6py9 | pdb_00006py9

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

spinqualitylabelsall models 6py9, resolution 2.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6py9 is a 4 chain structure with sequence from Phaseolus vulgaris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: AD9, CL, EDO, FE, FLC, FUC, GOL, NA, NAG, P4J, PGE, SO4, ZN Activity: Acid phosphatase, with EC number 3.1.3.2 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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 A 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 elements that modulate the substrate specificity of plant purple acid phosphatases: Avenues for improved phosphorus acquisition in crops.,Feder D, McGeary RP, Mitic N, Lonhienne T, Furtado A, Schulz BL, Henry RJ, Schmidt S, Guddat LW, Schenk G Plant Sci. 2020 May;294:110445. doi: 10.1016/j.plantsci.2020.110445. Epub 2020, Feb 14. PMID:32234228 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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