In silico characterization of a cyanobacterial plant-type isoaspartyl aminopeptidase/asparaginase

Abstract

Asparaginases are found in a range of organisms, although those found in cyanobacteria have been little studied, in spite of their great potential for biotechnological application. This study therefore sought to characterize the molecular structure of an L-asparaginase from the cyanobacterium Limnothrix sp. CACIAM 69d, which was isolated from a freshwater Amazonian environment. After homology modeling, model validation was performed using a Ramachandran plot, VERIFY3D, and the RMSD. We also performed molecular docking and dynamics simulations based on binding free-energy analysis. Structural alignment revealed homology with the isoaspartyl peptidase/asparaginase (EcAIII) from Escherichia coli. When compared to the template, our model showed full conservation of the catalytic site. In silico simulations confirmed the interaction of cyanobacterial isoaspartyl peptidase/asparaginase with its substrate, β-Asp-Leu dipeptide. We also observed that the residues Thr154, Thr187, Gly207, Asp218, and Gly237 were fundamental to protein-ligand complexation. Overall, our results suggest that L-asparaginase from Limnothrix sp. CACIAM 669d has similar properties to E. coli EcAIII asparaginase. Our study opens up new perspectives for the biotechnological exploitation of cyanobacterial asparaginases.

The effects of nature‐inspired amino acid substitutions on structural and biochemical properties of the E. coli L‐asparaginase EcAIII

“…The selection was based on two criteria: (i) distinct combinations of amino acid substitutions at 17 positions within the binding site of the substrate, and (ii) the overall sequence identity between 25% and 65% to the reference EcAIII sequence (Table S3 ). Currently, there are a limited number of Class 2 L‐asparaginases structures available (da Silva et al, 2018 ; Sajed et al, 2022 ; Sharma et al, 2022 ), so we have assembled a library of structures of predicted models and provided them as Supplementary Material .…”

Identification of L-asparaginases from Streptomyces strains with competitive activity and immunogenic profiles: a bioinformatic approach

“…In addition, we found that about 20% of species have ASNase isoforms. In that sense, many Gram-negative bacteria have at least two isozymes of the family PF00710.11 (Fernández & Zúñiga, 2006) and, in E. coli, the existence of a third isoenzyme has been recently reported (Da Silva et al, 2018). Historically, the genus Streptomyces has been attractive due to the wide repertoire of bioactive molecules produced.…”

Molecular Insight into Stereoselective ADME Characteristics of C20-24 Epimeric Epoxides of Protopanaxadiol by Docking Analysis

“…All the identical residues were highlighted in red color, and those similar residues in orange color respectively. Model validation to check any potential error or deviation from the normal protein is of the utmost importance for further structure-based docking study [33,34]. The alignment score of 0.023 and RMSD value of 0.753 Å ( Figure 3a) indicated a good alignment of multiple amino acid sequences between the template protein of 2IYA and homology model of UGT1A8, as well as the reasonability of the obtained homology model.…”