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Rare codons analysis, the structure determination, and investigation of the active site of L-asparaginase II of B. megaterium
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Safa Lotfi *    , Mojtaba Mortazavi |
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Abstract: (317 Views) |
Introduction: Currently, L-asparaginase II of Escherichia coli and Erwinia chrysanthemi are prescribed for the treatment of acute lymphoblastic leukemia (ALL) in children. However, due to their short half-life and side effects related to immunogenicity and glutaminase activity, the research to find new bacterial sources of L-asparaginase with higher therapeutic effects and minimal side effects has continued. In this regard, the L-asparaginase II of Bacillus megaterium has been studied in this research.
Materials & methods: Rare codons of the L-asparaginase II gene of B. megaterium were identified with ATGme server and amino acid residues related to these codons were determined. The third protein structure was predicted using three homology modeling-based servers and the quality of the models was studied with ERRAT and Verify3D servers. The amino acid residues of the active site were determined with PyMol software.
Results: The results showed that this gene has 73 rare codons and 27 very rare codons. All three servers (SWISS-MODEL, Phyre2, and I-TASSER) used L-asparaginase II of E. chrysanthemi as the template, and the model created by SWISS-MODEL had higher accuracy and quality than the other two models. The comparison of the active site residues of this enzyme with L-asparaginase II of E. chrysanthemi indicated that out of a total of 8 residues, 5 amino acids are similar and 3 amino acids are different. Glu63, Thr95 and Ala120 are replaced with Gln103, Ser135, and Ser160 in L-asparaginase II of B. megaterium. According to the previous published reports, the presence of glutamine instead of glutamate in the L-asparaginase II active site reduces glutaminase activity. The analysis of amino acids with rare codons showed that all three serine of active site possess rare codons. Therefore, due to the high number of rare codons and the fact that some of them are related to the active site residues, during the process of codon optimization, a detailed and comprehensive study should be carried out to ensure high protein production and its solubility in the E. coli expression system.
Conclusion: Summing up, the obtained results can help the process of designing and producing the L-asparaginase II enzyme with higher therapeutic properties and lower side effects. |
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| Keywords: Acute lymphoblastic leukemia (ALL), L-asparaginase II, Bacillus megaterium, Rare codons, SWISS-MODEL |
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Full-Text [PDF 1438 kb]
(104 Downloads)
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Type of Study: Research |
Subject:
Special
Received: 2026/02/24 | Accepted: 2025/08/1 | Published: 2025/08/1
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