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

Abstract

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

Keywords:

• Arginase
• crystal structure
• Thermus thermophilus
• L-ornithine
• arginine biosynthesis
• molecular dynamics simulation
• thermostability

Acknowledgements

The authors thank C. Kuroishi for cloning of the TTHA1496 gene. This work was supported by the RIKEN Structural Genomic/Proteomics Initiative (RSGI), the National Project on Protein Structural and Functional Analyses, Ministry of Education, Culture, Sports, Science and Technology of Japan. KP thanks Department of Biotechnology (DBT), Government of India for the resources. KP thanks DST-FIST, Government of India for the computational facilities sanctioned to the department (No: SR/FST/LSII-037/2014 (C) dt. 29.03.2016).

Disclosure statement

No potential conflict of interest was reported by the authors.

Funding

The author(s) reported there is no funding associated with the work featured in this article.