Crystallization and preliminary crystallographic data of purple acid phosphatase from red kidney bean

doi:10.1016/0022-2836(92)91012-E

Journal of Molecular Biology

Volume 224, Issue 2, 20 March 1992, Pages 511-513

https://doi.org/10.1016/0022-2836(92)91012-E Get rights and content

Abstract

Purple acid phosphatase from red kidney bean has been crystallized from ammonium sulfate solutions in the pH range from 3·5 to 5·5. The crystal form is tetragonal bipyramidal and the largest crystals grew up to 2·0 mm long. Systematic absences indicate one of the enantiomorphic space groups P4₁2₁2 (92) or P4₃2₁2 (96) with cell dimensions $a = b = 104·1(1) A ̊ and c = 308·7(2) A ̊$ . The asymmetric unit contains one dimer with M_r of 110,700, determined by ultraviolet-laser desorption mass spectrometry. The crystals, with a salt-free density of 1·12 g/cm³ and a water content of 67%, diffract to 3·5 Å.

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Cited by (21)

Purple acid phosphatase in the walls of tobacco cells
2008, Phytochemistry
Purple acid phosphatase isolated from the walls of tobacco cells appears to be a 220 kDa homotetramer composed of 60 kDa subunits, which is purple in color and which contains iron as its only metal ion. Although the phosphatase did not require dithiothreitol for activity and was not inhibited by phenylarsine oxide, the enzyme showed a higher catalytic efficiency (k_cat/K_m) for phosphotyrosine-containing peptides than for other substrates including p-nitrophenyl-phosphate and ATP. The phosphatase formed as a 120 kDa dimer in the cytoplasm and as a 220 kDa tetramer in the walls, where Brefeldin A blocked its secretion during wall regeneration. According to our double-immunofluorescence labeling results, the enzyme might be translocated through the Golgi apparatus to the walls at the interphase and to the cell plate during cytokinesis.
Cloning and comparative protein modeling of two purple acid phosphatase isozymes from sweet potatoes (Ipomoea batatas)
1999, Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology
The sequence of cDNA fragments of two isozymes of the purple acid phosphatase from sweet potato (spPAP1 and spPAP2) has been determined by 5′ and 3′ rapid amplification of cDNA ends protocols using oligonucleotide primers based on amino acid information. The encoded amino acid sequences of these two isozymes show an equidistance of 72–77% not only to each other, but also to the primary structure of the purple acid phosphatase from red kidney bean (kbPAP). A three-dimensional model of the active site has been constructed for spPAP2 on the basis of the kbPAP crystallographic structure that helps to explain the reported differences in the visible and EPR spectra of spPAP2 and kbPAP.
Structural and functional studies on model compounds of purple acid phosphatases and catechol oxidases
1999, Coordination Chemistry Reviews
The synthesis, single crystal X-ray crystallographic, magnetic and electrochemical characterization of eight representative symmetric and unsymmetric complexes as structural model compounds for active sites in PAPs is reported. A mixed valent diiron as well as an iron(III)–zinc(II) complex as models for the active, reduced form of mammalian and plant PAPs, respectively, were synthesized and characterized. Five diiron(III) compounds as structural models for the oxidized uteroferrin-phosphato and -arsenato complex and a model for the oxidized form of PAP from beef spleen are reported. In addition to the structural relevance the catalase and peroxidase activity of one of these model complexes is introduced. Further we summarize our recent research concerning synergistic investigations on catechol oxidase and on synthetic copper coordination complexes. The catechol oxidase is an important type 3 copper protein for the activation of dioxygen. The development of low-molecular weight catalysts should facilitate the oxidation of organic substances by O₂. In particular the reported copper(II) complexes may serve as structural and functional bioinorganic model compounds for the active sites of dioxygen binding and dioxygen activating copper proteins, respectively. These investigations provided a new X-ray crystallographically characterized type of peroxo copper(II) complexes with a μ₄-(η¹)₄ coordination mode.
Localization of the Fe(III)-Zn(II) purple acid phosphatase in dry kidney beans using immunofluorescence and immunogold electron microscopy
1998, Annals of Botany
Localization of purple acid phosphatase (PAP) from the seeds of kidney beans,Phaseolus vulgaris(L.), was performed using light and transmission electron microscopy. After rehydration and aqueous fixation, cryo-sections of bean cotyledon tissue showed a bright immunofluorescent signal in the cytoplasm of cells whereas cell walls and reserve materials (starch, protein bodies) remained unstained. In ultrathin sections of dry cotyledon tissue anhydrously fixed in acrolein vapour and embedded in Lowicryl resin, PAP mapped exclusively to ribosome-rich areas of the cytoplasm. In view of these results, we propose that kidney bean PAP might possibly be engaged in mechanisms involved in the triggering of seed dormancy.
Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures
1996, Journal of Molecular Biology
Purple acid phosphatase is a widely distributed non-specific phosphomonoesterase. X-ray structures of the dimeric 111-kDa Fe(III)-Zn(II) kidney bean purple acid phosphatase (kbPAP) complexed with phosphate, the product of the reaction, and with tungstate, a strong inhibitor of the phosphatase activity, were determined at 2.7 and 3.0 Å resolution, respectively. Furthermore the resolution of the unligated enzyme, recently solved at 2.9 Å could be extended to 2.65 Å with completely new data. The binding of both oxoanions is not accompanied by larger conformational changes in the enzyme structure. Small movements with a maximal coordinate shift of 1 Å are only observed for the active site residues His295 and His296. In the inhibitor complex as well as in the product complex, the oxoanion binds in a bidentate bridging mode to the two metal ions, replacing two of the presumed solvent ligands present in the unligated enzyme form. As also proposed for the unligated structure a bridging hydroxide ion completes the coordination spheres of both metal ions to octahedral arrangements. All three structures reported herein support a mechanism of phosphate ester hydrolysis involving interaction of the substrate with Zn(II) followed by a nucleophilic attack on the phosphorus by an Fe(III)-coordinated hydroxide ion. The negative charge evolving at the pentacoordinated transition state is probably stabilized by interactions with the divalent zinc and the imidazole groups of His202, His295, and His296, the latter protonating the leaving alcohol group.
X-ray absorption studies of the purple acid phosphatase from red kidney beans (native enzyme, metal exchanged form)
1995, Physica B: Physics of Condensed Matter
Purple acid phosphatase from red kidney beans (KBP) catalyzes the hydrolysis of activated phosphoric acid monoesters and contains a heterodinuclear Fe(III)Zn(II) core in its active site. Iron K-edge X-ray absorption data have been obtained for the native enzyme and for a metal exchanged derivative, where Zn(II) was substituted by Fe(III). The environment of the native enzyme consists of 2.5 O/N at 1.91 Å, 3 O/N at 2.09 Å, and 1 Zn at 4.05 Å. For the metal exchanged form we obtained 2.5 O/N at 1.94 Å, 2.5 O/N at 2.09 Å, and 1 Fe at 3.79 Å.

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Journal of Molecular Biology

Crystallization noteCrystallization and preliminary crystallographic data of purple acid phosphatase from red kidney bean

Abstract

Biochim. Biophys. Acta

Inorganica Chimica Acta

J. Mol. Biol

J. Mol. Biol

Properties of the Fe(II)-Fe(III) derivative of red kidney bean purple phosphatase. Evidence for a binuclear Zn-Fe center in the native enzyme

J. Amer. Chem. Soc

The S.E.R.C. (U.K.) Collaborative Computing Project No. 4, a Suite of Programs for Protein Crystallography

Density and apparent specific volume of proteins

Crystallization note
Crystallization and preliminary crystallographic data of purple acid phosphatase from red kidney bean