentration, migrates to a secondary binding site or into the solvent. Although L-Trp is spectroscopically silent at this site, it is still noticeable due to its pronounced effect on the CO association kinetics, which are significantly slower than those of L-Trp-free hIDO. L-Trp returns to its initial site only after CO has rebound to the heme iron.

Determinants of substrate internalization in the distal pocket of dehaloperoxidase hemoglobin of Amphitrite ornata.

Dehaloperoxidase (DHP) is a small heme protein in the coelom of the terebellid polychaete Amphitrite ornata. It can act both as an oxygen storage protein (hemoglobin function) and as a dehaloperoxidase (peroxidase function). The X-ray structure of the ferric form shows that the phenolic substrate can bind inside the protein, which is not the case for a typical peroxidase. In the present study, we have used CO-ligated DHP to mimic the distal pocket of the peroxidase DHP and to probe under which conditions both a halophenol and a diatomic ligand can be accommodated in the distal pocket. To vary the structure of the distal pocket, we have compared wild-type DHP and mutants H55V and H55R at different pH values, using flash photolysis in the visible and FTIR spectroscopy in the CO stretching bands. The latter technique is extremely sensitive to even small structural changes in the CO environment and thus can report substrate binding in the distal pocket. Our results on wild-type DHP and its variants indicate that halophenols and a diatomic ligand can indeed simultaneously be present in the distal pocket if the distal histidine is in the low-pH conformation, in which its side chain is swung out of the distal pocket. The markedly different pH dependencies of enzyme activity and substrate binding are not consistent with the hypothesis that substrate dehalogenation occurs within the interior of DHP.