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The initial step of the dephosphorylation of phosphotyrosine by the protein tyrosine phosphatases (PTPases) requires an active-site cysteine residue to be in its deprotonated (thiolate) form so as to make a nucleophilic attack on the phosphate to form a phosphoenzyme intermediate. At the same time, an active-site aspartic acid residue must be in its protonated form to serve as a general acid donating a proton to the leaving tyrosyl moiety. The protein must therefore provide an unusual electrostatic environment in the active site to maintain these protonation states in the free enzyme and in the Michaelis complex with the substrate, whose phosphate group is in the −2 charged form. We present electrostatic calculations for the pKa of the ionizable side chains of four different PTPases. The study includes Michaelis complexes with the substrate, as well as free enzymes. The calculations consistently predict that in the neutral to mildly acidic pH range, the active-site cysteine residue is deprotonated and the aspartic acid residue is protonated, as required for optimal catalysis. This prediction is made even for the Michaelis complexes. Good quantitative agreement with measured pKa values of the aspartic acid residues are obtained, while the calculated pKa values of the cysteine residue are generally much lower than experimental estimates, suggesting that the protonation of the (normally unprotonated) cysteine residue may induce a conformational change in the active site. An analysis is made of the electrostatic factors responsible for maintaining the functionally essential protonation states. The phosphate-binding loop, whose backbone dipolar groups and conserved arginine side chain are oriented so as to stabilize negative charge in the active site, is found to be particularly important. However, structural features that are not conserved across the PTPase family make significant contributions in particular cases. The PTPases use dipoles more than positive charges to stabilize negative charge in the active site, and this helps to prevent the destabilization of the general acid by the longer range interactions with positive charges. The use of a low protein dielectric constant in the calculations is essential to obtaining calculated protonation states that are consistent with the catalytic mechanism. Models using a higher dielectric constant bring the calculated cysteine pKa values closer to some reported experimental values for the free enzyme, but fail to predict the protonation of the general acid, or the maintenance of the thiolate form of the cysteine residue in the Michaelis complex.

Angiogenesis is a tightly controlled process in which signaling by the receptors for vascular endothelial growth factor (VEGF) plays a key role. In order to define signaling pathways downstream of VEGF receptors (VEGFR), the kinase domain of VEGFR2 (Flk-1) was used as a bait to screen a human fetal heart library in the yeast two-hybrid system. One of the signaling molecules identified in this effort was HCPTPA, a low molecular weight, cytoplasmic protein tyrosine phosphatase. Although HCPTPA possesses no identifiable phosphotyrosine binding domains (i.e. SH2 or phosphotyrosine binding domains), it bound specifically to active, autophosphorylated VEGFR2 but not to a mutated, kinase-inactive VEGFR2. Recombinant VEGFR2 and endogenous VEGFR2 were substrates for recombinant HCPTPA, and HCPTPA was co-expressed with VEGFR2 in endothelial cell lines, suggesting that HCPTPA may be a negative regulator of VEGFR2 signal transduction. To pursue this possibility, an adenovirus directing the expression of HCPTPA was constructed. When used to infect cultured endothelial cells, this adenovirus directed high level expression of HCPTPA that resulted in impairment of VEGF-mediated VEGFR2 autophosphorylation and mitogen-activated protein kinase activation. Adenovirus-mediated overexpression of HCPTPA also inhibited VEGF-induced cellular responses (endothelial cell migration and proliferation) and inhibited angiogenesis in the rat aortic ring assay. Taken together, these findings indicate that HCPTPA may be an important regulator of VEGF-mediated signaling and biological activity. Potential interactions with other signaling pathways and possible therapeutic implications are discussed.

The enzyme from almond that catalyzes the hydrolysis of the N-glycosidic linkage between asparagine and the oligosaccharide chain of glycopeptides and glycoproteins has been variously termed an N-glycosidase and an amidase enzyme. Using turkey ovomucoid glycopeptide as a substrate for the enzyme, we followed the hydrolysis reaction by 1H NMR spectroscopy. These kinetic data revealed a rapid hydrolysis of the substrate but a delayed appearance of the final product. This implied that an intermediate, most likely a 1-aminooligosaccharide, was formed during the reaction. Identification of the intermediate as a 1-beta-amino-N-acetylglucosamine-oligosaccharide was achieved by trapping it as the 1-acetamido derivative using acetic anhydride and subsequent analysis by 1H NMR. The data conclusively demonstrate that the enzyme catalyzes the hydrolysis of the glycopeptide to form an aspartic acid-containing polypeptide and an intermediate oligosaccharide amine. The latter derivative is hydrolyzed nonenzymatically to yield the final carbohydrate product. Thus, the enzyme is in fact an amidohydrolase (amidase) and not an N-glycosidase. The trivial name glycopeptidylamidase is suggested.

The 3'-termini of the mitochondrial 12 S and 16 S ribosomal RNAs from mouse L cells have been definitively characterized by mobility-shift RNA sequencing, RNase digestion followed by fingerprinting using two-dimensional homochromatography, and precise mapping of RNA-DNA duplexes using nuclease S1. The results have been correlated with the known DNA sequence of the rRNA region. The vast majority of the 12 S rRNA consists of a family of transcripts whose last template-encoded nucleotide corresponds to a position immediately adjacent to the 5' end of the tRNAVal gene in the DNA sequence. These transcripts are oligoadenylated at their 3'-ends with from 1 to about 5 adenylate residues that are not encoded in the DNA sequence. A minor proportion of the 12 S rRNA ends one nucleotide before the 12 S/tRNAVal gene boundary and is also oligoadenylated. In contrast, the 3'-termini of 16 S rRNA have considerably greater heterogeneity, with the genomic location of the last template-encoded nucleotide varying from the nucleotide immediately adjacent to the 5'-end of the tRNALeuUUR gene to any position up to 7 nucleotides downstream within the tRNALeuUUR gene sequence. These various 16 S rRNA transcripts are oligoadenylated to a somewhat greater degree than the 12 S rRNA. The extent of the 16 S rRNA 3' heterogeneity, as compared to the 12 S rRNA, suggests that the 16 S rRNA 3'-termini may be generated by a mechanism involving termination of transcription rather than by processing of a primary transcript. The data are similar to those reported for human mitochondrial rRNA 3'-termini, and support a general role for adenylation of 3'-termini in the termination or processing of mammalian mitochondrial RNAs.

The stereochemical course of the phospho transfer catalyzed by homogeneous human prostatic acid phosphatase was investigated using 31P nuclear magnetic resonance spectroscopy. Transphosphorylation from phenyl-(R)-[15O, 17O, 18O]phosphate to (S)-propane-1,2-diol occurs with overall retention of configuration at phosphorus. This stereochemical result is consistent with the interpretation that the hydrolysis of substrates by this enzyme proceeds by way of a covalent phosphoenzyme intermediate. Conditions for optimizing phospho transfer by this and related acid phosphatases have also been explored.

Fluorescence steady-state and lifetime measurements have been performed that permit the differentiation of the 2 intrinsic tryptophan residues in bovine low molecular weight phosphotyrosyl protein phosphatase (BPTP). Spectral information was obtained by use of two single-tryptophan mutant proteins, W39F and W49F, and the double mutant protein W39,49F. Fluorescence measurements show that Trp39 is characterized by a large blue shift, a low quantum yield, and a shorter mean lifetime compared to Trp49. Solute fluorescence quenching studies of W39F reveal that Trp49 is highly exposed to the aqueous environment. In contrast, Trp39 is situated within a hydrophobic core and is only partially accessible to quenching agents such as acrylamide, iodide ion, and cesium ion. The fluorescence contributions of Trp39 and Trp49 are additive, and their sum is equivalent to that observed for wild type BPTP. Calculated intramolecular distances between Trp39 or Trp49 and a 5-[[(acetylamino)-ethyl]amino]naphthalene-1- sulfonate group covalently bound at Cys12 or Cys17 of the respective protein mutants, place Trp49 within 10 A and Trp39 at least 20 A from the active site. The fluorescence decay of the single tryptophan mutants and, surprisingly, wild type BPTP were each adequately fitted as biexponentials. The latter is a consequence of the imprecision involved in determining actual minima in a three- and four-exponential fitting. Comparison of quenching results of wild type BPTP with those of the single tryptophan mutant proteins indicates that minor fluorescence components, easily resolved using a biexponential fitting for the mutant proteins, are unresolvable for wild type BPTP. These minor components skewed the weighted magnitudes and induced perturbations in lifetimes for the tryptophan fluorescence of wild type BPTP, which directly influenced the calculated values of Ksv and kq.

The low molecular weight protein-tyrosine phosphatase (low M(r) PTPase) is an 18-kDa cytoplasmic enzyme of unknown function that has been previously found in several vertebrates. Using an oligonucleotide probe derived from the active site sequence of the mammalian low M(r) PTPases, a Saccharomyces cerevisiae gene that encodes a homolog of this enzyme was cloned by low stringency hybridization. This gene, LTP1, together with a neighboring gene, TKL1, is shown to be located on the right arm of chromosome XVI. The deduced amino acid sequence of its 161-amino acid residue product shows a 39% average identity with that of the mammalian enzymes. The yeast Ltp1 protein was expressed in Escherichia coli, purified to homogeneity, and shown to possess PTPase activity. The recombinant Ltp1 efficiently hydrolyzes phosphotyrosine and a phosphotyrosine-containing peptide, Tyr531-fyn, but it shows low activity toward phosphoserine and phosphothreonine. The catalytic activity of Ltp1 toward a number of substrates was approximately 30-fold lower than the corresponding values measured for the bovine low M(r) PTPase. However, the yeast enzyme was markedly activated by adenine and some purine nucleosides and nucleotides, including cAMP and cGMP. In the case of adenine, the activity of Ltp1 was increased by approximately 30-fold. The high degree of evolutionary conservation of the low M(r) PTPases implies a significant role for this enzyme. However, neither the disruption of the LTP1 gene nor an approximately 10-fold overexpression of its product in S. cerevisiae caused any apparent phenotypic changes under the conditions tested. No proteins related to Ltp1 could be detected in extracts of the ltp1 null mutant, either by immunoblotting or by gel-filtration analysis accompanied by extended kinetic assays, consistent with the conclusion that LTP1 is the only low M(r) PTPase-encoding gene in S. cerevisiae.

The low molecular weight phosphotyrosine phosphatases (PTPases) constitute a distinctive class of phosphotyrosine phosphatases that is widely distributed among vertebrate and invertebrate organisms. In vertebrates, two isoenzymes of these low molecular weight PTPases are commonly expressed. The two human isoenzymes, HCPTPA and HCPTPB, differ in an alternatively spliced sequence (residues 40-73) referred to as the variable loop, resulting in isoenzymes that have different substrate specificities and inhibitor/activator responses. We present here the x-ray crystallographic structure of a human low molecular weight PTPase solved by molecular replacement to 2.2 A. The structure of human low molecular weight PTPase is compared with a structure representing the other isoenzyme in this PTPase class, in each case with a sulfonate inhibitor bound to the active site. Possible aromatic residue interactions with the phosphotyrosine substrate are proposed from an examination of the binding site of the inhibitors. Differences are observed in the variable loop region, which forms one wall and the floor of a long crevice leading from the active-site loop. A set of residues lying along this crevice (amino acids 49, 50, and 53) is suggested to be responsible for differences in substrate specificity in these two enzymes.

Conclusive evidence is presented that an acid phosphatase catalyzes phosphate (oxygen)-water exchange. Studies conducted with human prostatic acid phosphatase by two independent methods have established that, despite earlier reports to the contrary, the enzyme catalyzes an exchange reaction between oxygen atoms of phosphate ion and of water. Kinetic data were obtained both by chemical conversion to trimethyl phosphate followed by mass spectroscopy and by a totally independent method involving 31P isotope shift nuclear magnetic resonance spectroscopy. Analysis showed that the enzyme catalyzes the exchange in a random, noncoupled process. If any coupled exchange occurs, it must represent less than 10% of the total. By mass spectral analysis, catalytic rate constants kcat = 0.14 sec-1 (4 degrees) and 1.8 sec-1 (37.5 degrees) were obtained. By 31P nuclear magnetic resonance kcat = 1.6 sec-1 (31 degrees) was obtained. The energy of activation for the exchange reaction is approximately 13kcal mol-1. The kcat value for exchange is about 10-fold greater than that observed with Escherichia coli alkaline phosphatase.