Structural elements that modulate the substrate specificity of plant purple acid phosphatases: avenues for improved phosphorus acquisition in crops

Abstract

Phosphate acquisition by plants is an essential process that is directly implicated in the optimization of crop yields. Purple acid phosphatases (PAPs) are ubiquitous metalloenzymes, which catalyze the hydrolysis of a wide range of phosphate esters and anhydrides. While some plant PAPs display a preference for ATP as the substrate, others are efficient in hydrolyzing phytate or 2-phosphoenolpyruvate (PEP). PAP from red kidney bean (rkbPAP) is an efficient ATP-and ADPase, but has no activity towards phytate. The crystal structure of this enzyme in complex with an ATP analogue (to 2.20 Å resolution) provides insight into the amino acid residues that play an essential role in binding this substrate. Homology modelling was used to generate three-dimensional structures for the active sites of PAPs from tobacco (NtPAP) and Arabidopsis thaliana (AtPAP12 and AtPAP26) that are efficient in hydrolyzing phytate and PEP as substrates, respectively. In combination with substrate docking simulations and a phylogenetic analysis of 49 plant PAP sequences (including the first PAP sequences reported from Eucalyptus), several active site residues were identified that are important in defining the substrate specificities of plant PAPs. These results may inform bioengineering studies aimed at identifying and incorporating suitable plant PAP genes into crops to improve phosphorus use efficiency.Organic phosphorus sources increasingly supplement or replace inorganic fertilizer, and efficient phosphorus use of crops will lower the environmental footprint of agriculture while enhancing food production.

Advances in chilling injury of postharvest fruit and vegetable: Extracellular ATP aspects

“…Cold‐elicited eATP is primarily hydrolyzed by APYs or purine permeases (PUPs) on the cytomembrane to eAMP and Pi. eAMP can be hydrolyzed further by an unspecific 5′‐nucleotidase (5NT) to form extracellular adenosine (eAde), which can be transported into cells by equilibrative nucleoside transporters (ENTs) (Bernard et al., 2011) or converted into extracellular adenine (eAdo) by the cell‐wall‐bound nucleoside hydrolase (NSHs) and then transferred into the cells via a proton gradient by PUPs (Cao et al., 2014; Feder et al., 2020). As the breakdown products of eATP, Ade or Ado can be retrieved to supply the nucleotide pool, which is involved in iATP salvage for maintaining energy homeostasis in cells.…”

Structural and Functional Insight into the Mechanism of the Fe−S Cluster‐Dependent Dehydratase from Paralcaligenes ureilyticus

“…The two sites we now refer to as I and II (Figure 8). A probable location for site II is less than 5 Å from site I, suggesting the possibility that a dinuclear metal centre may be formed that resembles those found in metallohydrolases (e. g., purple acid phosphatases, [36,37] pesticide‐degrading hydrolases [38–41] or antibiotic‐degrading metallo‐β‐lactamases [42,43] ), reductases such as ribonucleotide reductase [44] or keto‐acid isomeroreductase [45,46] or oxygenases such as methane monooxygenase [47] …”

Selectivity in Enzymatic Phosphorus Recycling from Biopolymers: Isotope Effect, Reactivity Kinetics, and Molecular Docking with Fungal and Plant Phosphatases

“…This finding was in accordance with previous reports that sweet potato PAP exhibited a higher preference for small substrates like phosphoenolpyruvate compared to thale cress and wheat PAPs that accept bulkier substrates like phytate in their active sites. 63,64 We posit that the confined circular tunnel-shaped active site of sweet potato PAP may limit the access of the target phosphate moiety to the catalytic metals (Supporting Information, Appendix G). However, in accordance with the high preference of thale cress and wheat PAPs for P-monoester bonds, 63 the catalytic center of both enzymes oriented favorably with respect to a terminal P-monoester bond in RNA (Figure 4D and Supporting Information, Appendix G).…”

“…63,64 We posit that the confined circular tunnel-shaped active site of sweet potato PAP may limit the access of the target phosphate moiety to the catalytic metals (Supporting Information, Appendix G). However, in accordance with the high preference of thale cress and wheat PAPs for P-monoester bonds, 63 the catalytic center of both enzymes oriented favorably with respect to a terminal P-monoester bond in RNA (Figure 4D and Supporting Information, Appendix G). Among the plant PAPs, similar to the polyP complex, the red kidney bean PAP participated in the most favorable interactions to complex polyP and RNA, consistent with the specificity of this enzyme for multiphosphorylated ribonucleotides: 63 there was favorable orientation of metal cations (Fe 3+ and Zn 2+ ) with respect to a middle phosphate moiety in the polyP chain, a nearby water molecule (distance ∼2.6 Å), and the coordination of the metal catalytic center with the target phosphate moiety through 2 Hbond and 2 electrostatic interactions; the catalytic metals participated in 2 electrostatic interactions while targeting the P-diester bond in RNA (Figure 4D and Supporting Information, Appendix G).…”

“…However, in accordance with the high preference of thale cress and wheat PAPs for P-monoester bonds, 63 the catalytic center of both enzymes oriented favorably with respect to a terminal P-monoester bond in RNA (Figure 4D and Supporting Information, Appendix G). Among the plant PAPs, similar to the polyP complex, the red kidney bean PAP participated in the most favorable interactions to complex polyP and RNA, consistent with the specificity of this enzyme for multiphosphorylated ribonucleotides: 63 there was favorable orientation of metal cations (Fe 3+ and Zn 2+ ) with respect to a middle phosphate moiety in the polyP chain, a nearby water molecule (distance ∼2.6 Å), and the coordination of the metal catalytic center with the target phosphate moiety through 2 Hbond and 2 electrostatic interactions; the catalytic metals participated in 2 electrostatic interactions while targeting the P-diester bond in RNA (Figure 4D and Supporting Information, Appendix G). Interestingly, despite these enzyme-specific differences, our molecular simulations demonstrated that the active site residues of both plant and fungal APs engaged in a higher number of H-bonds and electrostatic interactions with polyP (5−17 interactions) compared to RNA (1−5 interactions) (Figure 4C,D).…”