9UFQ

Crystal structure of L-asparaginase from Thermococcus Sibiricus

Summary for 9UFQ

• Entry DOI: 10.2210/pdb9ufq/pdb
• Descriptor: asparaginase, GLYCINE (3 entities in total)
• Functional Keywords: l-asparaginase, hyperthermophilic enzyme, thermo-l-asparaginase, tsai, hydrolase
• Biological source: Thermococcus sibiricus
• Total number of polymer chains: 1
• Total formula weight: 36837.01

Authors

Matyuta, I.O.,Varfolomeeva, L.A.,Minyaev, M.E.,Dumina, M.,Zhdanov, D.,Zhgun, A.,Pokrovskaya, M.,Aleksandrova, S.,El'darov, M.,Popov, V.O.,Boyko, K.M. (deposition date: 2025-04-10, release date: 2025-06-11, Last modification date: 2025-07-09)

Primary citation

Dumina, M.V.,Zhdanov, D.D.,Veselovsky, A.V.,Pokrovskaya, M.V.,Aleksandrova, S.S.,Minyaev, M.E.,Varfolomeeva, L.A.,Matyuta, I.O.,Boyko, K.M.,Zhgun, A.A.
Hyperthermophilic L-Asparaginase from Thermococcus sibiricus and Its Double Mutant with Increased Activity: Insights into Substrate Specificity and Structure.
Int J Mol Sci, 26:-, 2025

PubMed Abstract: L-asparaginase (L-ASNase) is a key industrial enzyme significant for cancer therapy and the food industry for reducing dietary acrylamide. The hyperthermophilic L-ASNase from (TsAI) was previously shown to exhibit high activity and thermostability and is promising for biotechnology. To gain insights into structure-functional relationships of TsAI, determination of the substrate specificity, kinetic parameters, structural characterization, and molecular docking were performed. TsAI characteristics were compared with the TsAI mutant, which exhibited increased activity after a double mutation in the substrate-binding region. TsAI and TsAI were found to display high activity towards D-asparagine-62% and 21% of L-asparaginase activity, respectively-and low L-glutaminase coactivity of ~5%. Restoring the mesophilic-like triad GSQ in the mutant resulted in a two-fold increase in activity towards L-asparagine compared with TsAI. Crystal structures of TsAI forms solved at 1.9 Å resolution revealed that double mesophilic-like mutation increased the flexibility of the loop M51-L57, located in close proximity to the active site. Structural superposition and mutational analysis indicate that mobility of this loop is essential for the activity of thermo-ASNases. Molecular docking, without taking into account the temperature factor, showed that, in contrast to L-asparagine interaction, D-asparagine orientation in the TsAI and TsAI active sites is similar and not optimal for catalysis. Under real conditions, high temperatures can induce structural changes that reduce L-ASNase discrimination towards D-asparagine. Overall, the obtained structural and biochemical data provide a basis for a more detailed understanding of thermo-ASNase functioning and possibilities to engineer improved variants for future biotechnological application.

PubMed: 40564901
DOI: 10.3390/ijms26125437

Experimental method

X-RAY DIFFRACTION (1.9 Å)