Crystal structure analysis and molecular dynamics simulations of arginase from Thermus thermophilus

• Published in: Journal of biomolecular structure & dynamics 2023-09, Vol.41 (14), p.6811-6821
• Main Authors: K, Dhanalakshmi, Kuramitsu, Seiki, Yokoyama, Shigeyuki, Thirumananseri, Kumarevel, Ponnuraj, Karthe
• Format: Article
• Language: English
• Subjects: Arginase; arginine biosynthesis; crystal structure; L-ornithine; molecular dynamics simulation; thermostability; Thermus thermophilus
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2022.2112615

Arginase is a manganese-dependent metalloenzyme that catalyzes the hydrolysis of L-arginine to L-ornithine and urea. The product L-ornithine is an important component which has wide applications in the healthcare and pharmaceutical industry. Enzymatic biosynthesis of L-ornithine is one of the effective methods in which arginase is used as a bio-catalyst. Here, we report the crystal structure of arginase from Thermus thermophilus (TtArginase) in three different crystal forms. All structures were solved by molecular replacement and refined at 2.0 Å, 2.3 Å and 2.91 Å resolution respectively. TtArginase is compared with other structural homologs and the putative catalytic site residues were identified. To understand the thermophilic nature of TtArginase, the sequence and structural factors of TtArginase was compared with its mesophilic counterpart Bacillus subtilis arginase (BsArginase). To get insights on structural stability, molecular dynamics (MD) simulations were carried for TtArginase and BsArginase at three different temperatures (300 K, 333 K and 353 K). The results indicate that TtArginase is comparatively more stable than BsArginase. MD simulations were carried out in the absence of the metal ions at the active site which revealed high plasticity of the active site. The results suggest that metal ions are critical not only for the catalytic function, but also required for the maintenance of the proper active site geometry. Since arginase can be employed for large-scale industrial production of L-ornithine, the structural details of thermophilic arginases such as TtArginase will be helpful to engineer the protein to optimize its enzymatic action in a variety of conditions. Communicated by Ramaswamy H. Sarma