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

• Published in: Journal of molecular graphics & modelling 2019-01, Vol.86, p.35-42
• Main Authors: Bellini, Reinaldo G., Coronado, Mônika Aparecida, Paschoal, Alexandre Rossi, Gaudencio do Rêgo, Thaís, Hungria, Mariangela, Ribeiro de Vasconcelos, Ana Tereza, Nicolás, Marisa Fabiana
• Format: Article
• Language: English
• Subjects: Amidohydrolases - chemistry; Amino Acid Sequence; Amino Acids; Binding Sites; Bradyrhizobium - chemistry; Bradyrhizobium - enzymology; Bradyrhizobium japonicum; Catalytic Domain; d-amino acids; Docking; Hydrogen Bonding; Ligands; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Molecular modelling; N-Carbamoyl-d-amino acid amidohydrolase; Protein Binding; Protein Conformation
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2018.10.005

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. A reaction of hydrolysis transforming N-Carbamoyl-d-p-hydroxyphenylglycine (Cp-HPG) into the active compound D-p-hydroxyphenylglycine (D-HPG) can be effectively performed by the enzyme d-NCAase of the Brazilian Bradyrhizobium japonicum strain CPAC-15. [Display omitted] •A homodimeric structure for the enzyme d-NCAase of Bradyrhizobium japonicum, was successfully modelled.•Molecular modelling, docking, molecular dynam