Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications

Lucía Álvarez, Ariel Lewis-Ballester, Adrián Roitberg, Darío A. Estrin, Syun-Ru Yeh, Marcelo A. Marti, Luciana Capece

Research output: Contribution to journalArticle

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Abstract

Human indoleamine 2,3-dioxygenase catalyzes the oxidative cleavage of tryptophan to N-formyl kynurenine, the initial and rate-limiting step in the kynurenine pathway. Additionally, this enzyme has been identified as a possible target for cancer therapy. A 20-amino acid protein segment (the JK loop), which connects the J and K helices, was not resolved in the reported hIDO crystal structure. Previous studies have shown that this loop undergoes structural rearrangement upon substrate binding. In this work, we apply a combination of replica exchange molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure and dynamics of this protein region. Our simulations show that the JK loop can be divided into two regions: the first region (JK loopC) displays specific and well-defined conformations and is within hydrogen bonding distance of the substrate, while the second region (JK loopN) is highly disordered and exposed to the solvent. The peculiar flexible nature of JK loopN suggests that it may function as a target for post-translational modifications and/or a mediator for protein-protein interactions. In contrast, hydrogen bonding interactions are observed between the substrate and Thr379 in the highly conserved "GTGG" motif of JK loopC, thereby anchoring JK loopC in a closed conformation, which secures the appropriate substrate binding mode for catalysis. Site-directed mutagenesis experiments confirm the key role of this residue, highlighting the importance of the JK loopC conformation in regulating the enzymatic activity. Furthermore, the existence of the partially and totally open conformations in the substrate-free form suggests a role of JK loopC in controlling substrate and product dynamics.

Original languageEnglish (US)
Pages (from-to)2785-2793
Number of pages9
JournalBiochemistry
Volume55
Issue number19
DOIs
StatePublished - May 17 2016

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Indoleamine-Pyrrole 2,3,-Dioxygenase
Catalytic Domain
Kynurenine
Conformations
Substrates
Hydrogen Bonding
Site-Directed Mutagenesis
Mutagenesis
Proteins
Hydrogen bonds
Molecular Dynamics Simulation
Post Translational Protein Processing
Catalysis
Tryptophan
Amino Acids
Molecular dynamics
Enzymes
Crystal structure
Experiments
Neoplasms

ASJC Scopus subject areas

  • Biochemistry

Cite this

Álvarez, L., Lewis-Ballester, A., Roitberg, A., Estrin, D. A., Yeh, S-R., Marti, M. A., & Capece, L. (2016). Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications. Biochemistry, 55(19), 2785-2793. https://doi.org/10.1021/acs.biochem.6b00077

Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications. / Álvarez, Lucía; Lewis-Ballester, Ariel; Roitberg, Adrián; Estrin, Darío A.; Yeh, Syun-Ru; Marti, Marcelo A.; Capece, Luciana.

In: Biochemistry, Vol. 55, No. 19, 17.05.2016, p. 2785-2793.

Research output: Contribution to journalArticle

Álvarez, L, Lewis-Ballester, A, Roitberg, A, Estrin, DA, Yeh, S-R, Marti, MA & Capece, L 2016, 'Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications', Biochemistry, vol. 55, no. 19, pp. 2785-2793. https://doi.org/10.1021/acs.biochem.6b00077
Álvarez, Lucía ; Lewis-Ballester, Ariel ; Roitberg, Adrián ; Estrin, Darío A. ; Yeh, Syun-Ru ; Marti, Marcelo A. ; Capece, Luciana. / Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications. In: Biochemistry. 2016 ; Vol. 55, No. 19. pp. 2785-2793.
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