Refined structure of alkaline phosphatase from Escherichia coli at 2.8 Å resolution

Abstract

The structure of alkaline phosphatase from Escherichia coli has been determined to 2.8 Å resolution. The multiple isomorphous replacement electron density map of the dimer at 3.4 Å was substantially improved by molecular symmetry averaging and solvent flattening. From these maps, polypeptide chains of the dimer were built using the published amino acid sequence. Stereochemically restrained least-squares refinement of this model against native data, starting with 3.4 Å data and extending in steps to 2.8 Å resolution, proceeded to a final overall crystallographic R factor of 0.256. Alkaline phosphatase-phosphomonoester hydrolase (EC 3.1.3.1) is a metalloenzyme that forms an isologous dimer with two reactive centers 32 Å apart. The topology of the polypeptide fold of the subunit is of the α β class of proteins. Despite the similarities in the overall α β fold with other proteins, alkaline phosphatase does not have a characteristic binding cleft formed at the carboxyl end of the parallel sheet, but rather an active pocket that contains a cluster of three functional metal sites located off the plane of the central ten-stranded sheet. This active pocket is located near the carboxyl ends of four strands and the amino end of the antiparallel strand, between the plane of the sheet and two helices on the same side. Alkaline phosphatase is a non-specific phosphomonoesterase that hydrolyzes small phosphomonoesters as well as the phosphate termini of DNA. The accessibility calculations based on the refined co-ordinates of the enzyme show that the active pocket barely accommodates inorganic phosphate. Thus, the alcoholic or phenolic portion of the substrate would have to be exposed on the surface of the enzyme. Two metal sites, M1 and M2, 3.9 Å apart, are occupied by zinc. The third site, M3, 5 Å from site M2 and 7 Å from site M1, is occupied by magnesium or, in the absence of magnesium, by zinc. As with other zinc-containing enzymes, histidine residues are ligands to zinc site M1 (three) and to zinc site M2 (one). Ligand assignment and metal preference indicate that the crystallographically found metal sites M1, M2 and M3 correspond to the spectroscopically deduced metal sites A, B and C, respectively. Arsenate, a product analog and enzyme inhibitor, binds between Ser102 and zinc sites M1 and M2. The position of the guanidinium group of Arg166 is within hydrogen-bonding distance from the arsenate site. The structural disposition of those elements suggests that, despite the lack of protein acid and protein base functions, metals can activate both nucleophiles, Ser102 and water, necessary for double in-line nucleophilic displacement on phosphorus. Metal sites M1 and/or M2 can activate Ser102 and prepare the phosphate group for nucleophilic attack. They can stabilize the transition state along with Arg166 during bond formation and breakage. A second nucleophilic attack is performed by water during hydrolysis of phosphoserine intermediate. Comparison of the architecture of the active pocket with recent 31P and 113Cd nuclear magnetic resonance on covalent and non-covalent phosphoenzyme intermediates indicates the water molecule is most probably located on the M1 metal site.