6PY9

Crystal structure of red kidney bean purple acid phosphatase in complex with adenosine diphosphate metavanadate

Summary for 6PY9

• Entry DOI: 10.2210/pdb6py9/pdb
• Descriptor: Fe(3+)-Zn(2+) purple acid phosphatase, GLYCEROL, TRIETHYLENE GLYCOL, ... (15 entities in total)
• Functional Keywords: purple acid phosphatase, metallohydrolases, catalysis, phytase, atpase, agricultural biotechnology, metal binding protein, hydrolase
• Biological source: Phaseolus vulgaris (Kidney bean)
• Total number of polymer chains: 4
• Total formula weight: 224074.72

Authors

Feder, D.,Schenk, G.,Guddat, L.W.,McGeary, R.P.,Mitic, N.,Furtado, A.,Schulz, B.L.,Henry, R.J.,Schmidt, S. (deposition date: 2019-07-29, release date: 2020-04-29, Last modification date: 2024-10-23)

Primary citation

Feder, D.,McGeary, R.P.,Mitic, N.,Lonhienne, T.,Furtado, A.,Schulz, B.L.,Henry, R.J.,Schmidt, S.,Guddat, L.W.,Schenk, G.
Structural elements that modulate the substrate specificity of plant purple acid phosphatases: Avenues for improved phosphorus acquisition in crops.
Plant Sci., 294:110445-110445, 2020

PubMed 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. 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.

PubMed: 32234228
DOI: 10.1016/j.plantsci.2020.110445

Experimental method

X-RAY DIFFRACTION (2.2 Å)