title: Crystal structure of the deglycating enzyme Amadoriase I in its free form and substrate-bound complex.
abstract: Amadoriases, also known as fructosyl amine oxidases (FAOX), are enzymes that catalyze the de-glycosylation of fructosyl amino acids. As such, they are excellent candidates for the development of enzyme-based diagnostic and therapeutic tools against age- and diabetes-induced protein glycation. However, mostly because of the lack of a complete structural characterization of the different members of the family, the molecular bases of their substrate specificity have yet to be fully understood. The high resolution crystal structures of the free and the substrate-bound form of Amadoriase I shown herein allow for the identification of key structural features that account for the diverse substrate specificity shown by this class of enzymes. This is of particular importance in the context of the rather limited and partially incomplete structural information that has so far been available in the literature on the members of the FAOX family. Moreover, using molecular dynamics simulations, we describe the tunnel conformation and the free energy profile experienced by the ligand in going from bulk water to the catalytic cavity, showing the presence of four gating helices/loops, followed by an "L-shaped" narrow cavity. In summary, the tridimensional architecture of Amadoriase I presented herein provides a reference structural framework for the design of novel enzymes for diabetes monitoring and protein deglycation. Proteins 2016; 84:744-758. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Dipartimento Di Elettronica, Informazione E Bioingegneria, Politecnico Di Milano, Milano, 20133, Italy.
authors.forename: Federica
authors.initials: F
authors.lastname: Rigoldi
authors.affiliation: Dipartimento Di Elettronica, Informazione E Bioingegneria, Politecnico Di Milano, Milano, 20133, Italy.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Gautieri
authors.affiliation: Center for Nano Science and Technology @Polimi, Istituto Italiano Di Tecnologia, Milano, 20133, Italy.|Dipartimento Di Chimica, Materiali E Ingegneria Chimica "G. Natta", Politecnico Di Milano, Milano, 20133, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Dalle Vedove
authors.affiliation: Center for Nano Science and Technology @Polimi, Istituto Italiano Di Tecnologia, Milano, 20133, Italy.
authors.forename: Anna Paola
authors.initials: AP
authors.lastname: Lucarelli
authors.affiliation: Dipartimento Di Elettronica, Informazione E Bioingegneria, Politecnico Di Milano, Milano, 20133, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Vesentini
authors.affiliation: Center for Nano Science and Technology @Polimi, Istituto Italiano Di Tecnologia, Milano, 20133, Italy.
authors.forename: Emilio
authors.initials: E
authors.lastname: Parisini
mesh_terms: D000594:Amino Acid Oxidoreductases / Q000737:chemistry* / Q000378:metabolism*; D000595:Amino Acid Sequence; D001232:Aspergillus fumigatus / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism; D018360:Crystallography, X-Ray; D008239:Lysine / Q000031:analogs & derivatives / Q000378:metabolism; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D016415:Sequence Alignment; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: C033186:fructosyl-lysine; D000594:Amino Acid Oxidoreductases; C103012:amadoriase; D008239:Lysine
keywords: deglycating enzyme; enzyme structure; glycation; molecular modeling; protein crystallization