Phosphate forms an unusual tripodal complex with the Fe-Mn center of sweet potato purple acid phosphatase

Multi-omics analysis reveals the roles of purple acid phosphatases in organic phosphorus utilization by the tropical legume Stylosanthes guianensis

Stylo (Stylosanthes guianensis) is a tropical legume known for its exceptional tolerance to low phosphate (Pi), a trait believed to be linked to its high acid phosphatase (APase) activity. Previous studies have observed genotypic variations in APase activity in stylo; however, the gene encoding the crucial APase responsible for this variation remains unidentified. In this study, transcriptomic and proteomic analyses were employed to identify eight Pi starvation-inducible (PSI) APases belonging to the purple APase (PAP) family in the roots of stylo and seven in the leaves. Among these PSI-PAPs, SgPAP7 exhibited a significantly positive correlation in its expression levels with the activities of both internal APase and root-associated APase across 20 stylo genotypes under low-Pi conditions. Furthermore, the recombinant SgPAP7 displayed high catalytic activity toward adenosine 5'-diphosphate (ADP) and phosphoenolpyruvate (PEP) in vitro. Overexpression (OE) of SgPAP7 in Arabidopsis facilitated exogenous organic phosphorus utilization. Moreover, SgPAP7 OE lines showed lower shoot ADP and PEP levels than the wild type, implying that SgPAP7 is involved in the catabolism and recycling of endogenous ADP and PEP, which could be beneficial for plant growth in low-Pi soils. In conclusion, SgPAP7 is a key gene with a major role in stylo adaptation to low-Pi conditions by facilitating the utilization of both exogenous and endogenous organic phosphorus sources. It may also function as a PEP phosphatase involved in a glycolytic bypass pathway that minimizes the need for adenylates and Pi. Thus, SgPAP7 could be a promising target for improving tolerance of crops to low-Pi availability.

Towards a structural and functional analysis of the immunoglobulin-fold proteome

The immunoglobulin fold (Ig fold) domain is a super-secondary structural motif consisting of a sandwich with two layers of β-sheets that is present in many proteins with very diverse biological functions covering a wide range of physiological processes. This domain presents a modular architecture built with β strands connected by variable length loops that has a highly conserved structural core of four β-strands and quite variable β-sheet extensions in the two sandwich layers that enable both divergent and convergent evolutionary mechanisms in the known Ig fold proteome. The central role of this Ig fold's structural plasticity in the evolutionary success of antibodies in our immune system is well established. Nature has also utilized this Ig fold in all domains of life in many different physiological contexts that go way beyond the immune system. Here we will present a structural and functional overview of the utilization of the Ig fold in different biological processes and in different cellular contexts to highlight some of the innumerable ways that this structural motif can interact in multidomain proteins to enable their diversity of functions. This includes shareable specific protein structure visualizations behind those functions that serve as starting points for further explorations of the biomolecular interactions spanning the Ig fold proteome. This overview also highlights how this Ig fold is being utilized through natural adaptation, engineering, and even building from scratch for a range of biotechnological applications.

Impaired glycosylation of GmPAP15a, a root-associated purple acid phosphatase, inhibits extracellular phytate-P utilization in soybean

Phosphorus (P) is an essential nutrient, but easily fixed in soils. Therefore, most of soil P exists in the form of inaccessible organic phosphorus (Po), particularly phytate-P. Root-associated purple acid phosphatases (PAPs) are considered to play a crucial role in phosphate (Pi) scavenging in soils. However, evidence for regulating root-associated PAPs in utilization of extracellular phytate-P remain largely unknown in plants at both transcriptional and posttranslational levels. In this study, a Pi-starvation responsive GmPAP15a was identified in soybean (Glycine max). Overexpressing GmPAP15a led to significant increases in root-associated phytase activities, as well as total P content when phytate-P was supplied as the sole P resource in soybean hairy roots. Meanwhile, mass spectrometry (MS) analysis showed GmPAP15a was glycosylated at Asn144 and Asn502 , and its glycan structures of N-linked oligosaccharide chains exhibited microheterogeneity. Moreover, two homologues of AtPHR1, GmPHR9 and GmPHR32 were found to activate GmPAP15a transcription through luciferase activity analysis. Taken together, it is strongly suggested that GmPAP15a plays a vital role in phytate-P utilization in soybean, which might be regulated at both transcriptional and glycosylation modification levels. Our results highlight the GmPHR9/GmPHR32-GmPAP15a signalling pathway might present, and control phytate-P utilization in soybean.

Effect of sweet potato purple acid phosphatase on Pseudomonas aeruginosa flagellin-mediated inflammatory response in A549 cells

OBJECTIVE

The study was conducted to investigate the dephosphorylation of Pseudomonas aeruginosa flagellin (PA FLA) by sweet potato purple acid phosphatase (PAP) and the effect of the enzyme on the flagellin-mediated inflammatory response in the A549 lung epithelial cell line.

METHODS

The activity of sweet potato PAP on PA FLA was assayed at different pH (4, 5.5, 7, and 7.5) and temperature (25°C, 37°C, and 55°C) conditions. The release of interleukin-8 (IL-8) and the activation of nuclear factor kappa- light-chain-enhancer of activated B cells (NF-κB) in A549 cells exposed to PA FLA treated with or without sweet potato PAP was measured using IL-8 and NF-κB ELISA kits, respectively. The activation of toll-like receptor 5 (TLR5) in TLR5-overexpressing HEK-293 cells exposed to PA FLA treated with or without sweet potato PAP was determined by the secreted alkaline phosphatase-based assay.

RESULTS

The dephosphorylation of PA FLA by sweet potato PAP was favorable at pH 4 and 5.5 and highest at 55°C. PA-FLA treated with the enzyme decreased IL-8 release from A549 cells to about 3.5-fold compared to intact PA FLA at 1,000 ng/mL of substrate. Moreover, PA-FLA dephosphorylated by the enzyme repressed the activation of NF-κB in the cells compared to intact PA FLA. The activation of TLR5 by PA-FLA was highest in TLR-overexpressing HEK293 cells at a substrate concentration of 5,000 ng/mL, whereas PA FLA treated with the enzyme strongly repressed the activation of TLR5.

CONCLUSION

Sweet potato PAP has the potential to be a new alternative agent against the increased antibiotic resistance of P. aeruginosa and may be a new conceptual feed additive to control unwanted inflammatory responses caused by bacterial infections in animal husbandry.

Biomimetics for purple acid phosphatases: A historical perspective

Biomimetics hold potential for varied applications in biotechnology and medicine but have also attracted particular interest as benchmarks for the functional study of their more complex biological counterparts, e.g. metalloenzymes. While many of the synthetic systems adequately mimic some structural and functional aspects of their biological counterparts the catalytic efficiencies displayed are mostly far inferior due to the smaller size and the associated lower complexity. Nonetheless they play an important role in bioinorganic chemistry. Numerous examples of biologically inspired and informed artificial catalysts have been reported, designed to mimic a plethora of chemical transformations, and relevant examples are highlighted in reviews and scientific reports. Herein, we discuss biomimetics of the metallohydrolase purple acid phosphatase (PAP), examples of which have been used to showcase synergistic research advances for both the biological and synthetic systems. In particular, we focus on the seminal contribution of our colleague Prof. Ademir Neves, and his group, pioneers in the design and optimization of suitable ligands that mimic the active site of PAP.

Structure of a cereal purple acid phytase provides new insights to phytate degradation in plants

Grain phytate, a mixed metal ion salt of inositol hexakisphosphate, accounts for 60%-80% of stored phosphorus in plants and is a potent antinutrient of non-ruminant animals including humans. Through neofunctionalization of purple acid phytases (PAPhy), some cereals such as wheat and rye have acquired particularly high mature grain phytase activity. As PAPhy activity supplies phosphate, liberates metal ions necessary for seedling emergence, and obviates antinutrient effects of phytate, its manipulation and control are targeted crop traits. Here we show the X-ray crystal structure of the b2 isoform of wheat PAPhy induced during germination. This high-resolution crystal structure suggests a model for phytate recognition that, validated by molecular dynamics simulations, implicates elements of two sequence inserts (termed PAPhy motifs) relative to a canonical metallophosphoesterase (MPE) domain in forming phytate-specific substrate specificity pockets. These motifs are well conserved in PAPhys from monocot cereals, enzymes which are characterized by high specificity for phytate. Tested by mutagenesis, residues His229 in PAPhy motif 4 and Lys410 in the MPE domain, both conserved in PAPhys, are found to strongly influence phytase activity. These results explain the observed phytase activity of cereal PAPhys and open the way to the rational engineering of phytase activity in planta.

Phylogenetic and modelling analysis of purple acid phosphatase 18 (SiPAP18) from Setaria italica

Purple acid phosphatases belong to metallo-phosphatase family. Intracellular phosphatases are crucial for phosphorus (P) distribution in the cell and are highly induced in phosphorus-deprived conditions in the soil. Disparate PAP isoforms exist within discrete subcellular compartments in Setaria italica and their expression in P deprived conditions fosters phosphorus amelioration. We isolated the SiPAP18 gene and developed the homology SiPAP18 protein model based on the crystal structure of the Kidney bean PvPAP (PDB ID: 2QFP) as template (sequence similarity 42.7%) using Modeller 9.12 with adequate validation. Structure model analysis shows the significance of five conserved signatures with seven metal-paired amino acid residues during P-deprivation induced phosphorus amelioration.

New AlIIIZnII and AlIIICuII dinuclear complexes: Phosphatase-like activity and cytotoxicity

Herein, we report the synthesis and characterization of the first two Al^III(μ-OH)M^II (M = Zn (1) and Cu (2)) complexes with the unsymmetrical ligand H₂L{2-[[(2-hydroxybenzyl)(2-pyridylmethyl)]aminomethyl]-6-bis(pyridylmethyl)aminomethyl}-4-methylphenol. The complexes were characterized through elemental analysis, X-ray crystallography, IR spectroscopy, mass spectrometry and potentiometric titration. In addition, complex 2 was characterized by electronic spectroscopy. Kinetics studies on the hydrolysis of the model substrate bis(2,4-dinitrophenyl)phosphate by 1 and 2 show Michaelis-Menten behavior, with 1 being slightly more active (8.31%) than 2 (at pH 7.0). The antimicrobial effect of the compounds was studied using four bacterial strains (Staphylococcus aureus, Pseudomonas aeuruginosa, Shigella sonnei and Shigella dysenteriae) and for both complexes the inhibition of bacterial growth was superior to that caused by sulfapyridine, but inferior to that of tetracycline. The dark cytotoxicity and photocytotoxicity (under UV-A light) of the complexes in a chronic myelogenous leukemia cell line were investigated. Complexes 1 and 2 exhibited significant cytotoxic activity against K562 cells, which undergoes a 2-fold increase on applying 5 min of irradiation with UV-A light. Complex 2 was more effective and a good correlation between cytotoxicity and intracellular concentration was observed, the intracellular copper concentration required to inhibit 50% of cell growth being 3.5 × 10^-15 mol cell^-1.

Galvanic oxidation processes (GOPs): An effective direct electron transfer approach for organic contaminant oxidation

The activation of peroxymonosulfate (PMS) for organic contaminant oxidation usually relies on the formation of reactive oxygen species (ROSs). However, the ubiquitous anions and natural organic matter can easily scavenge ROSs and/or PMS, resulting in lower efficiencies and/or the formation of toxic byproducts. Relying on the unique long-distance electron transfer property, the recently developed Galvanic Oxidation Process (GOP) successfully achieved bisphenol A (BPA) degradation when BPA and PMS were physically separated in two reactors. In this study, we systematically investigated the performance of GOP at different PMS or BPA concentrations, pH, and ionic strength (IS) in both PMS and BPA solutions. The kinetic modeling employing the Langmuir-Hinshelwood model at different BPA concentrations suggested that although BPA and PMS were physically separated, the oxidation of the adsorbed BPA and reduction of the adsorbed PMS still followed a similar mechanism to that in traditional heterogeneous catalytic processes. The anions in the target water showed little impact on BPA degradation; higher IS enhanced the solution conductivity but inhibited BPA and electrode interactions, resulting in increased and then decrease BPA degradation rate. The electrodes presented high stability with a rate increase of 12% after 13 times of uses, and their hydration significantly facilitated BPA degradation but reduced the current by decreasing the potential difference between the anode and cathode. The graphite sheet itself without catalyst coating was also capable of shuttling electrons, while the use of a graphite fiber anode increased the BPA degradation by near 100% because of the larger surface area. The developed continuous stirred-tank reactor coupled with GOP (CSTR-GOP) achieved stable BPA degradation in less than 35 min and its scaling up is promising for future applications.

Rv2577 of Mycobacterium tuberculosis Is a Virulence Factor With Dual Phosphatase and Phosphodiesterase Functions

Tuberculosis, a lung disease caused by Mycobacterium tuberculosis (Mtb), is one of the ten leading causes of death worldwide affecting mainly developing countries. Mtb can persist and survive inside infected cells through modulation of host antibacterial attack, i.e., by avoiding the maturation of phagosome containing mycobacteria to more acidic endosomal compartment. In addition, bacterial phosphatases play a central role in the interplay between host cells and Mtb. In this study, we characterized the Rv2577 of Mtb as a potential alkaline phosphatase/phosphodiesterase enzyme. By an in vitro kinetic assay, we demonstrated that purified Rv2577 expressed in Mycobacterium smegmatis displays both enzyme activities, as evidenced by using the artificial substrates p-NPP and bis-(p-NPP). In addition, a three-dimensional model of Rv2577 allowed us to define the catalytic amino acid residues of the active site, which were confirmed by site-directed mutagenesis and enzyme activity analysis, being characteristic of a member of the metallophosphatase superfamily. Finally, a mutation introduced in Rv2577 reduced the replication of Mtb in mouse organs and impaired the arrest of phagosomes containing mycobacteria in early endosomes; which indicates Rv2577 plays a role in Mtb virulence.

Electronic Effect on Bimetallic Catalysts: Cleavage of Phosphodiester Mediated by Fe(III)-Zn(II) Purple Acid Phosphatase Mimics

The bimetallic system is an important strategy for the catalytic hydrolysis of phosphodiester. The purple acid phosphatase (PAPs) enzyme is a typical bimetallic catalyst in this field. Mechanistic details for the hydrolysis cleavage of the DNA dinucleotide analogue BNPP^- (BNPP^- = bis(p-nitrophenyl) phosphate) by hetero-binuclear [Fe^III(μ-OH)Zn^IIL]²⁺ complexes (L = 2-[N-bis(2-pyridylmethyl)-aminomethyl]-4-methyl-6-[N'-(2-pyridylmethyl)(2-hydroxybenzyl) aminomethyl] phenol) were investigated using density functional theory calculations. The catalysts with single-bridged hydroxyl and double-bridged hydroxyl groups were compared. The calculation results show that the doubly hydroxide-bridged complex could better bind to substrates. For the BNPP^- hydrolysis, the doubly hydroxide-bridged reactant isomerizes into a single hydroxide-bridged complex, and then the attack is initiated by the hydroxyl group on the iron center. In addition, the catalyst with the electron-donating group (Me) was determined to take precedence over electron-withdrawing groups (Br and NO₂ groups) in the hydrolysis reaction. This is because the substituents affect the high-lying occupied molecular orbitals, tuning the Lewis acidity of iron and pK_a values of the metal-bonded water. These factors influence the hydroxyl nucleophilicity, leading to changes in catalytic activity. To further examine substituent effects, the occupied orbital energies were calculated with several different substituent groups (-CF₃, -OMe, -OH, -NH₂, and -N(Me)₂). It was found that the HOMO or HOMO-1 energy decreases with the increase of the σ_p value. Further, the catalyst activity of the [Fe^III(μ-OH)Zn^IIL]²⁺ complexes was found to be mainly affected by the phenolate ligand (B) coordinated to the iron and zinc centers. These fundamental aspects of the hydrolysis reactions of BNPP^- catalyzed by [Fe^III(μ-OH)Zn^IIL]²⁺ complexes should contribute to improved understanding of the mechanism and to catalyst design involving hetero-binuclear metals complexes.

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

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. Crystal structures of this enzyme in complex with ATP analogues (to 2.20 and 2.60 Å resolution, respectively) complement the recent structure of rkbPAP with a bound ADP analogue (ChemBioChem 20 (2019) 1536). Together these complexes provide the first structural insight of a PAP in complex with molecules that mimic biologically relevant substrates. Homology modeling was used to generate three-dimensional structures for the active sites of PAPs from tobacco (NtPAP) and thale cress (AtPAP26) that are efficient in hydrolyzing phytate and PEP as preferred substrates, respectively. The combining of crystallographic data, substrate docking simulations and a phylogenetic analysis of 49 plant PAP sequences (including the first PAP sequences reported from Eucalyptus) resulted in the identification of several active site residues that are important in defining the substrate specificities of plant PAPs; of particular relevance is the identification of a motif ("REKA") that is characteristic for plant PAPs that possess phytase activity. These results may inform bioengineering studies aimed at identifying and incorporating suitable plant PAP genes into crops to improve phosphorus acquisition and 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.

Structural insights into phosphopantetheinyl hydrolase PptH from Mycobacterium tuberculosis

The amidinourea 8918 was recently reported to inhibit the type II phosphopantetheinyl transferase (PPTase) of Mycobacterium tuberculosis (Mtb), PptT, a potential drug-target that activates synthases and synthetases involved in cell wall biosynthesis and secondary metabolism. Surprisingly, high-level resistance to 8918 occurred in Mtb harboring mutations within the gene adjacent to pptT, rv2795c, highlighting the role of the encoded protein as a potentiator of the bactericidal action of the amidinourea. Those studies revealed that Rv2795c (PptH) is a phosphopantetheinyl (PpT) hydrolase, possessing activity antagonistic with respect to PptT. We have solved the crystal structure of Mtb's phosphopantetheinyl hydrolase, making it the first phosphopantetheinyl (carrier protein) hydrolase structurally characterized. The 2.5 Å structure revealed the hydrolases' four-layer (α/β/β/α) sandwich fold featuring a Mn-Fe binuclear center within the active site. A structural similarity search confirmed that PptH most closely resembles previously characterized metallophosphoesterases (MPEs), particularly within the vicinity of the active site, suggesting that it may utilize a similar catalytic mechanism. In addition, analysis of the structure has allowed for the rationalization of the previously reported PptH mutations associated with 8918-resistance. Notably, differences in the sequences and predicted structural characteristics of the PpT hydrolases PptH of Mtb and E. coli's acyl carrier protein hydrolase (AcpH) indicate that the two enzymes evolved convergently and therefore are representative of two distinct PpT hydrolase families.

Reclaiming Phosphate from Waste Solutions with Fe(III)-Polysaccharide Hydrogel Beads for Photo-Controlled-Release Fertilizer

Photoresponsive hydrogels from polysaccharides and Fe(III) were used as a new system to capture and release PO43- from waste solutions. Uptake of 0.6-1.5 mg of phosphate per gram of hydrogels was determined from 800 ppm phosphate solutions (pH 4.8-9.0). These beads also captured 1.2 mg g-1 of phosphate from animal waste (raw manure, 727 ppm phosphate, pH 7.6), which accounted for above 80% phosphate uptake. Irradiation of phosphate-loaded hydrogels degraded the gels due to the photochemistry of the Fe(III)-carboxylates, giving controlled phosphate release (∼81% after 7 days). No release (<2% after 7 days) was seen in the dark. Kale plant trials showed complete degradation of the hydrogels in ∼2 weeks under greenhouse conditions. Biomass analysis of kale treated with phosphate-loaded beads compared to controls indicated no signs of toxicity. These results show that Fe(III)-polysaccharide hydrogels were able to reclaim phosphates from waste solutions and can be used as a controlled-release fertilizer.

Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned?

Phosphoesterases hydrolyze the phosphorus oxygen bond of phosphomono-, di- or triesters and are involved in various important biological processes. Carboxylate and/or hydroxido-bridged dizinc(II) sites are a widespread structural motif in this enzyme class. Much effort has been invested to unravel the mechanistic features that provide the enormous rate accelerations observed for enzymatic phosphate ester hydrolysis and much has been learned by using simple low-molecular-weight model systems for the biological dizinc(II) sites. This review summarizes the knowledge and mechanistic understanding of phosphoesterases that has been gained from biomimetic dizinc(II) complexes, showing the power as well as the limitations of model studies.

Modeling the Active Site of the Purple Acid Phosphatase Enzyme with Hetero-Dinuclear Mixed Valence M(II)-Fe(III) [M = Zn, Ni, Co, and Cu] Complexes Supported over a [N6O] Unsymmetrical Ligand

The active site of the purple acid phosphatase enzyme has been successfully modeled by a series of hetero-dinuclear M(II)-Fe(III) [M = Zn, Ni, Co, and Cu] type complexes of an unsymmetrical [N₆O] ligand that contained a bridging phenoxide moiety and one imidazoyl and three pyridyl moieties as the terminal N-binding sites. In particular, the hetero-dinuclear complexes, {L[M^II(μ-OAc)₂Fe^III]}(ClO₄)₂ [M = Zn (3a), Ni (3b), Co (4a), and Cu (4b)], were obtained directly from the phenoxy-bridged ligand (HL), namely 2-{[bis(2-methylpyridyl)amino]methyl}-6-{[((1-methylimidazol-2-yl)methyl)(2-pyridylmethyl)amino]methyl}-4-t-butylphenol (2), upon sequential addition of Fe(ClO₄)₃·XH₂O and M(ClO₄)₂·6H₂O (M = Zn and Ni) or M(OAc)₂·XH₂O (M = Co and Cu), in a low-to-moderate (ca. 32-53%) yield. The temperature-dependent magnetic susceptibility measurements indicated weak antiferromagnetic coupling interactions occurring between the two metal centers in their high-spin states. All of the 3(a-b) and 4(a-b) complexes successfully carried out the hydrolysis of the bis(2,4-dinitrophenyl)phosphate (2,4-BDNPP) substrate in a mixed CH₃CN/H₂O (v/v 1:1) medium in the pH range of 5.5-10.5 at room temperature, thereby mimicking the functional activity of the native enzyme. The spectrophotometric titration suggested a monoaquated and dihydroxo species of the type {L[(H₂O)M^II(μ-OH)Fe^III(OH)]}²⁺ to be the catalytically active species for the phosphodiester hydrolysis reaction within the pH range of ca. 5.80-7.15. Last, the kinetic studies on the hydrolysis of the model substrate, 2,4-BDNPP, divulge a Michaelis-Menten-type behavior for all complexes.

Characterization of purple acid phosphatases involved in extracellular dNTP utilization in Stylosanthes

Stylo (Stylosanthes spp.) is a pasture legume predominant in tropical and subtropical areas, where low phosphorus (P) availability is a major constraint for plant growth. Therefore, stylo might exhibit superior utilization of the P pool on acid soils, particularly organic P. However, little is known about mechanisms of inorganic phosphate (Pi) acquisition employed by stylo. In this study, the utilization of extracellular deoxy-ribonucleotide triphosphate (dNTP) and the underlying physiological and molecular mechanisms were examined for two stylo genotypes with contrasting P efficiency. Results showed that the P-efficient genotype, TPRC2001-1, was superior to the P-inefficient genotype, Fine-stem, when using dNTP as the sole P source. This was reflected by a higher dry weight and total P content for TPRC2001-1 than for Fine-stem, which was correlated with higher root-associated acid phosphatase (APase) activities in TPRC2001-1 under low P conditions. Subsequently, three PAP members were cloned from TPRC2001-1: SgPAP7, SgPAP10, and SgPAP26 Expression levels of these three SgPAPs were up-regulated by Pi starvation in stylo roots. Furthermore, there was a higher abundance of transcripts of SgPAP7 and SgPAP10 in TPRC2001-1 than in Fine-stem. Subcellular localization analysis demonstrated that these three SgPAPs were localized on the plasma membrane. Overexpression of these three SgPAPs could result in significantly increased root-associated APase activities, and thus extracellular dNTP utilization in bean hairy roots. Taken together, the results herein suggest that SgPAP7, SgPAP10, and SgPAP26 may differentially contribute to root-associated APase activities, and thus control extracellular dNTP utilization in stylo.

Characterization of Wall Teichoic Acid Degradation by the Bacteriophage ϕ29 Appendage Protein GP12 Using Synthetic Substrate Analogs

The genetics and enzymology of the biosynthesis of wall teichoic acid have been the extensively studied, however, comparatively little is known regarding the enzymatic degradation of this biological polymer. The GP12 protein from the Bacillus subtilis bacteriophage ϕ29 has been implicated as a wall teichoic acid hydrolase. We have studied the wall teichoic acid hydrolase activity of pure, recombinant GP12 using chemically defined wall teichoic acid analogs. The GP12 protein had potent wall teichoic acid hydrolytic activity in vitro and demonstrated ∼13-fold kinetic preference for glycosylated poly(glycerol phosphate) teichoic acid compared with non-glycosylated. Product distribution patterns suggested that the degradation of glycosylated polymers proceeded from the hydroxyl terminus of the polymer, whereas hydrolysis occurred at random sites in the non-glycosylated polymer. In addition, we present evidence that the GP12 protein possesses both phosphodiesterase and phosphomonoesterase activities.

Metallophosphoesterases: structural fidelity with functional promiscuity

Calcineurin-like metallophosphoesterases (MPEs) form a large superfamily of binuclear metal-ion-centre-containing enzymes that hydrolyse phosphomono-, phosphodi- or phosphotri-esters in a metal-dependent manner. The MPE domain is found in Mre11/SbcD DNA-repair enzymes, mammalian phosphoprotein phosphatases, acid sphingomyelinases, purple acid phosphatases, nucleotidases and bacterial cyclic nucleotide phosphodiesterases. Despite this functional diversity, MPEs show a remarkably similar structural fold and active-site architecture. In the present review, we summarize the available structural, biochemical and functional information on these proteins. We also describe how diversification and specialization of the core MPE fold in various MPEs is achieved by amino acid substitution in their active sites, metal ions and regulatory effects of accessory domains. Finally, we discuss emerging roles of these proteins as non-catalytic protein-interaction scaffolds. Thus we view the MPE superfamily as a set of proteins with a highly conserved structural core that allows embellishment to result in dramatic and niche-specific diversification of function.

Catalytic mechanisms of metallohydrolases containing two metal ions

At least one-third of enzymes contain metal ions as cofactors necessary for a diverse range of catalytic activities. In the case of polymetallic enzymes (i.e., two or more metal ions involved in catalysis), the presence of two (or more) closely spaced metal ions gives an additional advantage in terms of (i) charge delocalisation, (ii) smaller activation barriers, (iii) the ability to bind larger substrates, (iv) enhanced electrostatic activation of substrates, and (v) decreased transition-state energies. Among this group of proteins, enzymes that catalyze the hydrolysis of ester and amide bonds form a very prominent family, the metallohydrolases. These enzymes are involved in a multitude of biological functions, and an increasing number of them gain attention for translational research in medicine and biotechnology. Their functional versatility and catalytic proficiency are largely due to the presence of metal ions in their active sites. In this chapter, we thus discuss and compare the reaction mechanisms of several closely related enzymes with a view to highlighting the functional diversity bestowed upon them by their metal ion cofactors.

A complex iron-calcium cofactor catalyzing phosphotransfer chemistry

Alkaline phosphatases play a crucial role in phosphate acquisition by microorganisms. To expand our understanding of catalysis by this class of enzymes, we have determined the structure of the widely occurring microbial alkaline phosphatase PhoX. The enzyme contains a complex active-site cofactor comprising two antiferromagnetically coupled ferric iron ions (Fe(3+)), three calcium ions (Ca(2+)), and an oxo group bridging three of the metal ions. Notably, the main part of the cofactor resembles synthetic oxide-centered triangular metal complexes. Structures of PhoX-ligand complexes reveal how the active-site metal ions bind substrate and implicate the cofactor oxo group in the catalytic mechanism. The presence of iron in PhoX raises the possibility that iron bioavailability limits microbial phosphate acquisition.

Crystal structure of the Bacillus subtilis phosphodiesterase PhoD reveals an iron and calcium-containing active site

The PhoD family of extra-cytoplasmic phosphodiesterases are among the most commonly occurring bacterial phosphatases. The exemplars for this family are the PhoD protein of Bacillus subtilis and the phospholipase D of Streptomyces chromofuscus. We present the crystal structure of B. subtilis PhoD. PhoD is most closely related to purple acid phosphatases (PAPs) with both types of enzyme containing a tyrosinate-ligated Fe³⁺ ion. However, the PhoD active site diverges from that found in PAPs and uses two Ca²⁺ ions instead of the single extra Fe²⁺, Mn²⁺, or Zn²⁺ ion present in PAPs. The PhoD crystals contain a phosphate molecule that coordinates all three active site metal ions and that is proposed to represent a product complex. A C-terminal helix lies over the active site and controls access to the catalytic center. The structure of PhoD defines a new phosphatase active site architecture based on Fe³⁺ and Ca²⁺ ions.

The structure of a purple acid phosphatase involved in plant growth and pathogen defence exhibits a novel immunoglobulin-like fold

Phosphatases function in the production, transport and recycling of inorganic phosphorus, which is crucial for cellular metabolism and bioenergetics, as well as in bacterial killing, since they are able to generate reactive oxygen species via Fenton chemistry. Diphosphonucleotide phosphatase/phosphodiesterase (PPD1), a glycoprotein plant purple acid phosphatase (PAP) from yellow lupin seeds, contains a bimetallic Fe-Mn catalytic site which is most active at acidic pH. Unlike other plant PAPs, PPD1 cleaves the pyrophosphate bond in diphosphonucleotides and the phosphodiester bond in various phosphodiesters. The homohexameric organization of PPD1, as revealed by a 1.65 Å resolution crystal structure and confirmed by solution X-ray scattering, is unique among plant PAPs, for which only homodimers have previously been reported. A phosphate anion is bound in a bidentate fashion at the active site, bridging the Fe and Mn atoms in a binding mode similar to that previously reported for sweet potato PAP, which suggests that common features occur in their catalytic mechanisms. The N-terminal domain of PPD1 has an unexpected and unique fibronectin type III-like fold that is absent in other plant PAPs. Here, the in vitro DNA-cleavage activity of PPD1 is demonstrated and it is proposed that the fibronectin III-like domain, which 'overhangs' the active site, is involved in DNA selectivity, binding and activation. The degradation of DNA by PPD1 implies a role for PPD1 in plant growth and repair and in pathogen defence.

Spectroscopic and mechanistic studies of dinuclear metallohydrolases and their biomimetic complexes

An enhanced understanding of the metal ion binding and active site structural features of phosphoesterases such as the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ), and the organophosphate degrading agent from Agrobacterium radiobacter (OpdA) have important consequences for potential applications. Coupled with investigations of the metalloenzymes, programs of study to synthesise and characterise model complexes based on these metalloenzymes can add to our understanding of structure and function of the enzymes themselves. This review summarises some of our work and illustrates the significance and contributions of model studies to knowledge in the area.

Biologically relevant heterodinuclear iron-manganese complexes

The heterodinuclear complexes [Fe(III)Mn(II)(L-Bn)(μ-OAc)(2)](ClO(4))(2) (1) and [Fe(II)Mn(II)(L-Bn)(μ-OAc)(2)](ClO(4)) (2) with the unsymmetrical dinucleating ligand HL-Bn {[2-bis[(2-pyridylmethyl)aminomethyl]]-6-[benzyl-2-(pyridylmethyl)aminomethyl]-4-methylphenol} were synthesized and characterized as biologically relevant models of the new Fe/Mn class of nonheme enzymes. Crystallographic studies have been completed on compound 1 and reveal an Fe(III)Mn(II)μ-phenoxobis(μ-carboxylato) core. A single location of the Fe(III) ion in 1 and of the Fe(II) ion in 2 was demonstrated by Mössbauer and (1)H NMR spectroscopies, respectively. An investigation of the temperature dependence of the magnetic susceptibility of 1 revealed a moderate antiferromagnetic interaction (J = 20 cm(-1)) between the high-spin Fe(III) and Mn(II) ions in 1, which was confirmed by Mössbauer and electron paramagnetic resonance (EPR) studies. The electrochemical properties of complex 1 are described. A quasireversible electron transfer at -40 mV versus Ag/AgCl corresponding to the Fe(III)Mn(II)/Fe(II)Mn(II) couple appears in the cyclic voltammogram. Thorough investigations of the Mössbauer and EPR signatures of complex 2 were performed. The analysis allowed evidencing of a weak antiferromagnetic interaction (J = 5.72 cm(-1)) within the Fe(II)Mn(II) pair consistent with that deduced from magnetic susceptibility measurements (J = 6.8 cm(-1)). Owing to the similar value of the Fe(II) zero-field splitting (D(Fe) = 3.55 cm(-1)), the usual treatment within the strong exchange limit was precluded and a full analysis of the electronic structure of the ground state of complex 2 was developed. This situation is reminiscent of that found in many diiron and iron-manganese enzyme active sites.

Binuclear metallohydrolases: complex mechanistic strategies for a simple chemical reaction

Binuclear metallohydrolases are a large family of enzymes that require two closely spaced transition metal ions to carry out a plethora of hydrolytic reactions. Representatives include purple acid phosphatases (PAPs), enzymes that play a role in bone metabolism and are the only member of this family with a heterovalent binuclear center in the active form (Fe(3+)-M(2+), M = Fe, Zn, Mn). Other members of this family are urease, which contains a di-Ni(2+) center and catalyzes the breakdown of urea, arginase, which contains a di-Mn(2+) center and catalyzes the final step in the urea cycle, and the metallo-β-lactamases, which contain a di-Zn(2+) center and are virulence factors contributing to the spread of antibiotic-resistant pathogens. Binuclear metallohydrolases catalyze numerous vital reactions and are potential targets of drugs against a wide variety of human disorders including osteoporosis, various cancers, antibiotic resistance, and erectile dysfunctions. These enzymes also tend to catalyze more than one reaction. An example is an organophosphate (OP)-degrading enzyme from Enterobacter aerogenes (GpdQ). Although GpdQ is part of a pathway that is used by bacteria to degrade glycerolphosphoesters, it hydrolyzes a variety of other phosphodiesters and displays low levels of activity against phosphomono- and triesters. Such a promiscuous nature may have assisted the apparent recent evolution of some binuclear metallohydrolases to deal with situations created by human intervention such as OP pesticides in the environment. OP pesticides were first used approximately 70 years ago, and therefore the enzymes that bacteria use to degrade them must have evolved very quickly on the evolutionary time scale. The promiscuous nature of enzymes such as GpdQ makes them ideal candidates for the application of directed evolution to produce new enzymes that can be used in bioremediation and against chemical warfare. In this Account, we review the mechanisms employed by binuclear metallohydrolases and use PAP, the OP-degrading enzyme from Agrobacterium radiobacter (OPDA), and GpdQ as representative systems because they illustrate both the diversity and similarity of the reactions catalyzed by this family of enzymes. The majority of binuclear metallohydrolases utilize metal ion-activated water molecules as nucleophiles to initiate hydrolysis, while some, such as alkaline phosphatase, employ an intrinsic polar amino acid. Here we only focus on catalytic strategies applied by the former group.