Structural analysis of a novel N-carbamoyl-D-amino acid amidohydrolase from a Brazilian Bradyrhizobium japonicum strain: In silico insights by molecular modelling, docking and molecular dynamics
In this work we performed several in silico analyses to describe the relevant structural aspects of an enzyme N-Carbamoyl-D-amino acid amidohydrolase (D-NCAase) encoded on the genome of the Brazilian strain CPAC 15 (=SEMIA 5079) of Bradyrhizobium japonicum, a nonpathogenic species belonging to the o...
| Autores: | , , , , , , |
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| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2019 |
| País: | Brasil |
| Institución: | Universidade Estadual Paulista (UNESP) |
| Repositorio: | Repositório Institucional da UNESP |
| Idioma: | inglés |
| OAI Identifier: | oai:repositorio.unesp.br:11449/188201 |
| Acceso en línea: | http://dx.doi.org/10.1016/j.jmgm.2018.10.005 http://hdl.handle.net/11449/188201 |
| Access Level: | acceso abierto |
| Palabra clave: | Bradyrhizobium japonicum D-amino acids Docking Molecular dynamics Molecular modelling N-Carbamoyl-D-amino acid amidohydrolase |
| Sumario: | In this work we performed several in silico analyses to describe the relevant structural aspects of an enzyme N-Carbamoyl-D-amino acid amidohydrolase (D-NCAase) encoded on the genome of the Brazilian strain CPAC 15 (=SEMIA 5079) of Bradyrhizobium japonicum, a nonpathogenic species belonging to the order Rhizobiales. D-NCAase has wide applications particularly in the pharmaceutical industry, since it catalyzes the production of D-amino acids such as D-p-hydroxyphenylglycine (D-HPG), an intermediate in the synthesis of β-lactam antibiotics. We applied a homology modelling approach and 50 ns of molecular dynamics simulations to predict the structure and the intersubunit interactions of this novel D-NCAase. Also, in order to evaluate the substrate binding site, the model was subjected to 50 ns of molecular dynamics simulations in the presence of N-Carbamoyl-d-p-hydroxyphenylglycine (Cp-HPG) (a D-NCAase canonical substrate) and water-protein/water-substrate interactions analyses were performed. Overall, the structural analysis and the molecular dynamics simulations suggest that D-NCAase of B. japonicum CPAC-15 has a homodimeric structure in solution. Here, we also examined the substrate specificity of the catalytic site of our model and the interactions with water molecules into the active binding site were comprehensively discussed. Also, these simulations showed that the amino acids Lys123, His125, Pro127, Cys172, Asp174 and Arg176 are responsible for recognition of ligand in the active binding site through several chemical associations, such as hydrogen bonds and hydrophobic interactions. Our results show a favourable environment for a reaction of hydrolysis that transforms N-Carbamoyl-d-p-hydroxyphenylglycine (Cp-HPG) into the active compound D-p-hydroxyphenylglycine (D-HPG). This work envisage the use of D-NCAase from the Brazilian Bradyrhizobium japonicum strain CPAC-15 (=SEMIA 5079) for the industrial production of D-HPG, an important intermediate for semi-synthesis of β-lactam antibiotics such as penicillins, cephalosporins and amoxicillin. |
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