4PV3

Crystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris in complex with Na+ cations

Summary for 4PV3

• Entry DOI: 10.2210/pdb4pv3/pdb
• Related: 1jn9 1k2x 1t3m 2gez 2zak 2zal 3c17 4PU6 4PV2 4gdt 4gdu 4gdv 4gdw 4hlo 4hlp
• Descriptor: L-ASPARAGINASE ALPHA SUBUNIT, L-ASPARAGINASE BETA SUBUNIT, SODIUM ION, ... (4 entities in total)
• Functional Keywords: metal binding sites, potassium coordination, k-dependent enzyme, ntn-hydrolase, plant protein, l-asparaginase, isoaspartyl aminopeptidase, amidohydrolase, hydrolase
• Biological source: Phaseolus vulgaris (French bean,kidney bean,string bean); More
• Total number of polymer chains: 4
• Total formula weight: 69372.81

Authors

Bejger, M.,Gilski, M.,Imiolczyk, B.,Jaskolski, M. (deposition date: 2014-03-14, release date: 2014-09-03, Last modification date: 2023-11-08)

Primary citation

Bejger, M.,Imiolczyk, B.,Clavel, D.,Gilski, M.,Pajak, A.,Marsolais, F.,Jaskolski, M.
Na+/K+ exchange switches the catalytic apparatus of potassium-dependent plant L-asparaginase
Acta Crystallogr.,Sect.D, 70:1854-1872, 2014

PubMed Abstract: Plant-type L-asparaginases, which are a subclass of the Ntn-hydrolase family, are divided into potassium-dependent and potassium-independent enzymes with different substrate preferences. While the potassium-independent enzymes have already been well characterized, there are no structural data for any of the members of the potassium-dependent group to illuminate the intriguing dependence of their catalytic mechanism on alkali-metal cations. Here, three crystal structures of a potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris (PvAspG1) differing in the type of associated alkali metal ions (K(+), Na(+) or both) are presented and the structural consequences of the different ions are correlated with the enzyme activity. As in all plant-type L-asparaginases, immature PvAspG1 is a homodimer of two protein chains, which both undergo autocatalytic cleavage to α and β subunits, thus creating the mature heterotetramer or dimer of heterodimers (αβ)2. The αβ subunits of PvAspG1 are folded similarly to the potassium-independent enzymes, with a sandwich of two β-sheets flanked on each side by a layer of helices. In addition to the `sodium loop' (here referred to as the `stabilization loop') known from potassium-independent plant-type asparaginases, the potassium-dependent PvAspG1 enzyme contains another alkali metal-binding loop (the `activation loop') in subunit α (residues Val111-Ser118). The active site of PvAspG1 is located between these two metal-binding loops and in the immediate neighbourhood of three residues, His117, Arg224 and Glu250, acting as a catalytic switch, which is a novel feature that is identified in plant-type L-asparaginases for the first time. A comparison of the three PvAspG1 structures demonstrates how the metal ion bound in the activation loop influences its conformation, setting the catalytic switch to ON (when K(+) is coordinated) or OFF (when Na(+) is coordinated) to respectively allow or prevent anchoring of the reaction substrate/product in the active site. Moreover, it is proposed that Ser118, the last residue of the activation loop, is involved in the potassium-dependence mechanism. The PvAspG1 structures are discussed in comparison with those of potassium-independent L-asparaginases (LlA, EcAIII and hASNase3) and those of other Ntn-hydrolases (AGA and Tas1), as well as in the light of noncrystallographic studies.

PubMed: 25004963
DOI: 10.1107/S1399004714008700

Experimental method

X-RAY DIFFRACTION (2.09 Å)