title: New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models.
abstract: Tyrosine ammonia lyase (TAL) catalyzes the deamination of tyrosine to p-coumaric acid in purple phototropic bacteria and Actinomycetales. The enzyme is used in bioengineering and has the potential to be used industrially. It belongs to a family of enzymes that uses a 4-methylidene-imidazole-5-one (MIO) cofactor to catalyze the deamination amino acids. In the present work, we used a QM/MM and a QM cluster models of TAL to explore two putative reaction paths for its catalytic mechanism. Part of the N-MIO mechanism was previously studied by computational methods. We improved on previous studies by using a larger, more complete model of the enzyme, and by describing the complete reaction path. The activation energy for this mechanism, in agreement with the previous study, is 28.5 kcal/mol. We also found another reaction path that has overall better kinetics and reaches the products in a single reaction step. The barrier for this Single-Step mechanism is 16.6 kcal/mol, which agrees very well with the experimental kcat of 16.0 kcal/mol. The geometrical parameters obtained for the cluster and QM/MM models are very similar, despite differences in the relative energies. This means that both approaches are capable of describing the correct catalytic path of TAL.
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; Dipartimento di Chimica, Università della Calabria, 87036 Arcavacata di Rende, Italy.
authors.forename: Gaspar P
authors.initials: GP
authors.lastname: Pinto
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; Dipartimento di Chimica, Università della Calabria, 87036 Arcavacata di Rende, Italy.
authors.forename: António J M
authors.initials: AJ
authors.lastname: Ribeiro
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Ramos
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
authors.forename: Pedro A
authors.initials: PA
authors.lastname: Fernandes
authors.affiliation: Dipartimento di Chimica, Università della Calabria, 87036 Arcavacata di Rende, Italy.
authors.forename: Marirosa
authors.initials: M
authors.lastname: Toscano
authors.affiliation: Dipartimento di Chimica, Università della Calabria, 87036 Arcavacata di Rende, Italy. Electronic address: nrusso@unical.it.
authors.forename: Nino
authors.initials: N
authors.lastname: Russo
mesh_terms: D000642:Ammonia-Lyases / Q000737:chemistry / Q000378:metabolism*; D055162:Biocatalysis; D003067:Coenzymes / Q000378:metabolism; D007093:Imidazoles / Q000378:metabolism; D008958:Models, Molecular; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D011789:Quantum Theory
chemical_list: C479280:4-methylideneimidazole-5-one; D003067:Coenzymes; D007093:Imidazoles; D000642:Ammonia-Lyases; C023208:L-tyrosine ammonia-lyase
keywords: Catalytic mechanism; DFT; Enzymatic catalysis; QM; QM/MM; Tyrosine ammonia lyase