Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis

Catalytic promiscuity and the evolution of new enzymatic activities

Several contemporary enzymes catalyze alternative reactions distinct from their normal biological reactions. In some cases the alternative reaction is similar to a reaction that is efficiently catalyzed by an evolutionary related enzyme. Alternative activities could have played an important role in the diversification of enzymes by providing a duplicated gene a head start towards being captured by adaptive evolution.

Hysteretic enzyme adaptation to environmental pH: change in storage pH of alkaline phosphatase leads to a pH-optimum in the opposite direction to the applied change

The activity of alkaline phosphatase (AP) shows a change in optimum pH in the opposite direction to the applied change in storage pH. Typically, a change in storage pH from 9.8 to 8.5 results in a (reversible) change of the pH-optimum from 10.0 to 10.8. Protein fluorescence analysis shows that this response is probably due to conformational changes induced by the different storage conditions. As storage pH increases, a more 'open' or less 'compact' conformation is attained. Analysis of the diprotic model (a model which describes possible pH-responses of enzymes) indicates, that, as the AP conformation is getting more 'open' an increase in the dissociation of activity-regulating protons of AP occurs. This leads to a decrease in pH-optimum, precisely as found in the experiment. The prerequisite for such a response, however, is that the conformational adaptation to environmental assay pH is slow (hysteretic) when compared with assay time (400 s). The relaxation time of this adaptation was found to be in the order of 2 h.

A model of the transition state in the alkaline phosphatase reaction

A high resolution crystal structure of Escherichia coli alkaline phosphatase in the presence of vanadate has been refined to 1.9 A resolution. The vanadate ion takes on a trigonal bipyramidal geometry and is covalently bound by the active site serine nucleophile. A coordinated water molecule occupies the axial position opposite the serine nucleophile, whereas the equatorial oxygen atoms of the vanadate ion are stabilized by interactions with both Arg-166 and the zinc metal ions of the active site. This structural complex supports the in-line displacement mechanism of phosphomonoester hydrolysis by alkaline phosphatase and provides a model for the proposed transition state in the enzyme-catalyzed reaction.

An artificial transmembrane segment directs SecA, SecB, and electrochemical potential-dependent translocation of a long amino-terminal tail

Many integral membrane proteins contain an amino-terminal segment, often referred to as an N-tail, that is translocated across a membrane. In many cases, translocation of the N-tail is initiated by a cleavable, amino-terminal signal peptide. For N-tail proteins lacking a signal peptide, translocation is initiated by a transmembrane segment that is carboxyl to the translocated segment. The mechanism of membrane translocation of these segments, although poorly understood, has been reported to be independent of the protein secretion machinery. In contrast, here we describe alkaline phosphatase mutants containing artificial transmembrane segments that demonstrate that translocation of a long N-tail across the membrane is dependent upon SecA, SecB, and the electrochemical potential in the absence of a signal peptide. The corresponding mutants containing signal peptides also use the secretion machinery but are less sensitive to inhibition of its components. We present evidence that inhibition of SecA by sodium azide is incomplete even at high concentrations of inhibitor, which suggests why SecA-dependent translocation may not have been detected in other systems. Furthermore, by varying the charge around the transmembrane segment, we find that in the absence of a signal peptide, the orientation of the membrane-bound alkaline phosphatase is dictated by the positive inside rule. However, the presence of a signal peptide is an overriding factor in membrane orientation and renders all mutants in an Nout-Cin orientation.

Mechanistic alternatives in phosphate monoester hydrolysis: what conclusions can be drawn from available experimental data?

Phosphate monoester hydrolysis reactions in enzymes and solution are often discussed in terms of whether the reaction pathway is associative or dissociative. Although experimental results for solution reactions have usually been considered as evidence for the second alternative, a closer thermodynamic analysis of observed linear free energy relationships shows that experimental information is consistent with the associative, concerted and dissociative alternatives.

Proline isomerization is unlikely to be the cause of slow annealing and reactivation during the folding of alkaline phosphatase

The in vitro folding of Escherichia coli alkaline phosphatase (AP) from the guanidine hydrochloride (GdnHCl) denatured state is characterized by a significant slow phase in the post activational recovery of native protein lability (probed by the susceptibility to GdnHCl denaturation and occurring on the time scale of days) as well as a slow phase in the recovery of activity (on the time scale of minutes). Slow folding events have often been attributed to cis-trans isomerizations of X-Pro peptide bonds, a plausible explanation for AP, which contains 21 prolines per subunit. To investigate the role of proline isomerization in the two measures of refolding mentioned above, we have performed "double-jump" GdnHCl denaturation/renaturation experiments, with a third jump, where the rate of unfolding of refolded protein upon exposure to denaturant was added to assess the rate of change of lability. Our measurements of the time evolution of both the lability and the reactivation of refolded AP as a function of denaturation time show that proline isomerization is unlikely to be the cause of either of these slow events in the refolding of AP. The conclusions are further confirmed by the absence of proline isomerization effects when AP is refolded in the presence of human and periplasmic E. coli peptidyl-prolyl isomerase.

Macrocyclic Heterodinuclear Zn(II)Pb(II) Complexes: Synthesis, Structures, and Hydrolytic Function toward Tris(p-nitrophenyl) Phosphate

A heterodinuclear Zn(II)Pb(II) complex ZnPb(L)(ClO(4))(2).2H(2)O (1) has been obtained where (L)(2)(-) is an unsymmetric macrocycle derived from the 2:1:1 condensation of 2,6-diformyl-4-methylphenol, ethylenediamine and diethylenetriamine and has the "salen"- and "saldien"-like metal-binding sites sharing the phenolic moiety. Its DMF adduct, ZnPb(L)(ClO(4))(2).MeOH.2DMF (1'), crystallizes in the triclinic space group P&onemacr; with a = 14.457(4) Å, b = 14.795(6) Å, c = 10.307(9) Å, alpha = 109.04(5) degrees, beta = 96.24(5) degrees, gamma = 102.56(3) degrees, V = 1995(2) Å(3), and Z = 2. The refinement converges with R = 0.058 and R(w) = 0.060 for 3532 reflections with |F(0)| > 3sigma(|F(0)|). It has a discrete heterodinuclear core with the Zn(II) in the "salen" site and the Pb(II) in the "saldien" site of the macrocycle (L)(2)(-). The Zn has a square-pyramidal geometry together with a methanol oxygen, and the Pb has a seven-coordinate geometry together with one DMF oxygen and one perchlorate oxygen. The complex 1 is converted into [ZnPb(L)(OH)ClO(4)]H(2)O (2) under a weak alkaline condition. Its anhydrous form, [ZnPb(L)(OH)]ClO(4) (2), crystallizes in the monoclinic space group C2/c with a = 25.835(4) Å, b = 13.190(6) Å, c = 16.553 Å, beta = 106.31(2) degrees, V = 5413(2) Å(3), and Z = 8. The refinement converges with R = 0.038 and R(w) = 0.029 for 3944 reflections with |F(0)| > 3sigma(|F(0)|). It has a dimer structure of a dinuclear {ZnPb(L)(OH)}(+) unit having the Zn(II) in the "salen" site and the Pb(II) in the "saldien" site of the macrocycle. The hydroxide is bound to the Zn(II) to afford a square-pyramidal geometry about the metal. The dimeric core [ZnPb(L)(OH)](2)(2+) is formed by the bridge of the hydroxide oxygen to the Pb of the adjacent molecule and vice versa. The geometry about the Pb in the dimer structure is a pentagonal pyramid showing a distortion to "umbrella-like" structure, with the bridging hydroxide oxygen at the apex. In a DMSO solution, an equilibrium exists between the dimeric and monomeric species: [{ZnPb(L)(OH)}(2)](2+) right harpoon over left harpoon 2[ZnPb(L)(OH)](+). On the basis of (31)P NMR and visible spectra, 2 is shown to hydrolyze tris(p-nitorophenyl) phosphate (TNP) into bis(p-nitrophenyl) phosphate (BNP) in DMSO. 1 also exhibits a low activity to hydrolyze TNP into BNP due to the equilibrium [ZnPb(L)(H(2)O)](2+) right harpoon over left harpoon [ZnPb(L)(OH)](+) + H(+). From the reaction mixture with 2, a BNP complex [ZnPb(L)(BNP)]ClO(4) (3) has been isolated. 3 crystallizes in the triclinic space group P&onemacr; with a = 13.494(9) Å, b = 13.88(1) Å, c = 12.765(8) Å, alpha = 94.71(6) degrees, beta = 97.02(6) degrees, gamma = 61.68(5) degrees, V = 2088(2) Å(3), Z = 2. The refinement converges with R = 0.044 and R(w) = 0.056 for 6070 reflections with |F(0)| > 3sigma(|F(0)|). The BNP(-) group bridges the pair of metal ions through its two oxygens, together with two phenolic oxygens of (L)(2)(-). On the basis of the above findings, a mechanistic scheme for the TNP hydrolysis by 2 is proposed; a TNP molecule is bound to the Pb center, and the hydroxide on the adjacent Zn ion attacks the phosphorus nucleus of TNP, leading to the formation of the BNP complex 3.

The R78K and D117E active-site variants of Saccharomyces cerevisiae soluble inorganic pyrophosphatase: structural studies and mechanistic implications

We have solved the structure of two active-site variants of soluble inorganic pyrophosphatases (PPase), R78K and D117K, at resolutions of 1.85 and 2.15 A and R-factors of 19.5% and 18.3%, respectively. In the R78K variant structure, the high-affinity phosphate group (P1) is missing, consistent with the wild-type structure showing a bidentate interaction between P1 and Arg78, and solution data showing a decrease in P1 affinity in the variant. The structure explains why the mutation affects P1 and pyrophosphate binding much more than would be expected by the loss of one hydrogen bond: Lys78 forms an ion-pair with Asp71, precluding an interaction with P1. The R78K variant also provides the first direct evidence that the low-affinity phosphate group (P2) can adopt the structure that we believe is the immediate product of hydrolysis, with one of the P2 oxygen atoms co-ordinated to both activating metal ions (M1 and M2). If so, the water molecule (Wat1) between M1 and M2 in wild-type PPase is, indeed, the attacking nucleophile. The D117E variant structure likewise supports our model of catalysis, as the Glu117 variant carboxylate group is positioned where Wat1 is in the wild-type: the potent Wat1 nucleophile is replaced by a carboxylate co-ordinated to two metal ions. Alternative confirmations of Glu117 may allow Wat1 to be present but at much reduced occupancy, explaining why the pKa of the nucleophile increases by three pH units, even though there is relatively little distortion of the active site. These new structures, together with parallel functional studies measuring catalytic efficiency and ligand (metal ion, PPi and Pi) binding, provide strong evidence against a proposed mechanism in which Wat1 is considered unimportant for hydrolysis. They thus support the notion that PPase shares mechanistic similarity with the "two-metal ion" mechanism of polymerases.

Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases

The 2.15-A resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed with DNA and Ca2+ ions reveals two divalent metals bound in one of the active sites. One of these metals is ligated through an inner-sphere water molecule to the phosphate group located 3' to the scissile phosphate. A second inner-sphere water on this metal is positioned approximately in-line for attack on the scissile phosphate. This structure corroborates the observation that the pro-SP phosphoryl oxygen on the adjacent 3' phosphate cannot be modified without severe loss of catalytic efficiency. The structural equivalence of key groups, conserved in the active sites of EcoRV, EcoRI, PvuII, and BamHI endonucleases, suggests that ligation of a catalytic divalent metal ion to this phosphate may occur in many type II restriction enzymes. Together with previous cocrystal structures, these data allow construction of a detailed model for the pretransition state configuration in EcoRV. This model features three divalent metal ions per active site and invokes assistance in the bond-making step by a conserved lysine, which stabilizes the attacking hydroxide ion nucleophile.

Biphasic denaturation of human placental alkaline phosphatase in guanidinium chloride

Human placental alkaline phosphatase is a membrane-anchored dimeric protein. Unfolding of the enzyme by guanidinium chloride (GdmCl) caused a decrease of the fluorescence intensity and a large red-shifting of the protein fluorescence maximum wavelength from 332 to 346 nm. The fluorescence changes were completely reversible upon dilution. GdmCl induced a clear biphasic fluorescence spectrum change, suggesting that a three-state unfolding mechanism with an intermediate state was involved in the denaturation process. The half unfolding GdmCl concentrations, [GdmCl]0.5, corresponding to the two phases were 1.45 M and 2.50 M, respectively. NaCl did not cause the same effect as GdmCl, indicating that the GdmCl-induced biphasic denaturation is not a salt effect. The decrease in fluorescence intensity was monophasic, corresponding to the first phase of the denaturation process with [GdmCl]0.5 = 1.37 M and reached a minimum at 1.5 M GdmCl, where the enzyme remained completely active. The enzymatic activity lost started at 2.0 M GdmCl and was monophasic but coincided with the second-phase denaturation with [GdmCl]0.5 = 2.46 M. Inorganic phosphate provides substantial protection of the enzyme against GdmCl inactivation. Determining the molecular weight by sucrose-density gradient ultracentrifugation revealed that the enzyme gradually dissociates in both phases. Complete dissociation occurred at [GdmCl] > 3 M. The dissociated monomers reassociated to dimers after dilution of the GdmCl concentration. Refolding kinetics for the first-phase denaturation is first-order but not second-order. The biphasic phenomenon thereby was a mixed dissociation-denaturation process. A completely folded monomer never existed during the GdmCl denaturation. The biphasic denaturation curve thereby clearly demonstrates an enzymatically fully active intermediate state, which could represent an active-site structure intact and other structure domains partially melted intermediate state.

Allotype immunoglobulin enhances alkaline phosphatase activity: implications for the inflammatory response

To understand the interactions among components of the immune/inflammation response, we studied the effects of immunoglobulins on the phosphatase activity of alkaline phosphatase in vitro. Bovine intestinal alkaline phosphatase was incubated with substrate in the presence of allotypic and xenotypic immunoglobulin. We found that bovine but not rabbit immunoglobulin enhanced the phosphatase activity of bovine intestinal alkaline phosphatase. Similarly, human but not bovine immunoglobulin G enhanced human placental alkaline phosphatase activity. By enhancing alkaline phosphatase activity, immunoglobulins bound to alkaline phosphatase may assist physiologic transport functions and enhance resolution of the inflammatory response. Further, in clinical conditions with high immunoglobulin concentrations, the serum alkaline phosphatase recorded may have spuriously high values.

Genetic complexity, structure, and characterization of highly active bovine intestinal alkaline phosphatases

Mammalian alkaline phosphatases (APs) display 10-100-fold higher kcat values than do bacterial APs. To begin uncovering the critical residues that determine the catalytic efficiency of mammalian APs, we have compared the sequence of two bovine intestinal APs, i.e. a moderately active isozyme (bovine intestinal alkaline phosphatase, bIAP I, approximately 3,000 units/mg) previously cloned in our laboratory, and a highly active isozyme (bIAP II, approximately 8, 000 units/mg) of hitherto unknown sequence. An unprecedented level of complexity was revealed for the bovine AP family of genes during our attempts to clone the bIAP II cDNA from cow intestinal RNAs. We cloned and characterized two novel full-length IAP cDNAs (bIAP III and bIAP IV) and obtained partial sequences for three other IAP cDNAs (bIAP V, VI, and VII). Moreover, we identified and partially cloned a gene coding for a second tissue nonspecific AP (TNAP-2). However, the cDNA for bIAP II, appeared unclonable. The sequence of the entire bIAP II isozyme was determined instead by a classical protein sequencing strategy using trypsin, carboxypeptidase, and endoproteinase Lys-C, Asp-N, and Glu-C digestions, as well as cyanogen bromide cleavage and NH2-terminal sequencing. A chimeric bIAP II cDNA was then constructed by ligating wild-type and mutagenized fragments of bIAP I, III, and IV to build a cDNA encoding the identified bIAP II sequence. Expression and enzymatic characterization of the recombinant bIAP I, II, III, and IV isozymes revealed average kcat values of 1800, 5900, 4200, and 6100 s-1, respectively. Comparison of the bIAP I and bIAP II sequences identified 24 amino acid positions as likely candidates to explain differences in kcat. Site-directed mutagenesis and kinetic studies revealed that a G322D mutation in bIAP II reduced its kcat to 1300 s-1, while the converse mutation, i.e. D322G, in bIAP I increased its kcat to 5800 s-1. Other mutations in bIAP II had no effect on its kinetic properties. Our data clearly indicate that residue 322 is the major determinant of the high catalytic turnover in bovine IAPs. This residue is not directly involved in the mechanism of catalysis but is spatially sufficiently close to the active site to influence substrate positioning and hydrolysis of the phosphoenzyme complex.

Alcoholysis of Urea Catalyzed by Palladium(II) Complexes

The palladium(II) aqua complex cis-[Pd(en)(H(2)O)(2)](2+) catalyzes the alcoholysis of urea into alkyl carbamate and ammonia. The observed rate constants for the ester formation fall in the range from 1.8 x 10(-)(5) to 5.9 x 10(-)(1) min(-)(1) at 313 K and pH 3.3, depending on the alcohol. This catalyzed reaction is at least 10(5) times faster than the uncatalyzed alcoholysis of urea under the same conditions. This is the first example of catalytic, nonhydrolytic cleavage of the amide bond in urea. The following steps in the mechanism of the methanolysis reaction are studied quantitatively: binding of urea to the catalyst in the presence of various alcohols or various concentrations of water, direct methanolysis of O-bound and N-bound urea, formation of carbamic acid (NH(2)COOH) coordinated to palladium(II) via the nitrogen atom, methanolysis of this intermediate, and the fast dissociation resulting in free methyl carbamate. Ammonia, a product of alcoholysis, inhibits this reaction by binding to palladium(II). When, however, ammonia is sequestered by the silver(I) cation, alcoholysis becomes relatively fast, and catalytic turnover is achieved. Various alcohols are compared in their reactivity toward urea. The effects of nucleophilicity, steric bulk, size, and additional hydroxyl groups (in diols) are examined. The intramolecular alcoholysis in the 2,6-dithia-1,8-octanediol complex cis-[Pd(C(6)H(14)O(2)S(2))(H(2)O)(2)](2+) results in at least 100-fold rate enhancement relative to the intermolecular alcoholysis by cis-[Pd(en)(H(2)O)(2)](2+). Alkyl carbamates do not hydrolyze further into carbamic acid and alcohol. Aryl carbamates do hydrolyze further, and this reaction requires the palladium(II) aqua complex as a catalyst. Carbamic acid then spontaneously decomposes into carbon dioxide and ammonia. Observed rate constants for the appearance and disappearance of aryl carbamates agree with the relative nucleophilicities of aryl alcohols. This study of the catalysis by a metal complex may contribute to the understanding of the metalloenzyme urease. We propose a new method, alcoholysis, for cleaving amide bonds in peptides and proteins.

A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases

Sequence analysis of the probable archaeal phosphoglycerate mutase resulted in the identification of a superfamily of metalloenzymes with similar metal-binding sites and predicted conserved structural fold. This superfamily unites alkaline phosphatase, N-acetylgalactosamine-4-sulfatase, and cerebroside sulfatase, enzymes with known three-dimensional structures, with phosphopentomutase, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, phosphoglycerol transferase, phosphonate monoesterase, streptomycin-6-phosphate phosphatase, alkaline phosphodiesterase/nucleotide pyrophosphatase PC-1, and several closely related sulfatases. In addition to the metal-binding motifs, all these enzymes contain a set of conserved amino acid residues that are likely to be required for the enzymatic activity. Mutational changes in the vicinity of these residues in several sulfatases cause mucopolysaccharidosis (Hunter, Maroteaux-Lamy, Morquio, and Sanfilippo syndromes) and metachromatic leucodystrophy.

Analysis of zinc binding sites in protein crystal structures

The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.

Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution

Detection of recurring three-dimensional side-chain patterns is a potential means of inferring protein function. This paper presents a new method for detecting such patterns and discusses various implications. The method allows detection of side-chain patterns without any prior knowledge of function, requiring only protein structure data and associated multiple sequence alignments. A recursive, depth-first search algorithm finds all possible groups of identical amino acids common to two protein structures independent of sequence order. The search is highly constrained by distance constraints, and by ignoring amino acids unlikely to be involved in protein function. A weighted root-mean-square deviation (RMSD) between equivalenced groups of amino acids is used as a measure of similarity. The statistical significance of any RMSD is assigned by reference to a distribution fitted to simulated data. Searches with the Ser/His/Asp catalytic triad, a His/His porphyrin binding pattern, and the zinc-finger Cys/Cys/His/His pattern are performed to test the method on known examples. An all-against-all comparison of representatives from the structural classification of proteins (SCOP) is performed, revealing several new examples of evolutionary convergence to common patterns of side-chains within different tertiary folds and in different orders along the sequence. These include a di-zinc binding Asp/Asp/His/His/Ser pattern common to alkaline phosphatase/bacterial aminopeptidase, and an Asp/Glu/His/His/Asn/Asn pattern common to the active sites of DNase I and endocellulase E1. Implications for protein evolution, function prediction and the rational design of functional regulators are discussed.

A novel protein modification generating an aldehyde group in sulfatases: its role in catalysis and disease

In multiple sulfatase deficiency, a rare human lysosomal storage disorder, all known sulfatases are synthesized as catalytically poorly active polypeptides. Analysis of the latter has shown that they lack a protein modification that was detected in all members of the sulfatase family. This novel protein modification generates a 2-amino-3-oxopropanoic acid (C alpha-formylglycine) residue by oxidation of the thiol group of a cysteine that is conserved among all eukaryotic sulfatases. The oxidation occurs in the endoplasmic reticulum at a stage when the nascent polypeptide is not yet folded. The aldehyde is part of the catalytic site and is likely to act as an aldehyde hydrate. One of the geminal hydroxyl groups accepts the sulfate during sulfate ester cleavage leading to the formation of a covalently sulfated enzyme intermediate. The other hydroxyl is required for the subsequent elimination of the sulfate and regeneration of the aldehyde group. In some prokaryotic members of the sulfatase gene family, the DNA sequence predicts a serine residue, and not a cysteine. Analysis of one of these prokaryotic sulfatases, however, revealed the presence of the C alpha-formylglycine indicating that the aldehyde group is essential for all members of the sulfatase family and that it can be generated from either cysteine or serine.

Kinetic and X-ray structural studies of three mutant E. coli alkaline phosphatases: insights into the catalytic mechanism without the nucleophile Ser102

Escherichia coli alkaline phosphatase (EC 3.1.3.1) is a non-specific phosphomonoesterase that catalyzes the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol. We investigated the nature of the primary nucleophile, fulfilled by the deprotonated Ser102, in the catalytic mechanism by mutating this residue to glycine, alanine and cysteine. The efficiencies of the S102G, S102A and S102C enzymes were 6 x 10(5)-fold, 10(5)-fold and 10(4)-fold lower than the wild-type enzyme, respectively, as measured by the kcat/Km ratio, still substantially higher than the non-catalyzed reaction. In order to investigate the structural details of the altered active site, the enzymes were crystallized and their structures determined. The enzymes crystallized in a new crystal form corresponding to the space group P6322. Each structure has phosphate at each active site and shows little departure from the wild-type model. For the S102G and S102A enzymes, the phosphate occupies the same position as in the wild-type enzyme, while in the S102C enzyme it is displaced by 2.5 A. This kinetic and structural study suggests an explanation for differences in catalytic efficiency of the mutant enzymes and provides a means to study the nature and strength of different nucleophiles in the same environment. The analysis of these results provides insight into the mechanisms of other classes of phosphatases that do not utilize a serine nucleophile.

Zinc enzymes

The number of zinc enzymes for which detailed structural and mechanistic data, including high resolution crystal structures, are available is increasing rapidly. The new findings continue to support the conclusion that the majority of zinc enzymes catalyze hydrolysis or closely related transfer reactions. In a protein environment, tetrahedral or 5-coordinate Zn2+ is ideally suited to activate a coordinated water (frequently a Zn2+--OH) as a nucleophile attacking the carbonyl carbon of a peptide bond, the carbon of carbon dioxide or the phosphorus of a phosphate ester. Protein-bound Zn2+ can function catalytically by forming mixed complexes with the substrate, either by expanding its coordination sphere or by exchanging a ligand. Formation of protein-Zn2+-substrate bonds can position the substrate or polarize its electron distribution to facilitate further steps in the reaction.

Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates

A two-metal-ion catalytic mechanism has previously been proposed for several phosphoryl-transfer enzymes. In order to extend the structural basis of this mechanism, crystal structures of three single-stranded DNA substrates bound to the 3'-5' exonucleolytic active site of the large fragment of DNA polymerase I from Escherichia coli have been elucidated. The first is a 2.1 A resolution structure of a Michaelis complex between the large fragment (or Klenow fragment, KF) and a single-stranded DNA substrate, stabilized by low pH and flash-freezing. The positions and identities of the catalytic metal ions, a Zn2+ at site A and a Mg2+ at site B, have been clearly established. The structural and kinetic consequences of sulfur substitutions in the scissile phosphate have been explored. A complex with the Rp isomer of phosphorothioate DNA, refined at 2.2 A resolution, shows Zn2+ bound to both metal sites and a mispositioning of the substrate and attacking nucleophile. The complex with the Sp phosphorothioate at 2. 3 A resolution reveals that metal ions do not bind in the active site, having been displaced by a bulky sulfur atom. Steady-state kinetic experiments show that catalyzed hydrolysis of the Rp isomer was reduced only about 15-fold, while no enzyme activity could be detected with the Sp phosphorothioate, consistent with the structural observations. Furthermore, Mn2+ could not rescue the activity of the exonuclease on the Sp phosphorothioate. Taken together, these studies confirm and extend the proposed two-metal-ion exonuclease mechanism and provide a structural context to explain the effects of sulfur substitutions on this and other phosphoryl-transfer enzymes. These experiments also suggest that the possibility of metal-ion exclusion be taken into account when interpreting the results of Mn2+ rescue experiments.

Sulfatases, trapping of the sulfated enzyme intermediate by substituting the active site formylglycine

Sulfatases contain an active site formylglycine residue that is generated by post-translational modification. Crystal structures of two lysosomal sulfatases revealed significant similarity to the catalytic site of alkaline phosphatase containing a serine at the position of formylglycine. To elucidate the catalytic mechanism of sulfate ester hydrolysis, the formylglycine of arylsulfatases A and B was substituted by serine. These mutants upon incubation with substrate were covalently sulfated at the introduced serine. This sulfated enzyme intermediate was stable at pH 5. At alkaline pH it was slowly hydrolyzed. These characteristics are analogous to that of alkaline phosphatase which forms a phosphoserine intermediate that is stable at pH 5, but is hydrolyzed at alkaline pH. In wild-type sulfatases the hydroxyl needed for formation of the sulfated enzyme intermediate is provided by the aldehyde hydrate of the formylglycine. The second, non-esterified hydroxyl of the aldehyde hydrate is essential for rapid desulfation of the enzyme at acidic pH, which most likely occurs by elimination. The lack of this second hydroxyl in the serine mutants explains the trapping of the sulfated enzyme intermediate. Thus, in acting as a geminal diol the formylglycine residue allows for efficient ester hydrolysis in an acidic milieu.

Solvent kinetic isotope effects of human placental alkaline phosphatase in reverse micelles

Human placental alkaline phosphatase was embedded in a reverse micellar system prepared by dissolving the surfactant sodium bis(2-ethylhexyl) sulphosuccinate (Aerosol-OT) in 2,2, 4-trimethylpentane. This microemulsion system provides a convenient instrumental tool to study the possible kinetic properties of the membranous enzyme in an immobilized form. The pL (pH/p2H) dependence of hydrolysis of 4-nitrophenyl phosphate has been examined over a pL range of 8.5-12.5 in both aqueous and reverse micellar systems. Profiles of log V versus pL were Ha-bell shaped in the acidic region but reached a plateau in the basic region in which two pKa values of 9.01-9.71 and 9.86-10.48, respectively, were observed in reverse micelles. However, only one pKa value of 9.78-10.27 in aqueous solution was detected. Profiles of log V/K versus pL were bell-shaped in the acidic region. However, they were wave-shaped in the basic region in which a residue of pKa 9.10-9.44 in aqueous solution and 8.07-8.78 in reverse micelles must be dehydronated for the reaction to reach an optimum. The V/K value shifted to a lower value upon dehydronation of a pKa value of 9.80-10.62 in aqueous solution and 11.23-12.17 in reverse micelles. Solvent kinetic isotope effects were measured at three pL values. At pL 9.5, the observed isotope effect was a product of equilibrium isotope effect and a kinetic isotope effect; at pL 10.4, the log V/K value was identical in water and deuterium. The deuterium kinetic isotope effect on V/K was 1.14 in an aqueous solution and 1.16 in reverse micelles. At pL 11.0 at which the log V values reached a plateau in either solvent system, the deuterium kinetic isotope effect on V was 2.08 in an aqueous solution and 0.62 in reverse micelles. Results from a proton inventory experiment suggested that a hydron transfer step is involved in the transition state of the catalytic reaction. The isotopic fractionation factor (pi) for deuterium for the transition state (piT) increased when the pH of the solution was raised. At pL 11.0, the piT was 1.07 in reverse micelles, which corresponds to the inverse-isotope effect of the reaction in this solvent system. Normal viscosity effects on kcat and kcat/Km were observed in aqueous solution, corresponding to a diffusional controlled physical step as the rate-limiting step. We propose that the rate-limiting step of the hydrolytic reaction changes from phosphate releasing in aqueous solution to a covalent phosphorylation or dephosphorylation step in reverse micelles.

Human placental alkaline phosphatase: expression in Pichia pastoris, purification and characterization of the enzyme

The soluble form of human placental alkaline phosphatase (PLAP) was expressed in the methylotrophic yeast Pichia pastoris and the expression product was purified and characterized. Yeast-derived PLAP (yPLAP) was secreted into the medium to the level of 2 mg/liter. yPLAP displayed kinetic properties similar to those reported earlier for the membrane-bound PLAP. Purified yPLAP had specific activity of 774 U/mg and appeared in two subunit sizes, ca. 62 and 65 kDa. This difference was due to heterogenous N-glycosylation. Purified yPLAP appeared as multiple forms in isoelectric focusing in pI range of 4.2 to 5.2. The expression system is discussed in comparison to previously reported expression systems.

Synthesis of Some Copper(II)-Chelating (Dialkylamino)pyridine Amphiphiles and Evaluation of Their Esterolytic Capacities in Cationic Micellar Media

Three new (dialkylamino)pyridine (DAAP)-based ligand amphiphiles 3-5 have been synthesized. All of the compounds possess a metal ion binding subunit in the form of a 2,6-disubstituted DAAP moiety. In addition, at least one ortho-CH(2)OH substituent is present in all the ligands. Complex formation by these ligands with various metal ions were examined under micellar conditions, but only complexes with Cu(II) ions showed kinetically potent esterolytic capacities under micellar conditions. Complexes with Cu(II) were prepared in host comicellar cetyltrimethylammonium bromide (CTABr) media at pH 7.6. Individual complexes were characterized by UV-visible absorption spectroscopy and electron paramagnetic resonance spectroscopy. These metallomicelles speed the cleavage of the substrates p-nitrophenyl hexanoate or p-nitrophenyl diphenyl phosphate. To ascertain the nature of the active esterolytic species, the stoichiometries of the respective Cu(II) complexes were determined from the kinetic version of Job's plot. In all the instances, 2:1 complex ligand/Cu(II) ion are the most kinetically competent species. The apparent pK(a) values of the Cu(II)-coordinated hydroxyl groups of the ligands 3, 4, and 5, in the comicellar aggregate, are 7.8, 8.0, and 8.0, respectively, as estimated from the rate constant vs pH profiles of the ester cleavage reactions. The nucleophilic metallomicellar reagents and the second-order "catalytic" rate constants toward esterolysis of the substrate p-nitrophenyl hexanoate (at 25 degrees C, pH 7.6) are 37.5 for 3, 11.4 for 4, and 13.8 for 5. All catalytic systems comprising the coaggregates of 3, 4, or 5 and CTABr demonstrate turnover behavior in the presence of excess substrate.

Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments

The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex between the anti HIV-1 gag ribozyme and its abortive DNA substrate manifests in the detection of a continuous track of A.T base pairs; this suggests that the interaction between the ribozyme and its DNA substrate is stronger than the one observed in the case of the free ribozyme where the bases in stem I and stem III regions interact strongly with the ribozyme core region (Sarma, R. H., et al. FEBS Letters 375, 317-23, 1995). The complex formation provides certain guidelines in the design of suitable therapeutic ribozymes. If the residues in the ribozyme stem regions interact with the conserved core, it may either prevent or interfere with the formation of a catalytically active tertiary structure.

Purification and characterization of alkaline phosphatase from Thermotoga neapolitana

A hyperthermophilic alkaline phosphatase was purified from Thermotoga neapolitana by heat treatment at 100 degrees C in the presence of Co2+ followed by ion-exchange and affinity chromatographies. The enzyme was purified 2,880-fold with 44% yield. The purified enzyme showed a single protein band of M(r) 45,000 on SDS-PAGE and an apparent molecular weight of 87,000 estimated by gel filtration chromatography. This suggested a homogenous dimer structure. The optimal pH and temperature for enzyme activity were 9.9 and 85 degrees C, respectively. Under optimal conditions, T. neapolitana alkaline phosphatase displayed 30% higher activity than calf intestine alkaline phosphatase did with p-nitrophenyl-phosphate as substrate. The hyperthermostable enzyme had a half-life of 238 min at 90 degrees C and K(m) and Vmax values of 183 microM and 1,352 U mg-1, respectively. Co2+ enhanced the enzyme activity, thermostability, and ligand affinity during column chromatography. The alkaline phosphatase was twice as active with Co2+ than with either Zn2+ or Mn2+ as the metal cofactor.

Structure and function of the low Mr phosphotyrosine protein phosphatases

Phosphotyrosine protein phosphatases (PTPases) catalyse the hydrolysis of phosphotyrosine residues in proteins and are hence implicated in the complex mechanism of the control of cell proliferation and differentiation. The low Mr PTPases are a group of soluble PTPases displaying a reduced molecular mass; in addition, a group of low molecular mass dual specificity (ds)PTPases which hydrolyse phosphotyrosine and phosphoserine/threonine residues in proteins are known. The enzymes belonging to the two groups are unrelated to each other and to other PTPase classes except for the presence of a CXXXXXRS/T sequence motif containing some of the catalytic residues (active site signature) and for the common catalytic mechanism, clearly indicating convergent evolution. The low Mr PTPases have a long evolutionary history since microbial (prokaryotic and eukaryotic) counterparts of both tyrosine-specific and dsPTPases have been described. Despite the relevant number of data reported on the structural and catalytic features of a number of low Mr PTPases, only limited information is presently available on the substrate specificity and the true biological roles of these enzymes, in prokaryotic, yeast and eukaryotic cells.

Mammalian alkaline phosphatases are allosteric enzymes

Mammalian alkaline phosphatases (APs) are zinc-containing metalloenzymes encoded by a multigene family and functional as dimeric molecules. Using human placental AP (PLAP) as a paradigm, we have investigated whether the monomers in a given PLAP dimer are subject to cooperativity during catalysis following an allosteric model or act via a half-of-sites model, in which at any time only one single monomer is operative. Wild type and mutant PLAP homodimers and heterodimers were produced by stably transfecting Chinese hamster ovary cells with mutagenized PLAP cDNAs followed by enzyme extraction, purification, and characterization. [Gly429]PLAP manifested negative cooperativity when partially metalated as a consequence of the reduced affinity of the incompletely metalated AP monomers for the substrate. Upon full metalation with Zn2+, however, the negative cooperativity disappeared. To distinguish between an allosteric and a half-of-sites model, a [Gly429]PLAP-[Ser84]PLAP heterodimer was produced by combining monomers displaying high and low sensitivity to the uncompetitive inhibitor L-Leu as well as a [Gly429]PLAP-[Ala92]PLAP heterodimer combining a catalytically active and inactive monomer, respectively. The L-Leu inhibition profile of the [Gly429]PLAP-[Ser84]PLAP heterodimer was intermediate to that for each homodimer as predicted by the allosteric model. Likewise, the [Gly429]PLAP-[Ala92]PLAP heterodimer was catalytically active, confirming that AP monomers act independently of each other. Although heterodimers are structurally asymmetrical, they migrate in starch gels with a smaller than expected weighted electrophoretic mobility, are more stable to heat denaturation than expected, and are more sensitive to L-Leu inhibition than predicted by a strict noncooperative model. We conclude that fully metalated mammalian APs are noncooperative allosteric enzymes but that the stability and catalytic properties of each monomer are controlled by the conformation of the second AP subunit.

Trapping and visualization of a covalent enzyme-phosphate intermediate

Using a mutant version of E. coli alkaline phosphatase, we succeeded in trapping and determining the structure of the phospho-enzyme intermediate. The X-ray structure also revealed the catalytic water molecule, bound to one of the active site zinc ions, positioned ideally for the apical attack necessary for the hydrolysis of the intermediate.

The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase

The crystal structure of an enzyme-substrate complex with histidyl-tRNA synthetase from Escherichia coli, ATP, and the amino acid analog histidinol is described and compared with the previously obtained enzyme-product complex with histidyl-adenylate. An active site arginine, Arg-259, unique to all histidyl-tRNA synthetases, plays the role of the catalytic magnesium ion seen in seryl-tRNA synthetase. When Arg-259 is substituted with histidine, the apparent second order rate constant (kcat/Km) for the pyrophosphate exchange reaction and the aminoacylation reaction decreases 1,000-fold and 500-fold, respectively. Crystals soaked with MnCl2 reveal the existence of two metal binding sites between beta- and gamma-phosphates; these sites appear to stabilize the conformation of the pyrophosphate. The use of both conserved metal ions and arginine in phosphoryl transfer provides evidence of significant early functional divergence of class II aminoacyl-tRNA synthetases.

Using guanidinium groups for the recognition of RNA and as catalysts for the hydrolysis of RNA

The guanidinium functional group is commonly used in nature to recognize and bind anions through ion pairing and hydrogen bonding. Specific hydrogen-bonding patterns can be found in crystal structures of simple guanidinium salts. Analysis of these simple salts reveals a variety of features which are found in natural systems. These features have been applied to a series of artificial phosphodiesterases for RNA. These receptors incorporate guanidinium groups positioned to mimic the hydrogen-bonding patterns found in simple guanidinium salts and natural enzymes. This paper outlines general guanidinium hydrogen-bonding patterns. Next, the complexation of phosphodiesters with a series of artificial receptors are analyzed in terms of counterions, solvent mixtures, and cavity flexibility. In addition, strategies to enhance catalysis through a pKa analysis of phosphoranes are addressed. Next, we describe how our findings were incorporated into second generation receptors/catalysts. Finally, our future work is discussed.