Journal:Acta Cryst D:S205979832500292X

Unique double-helical packing of protein molecules in the crystal of K-independent L-asparaginase from common bean

Dr Joanna Loch ^[1]

Molecular Tour
L-Asparaginases are enzymes that catalyze the hydrolysis of L-asparagine into L-aspartic acid and ammonia. This reaction is crucial for nitrogen metabolism in plants, as L-asparagine serves as a major nitrogen storage and transport molecule. Plant (Class 2) L-asparaginases are classified into two main types based on their dependency on potassium (K) ions: K-dependent and K-independent enzymes. K-dependent L-asparaginases require the presence of potassium ions for their enzymatic activity.

In common bean (Phaseolus vulgaris), there are two K-dependent L-asparaginases, PvAIII(K)-1 and PvAIII(K)-2, encoded by the PvAspG1 and PvAspG2 genes, respectively. These enzymes play a significant role in nitrogen assimilation and are regulated by environmental factors such as light. K-independent L-asparaginases, on the other hand, do not require potassium ions for their activity.

The genome of common bean encodes one K-independent L-asparaginase, PvAIII, expressed by the PvAsp-T2 gene.The enzyme shows a higher affinity for β-peptides than for L-asparagine, suggesting that its physiological role may be more related to detoxification processes rather than basic L-asparagine metabolism. This discovery highlights the importance of PvAIII in managing toxic protein degradation products in plants.

The K-independent L-asparaginase (PvAIII) from the common bean exhibits an extraordinary crystal structure (PDB ID: 9HNC). This structure is characterized by a rare P2 space-group symmetry and a unique pseudosymmetric double-helical packing, containing 32 protein chains in the asymmetric unit. The structure's uniqueness arises from the ability of the PvAIII molecule to form extensive intermolecular β-sheets, the incomplete degradation of the interdomain flexible linker, and the presence of intermolecular hydrogen bonds that connect adjacent protein chains.

Helical arrangements in crystal structures are relatively common in nature, but the double-helical packing observed in PvAIII is particularly remarkable among proteins. This unique packing is likely a result of specific molecular interactions promoted by the crystallization conditions. Such double-helical structures are more commonly associated with nucleic acids like DNA, making the discovery in PvAIII significant. Understanding these helical arrangements can provide broader insights into protein stability and function, potentially influencing the design of new protein-based applications.

Packing of PvAIII molecules in the crystal.

(A) Asymmetric unit containing two coiled arrangements of chains A-H (green shades) and I-P (magenta shades). (B) Translation along [001] generates the first strand of superhelix A-H and the first strand of superhelix I-P. (C) The second strands of both superhelices are generated by the crystallographic twofold axis along [010].

References

1. ↑ Loch JI, Pieróg I, Imiołczyk B, Barciszewski J, Marsolais F, Gilski M, Jaskolski M. Unique double-helical packing of protein molecules in the crystal of potassium-independent L-asparaginase from common bean. Acta Crystallogr D Struct Biol. 2025 May 1;81(Pt 5):252-264. PMID:40243630 doi:10.1107/S205979832500292X