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

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),...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Álvarez, L., Lewis-Ballester, A., Roitberg, A., Estrin, D.A., Yeh, S.-R., Marti, M.A., Capece, L.
Formato:	JOUR
Materias:	Amino acids Binding energy Bins Catalysis Conformations Enzyme activity Hydrogen bonds Molecular dynamics Mutagenesis Proteins Hydrogen bonding interactions Indoleamine 2 ,3-dioxygenase Post-translational modifications Protein-protein interactions Replica-exchange molecular dynamics simulations Site directed mutagenesis Structural rearrangement Structure and dynamics Crystal structure indoleamine 2,3 dioxygenase kynurenine tryptophan indoleamine 2,3-dioxygenase 1, human Article binding site cancer therapy catalyst comparative study conformational transition crystal structure enzyme activity enzyme structure human hydrogen bond molecular dynamics priority journal protein protein interaction protein purification protein secondary structure signal transduction site directed mutagenesis static electricity catalysis chemistry genetics metabolism protein domain protein motif structure activity relation X ray crystallography Amino Acid Motifs Crystallography, X-Ray Humans Indoleamine-Pyrrole 2,3,-Dioxygenase Mutagenesis, Site-Directed Protein Domains Structure-Activity Relationship
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_00062960_v55_n19_p2785_Alvarez
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_00062960_v55_n19_p2785_Alvarez
record_format	dspace
spelling	todo:paper_00062960_v55_n19_p2785_Alvarez2023-10-03T14:04:36Z Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications Álvarez, L. Lewis-Ballester, A. Roitberg, A. Estrin, D.A. Yeh, S.-R. Marti, M.A. Capece, L. Amino acids Binding energy Bins Catalysis Conformations Enzyme activity Hydrogen bonds Molecular dynamics Mutagenesis Proteins Hydrogen bonding interactions Indoleamine 2 ,3-dioxygenase Post-translational modifications Protein-protein interactions Replica-exchange molecular dynamics simulations Site directed mutagenesis Structural rearrangement Structure and dynamics Crystal structure indoleamine 2,3 dioxygenase kynurenine tryptophan indoleamine 2,3 dioxygenase indoleamine 2,3-dioxygenase 1, human Article binding site cancer therapy catalyst comparative study conformational transition crystal structure enzyme activity enzyme structure human hydrogen bond molecular dynamics priority journal protein protein interaction protein purification protein secondary structure signal transduction site directed mutagenesis static electricity catalysis chemistry genetics metabolism protein domain protein motif structure activity relation X ray crystallography Amino Acid Motifs Catalysis Crystallography, X-Ray Humans Indoleamine-Pyrrole 2,3,-Dioxygenase Mutagenesis, Site-Directed Protein Domains Structure-Activity Relationship 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. © 2016 American Chemical Society. Fil:Estrin, D.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Marti, M.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Capece, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_00062960_v55_n19_p2785_Alvarez
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Amino acids Binding energy Bins Catalysis Conformations Enzyme activity Hydrogen bonds Molecular dynamics Mutagenesis Proteins Hydrogen bonding interactions Indoleamine 2 ,3-dioxygenase Post-translational modifications Protein-protein interactions Replica-exchange molecular dynamics simulations Site directed mutagenesis Structural rearrangement Structure and dynamics Crystal structure indoleamine 2,3 dioxygenase kynurenine tryptophan indoleamine 2,3 dioxygenase indoleamine 2,3-dioxygenase 1, human Article binding site cancer therapy catalyst comparative study conformational transition crystal structure enzyme activity enzyme structure human hydrogen bond molecular dynamics priority journal protein protein interaction protein purification protein secondary structure signal transduction site directed mutagenesis static electricity catalysis chemistry genetics metabolism protein domain protein motif structure activity relation X ray crystallography Amino Acid Motifs Catalysis Crystallography, X-Ray Humans Indoleamine-Pyrrole 2,3,-Dioxygenase Mutagenesis, Site-Directed Protein Domains Structure-Activity Relationship
spellingShingle	Amino acids Binding energy Bins Catalysis Conformations Enzyme activity Hydrogen bonds Molecular dynamics Mutagenesis Proteins Hydrogen bonding interactions Indoleamine 2 ,3-dioxygenase Post-translational modifications Protein-protein interactions Replica-exchange molecular dynamics simulations Site directed mutagenesis Structural rearrangement Structure and dynamics Crystal structure indoleamine 2,3 dioxygenase kynurenine tryptophan indoleamine 2,3 dioxygenase indoleamine 2,3-dioxygenase 1, human Article binding site cancer therapy catalyst comparative study conformational transition crystal structure enzyme activity enzyme structure human hydrogen bond molecular dynamics priority journal protein protein interaction protein purification protein secondary structure signal transduction site directed mutagenesis static electricity catalysis chemistry genetics metabolism protein domain protein motif structure activity relation X ray crystallography Amino Acid Motifs Catalysis Crystallography, X-Ray Humans Indoleamine-Pyrrole 2,3,-Dioxygenase Mutagenesis, Site-Directed Protein Domains Structure-Activity Relationship Álvarez, L. Lewis-Ballester, A. Roitberg, A. Estrin, D.A. Yeh, S.-R. Marti, M.A. Capece, L. Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications
topic_facet	Amino acids Binding energy Bins Catalysis Conformations Enzyme activity Hydrogen bonds Molecular dynamics Mutagenesis Proteins Hydrogen bonding interactions Indoleamine 2 ,3-dioxygenase Post-translational modifications Protein-protein interactions Replica-exchange molecular dynamics simulations Site directed mutagenesis Structural rearrangement Structure and dynamics Crystal structure indoleamine 2,3 dioxygenase kynurenine tryptophan indoleamine 2,3 dioxygenase indoleamine 2,3-dioxygenase 1, human Article binding site cancer therapy catalyst comparative study conformational transition crystal structure enzyme activity enzyme structure human hydrogen bond molecular dynamics priority journal protein protein interaction protein purification protein secondary structure signal transduction site directed mutagenesis static electricity catalysis chemistry genetics metabolism protein domain protein motif structure activity relation X ray crystallography Amino Acid Motifs Catalysis Crystallography, X-Ray Humans Indoleamine-Pyrrole 2,3,-Dioxygenase Mutagenesis, Site-Directed Protein Domains Structure-Activity Relationship
description	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. © 2016 American Chemical Society.
format	JOUR
author	Álvarez, L. Lewis-Ballester, A. Roitberg, A. Estrin, D.A. Yeh, S.-R. Marti, M.A. Capece, L.
author_facet	Álvarez, L. Lewis-Ballester, A. Roitberg, A. Estrin, D.A. Yeh, S.-R. Marti, M.A. Capece, L.
author_sort	Álvarez, L.
title	Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications
title_short	Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications
title_full	Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications
title_fullStr	Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications
title_full_unstemmed	Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications
title_sort	structural study of a flexible active site loop in human indoleamine 2,3-dioxygenase and its functional implications
url	http://hdl.handle.net/20.500.12110/paper_00062960_v55_n19_p2785_Alvarez
work_keys_str_mv	AT alvarezl structuralstudyofaflexibleactivesiteloopinhumanindoleamine23dioxygenaseanditsfunctionalimplications AT lewisballestera structuralstudyofaflexibleactivesiteloopinhumanindoleamine23dioxygenaseanditsfunctionalimplications AT roitberga structuralstudyofaflexibleactivesiteloopinhumanindoleamine23dioxygenaseanditsfunctionalimplications AT estrinda structuralstudyofaflexibleactivesiteloopinhumanindoleamine23dioxygenaseanditsfunctionalimplications AT yehsr structuralstudyofaflexibleactivesiteloopinhumanindoleamine23dioxygenaseanditsfunctionalimplications AT martima structuralstudyofaflexibleactivesiteloopinhumanindoleamine23dioxygenaseanditsfunctionalimplications AT capecel structuralstudyofaflexibleactivesiteloopinhumanindoleamine23dioxygenaseanditsfunctionalimplications
_version_	1807316469990555648

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

Ejemplares similares