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PubMed1998

Molecular cloning, expression, and site-directed mutagenesis of inorganic pyrophosphatase from Thermus thermophilus HB8.

The genomic DNA encoding the inorganic pyrophosphatase from an extremely thermophilic bacterium, Thermus thermophilus HB8 (ATCC27634), was isolated by colony hybridization with a probe designed as a part of gene amplified by the PCR method, which was derived from the partial amino acid sequence of the enzyme. The DNA was cloned into a plasmid vector, pUC118, after digestion with BamHI. The inserted nucleotide fragment was about 1.8 kbp in length and the nucleotide sequence included a 525 bp open reading frame. The deduced amino acid sequence was completely identical with that of the enzyme determined by automated Edman analysis of peptide fragments isolated from digests obtained with Staphylococcus aureus V8 protease and Achromobacter protease I, and also from products obtained on chemical cleavage with cyanogen bromide and 70% formic acid. The subunit of this enzyme is composed of 174 amino acid residues with a calculated molecular weight of 19,084. Then, the gene was overexpressed in Escherichia coli BL21 (DE3) using a plasmid vector, pET15b, system. The recombinant enzyme was fully active, and exhibited higher thermostability than the E. coli enzyme. Amino acid residues located on the surface of the recombinant enzyme were determined by means of limited proteolysis, and the results revealed that the environment of Lys residues is almost the same as the crystal structure reported previously [Teplyakov, A. et al. (1994) Protein Sci. 3, 1098-1107]. Furthermore, the roles of two tryptophan residues were investigated by site-directed mutagenesis, which indicated that they may be responsible for the structural integrity and thermostability.

Amino Acid Sequence↗
PubMed1999

Primary structure, expression, and site-directed mutagenesis of inorganic pyrophosphatase from Bacillus stearothermophilus.

The complete primary structure of inorganic pyrophosphatase [EC 3.6. 1.1] from Bacillus stearothermophilus (ATCC 12016) was determined at the amino acid level by automated Edman degradation. The subunit of the enzyme consists of 164 amino acid residues with a calculated molecular mass of 18,796. The amino acid sequence of the enzyme is almost identical to that of thermophilic bacterium PS-3. Based on the determined primary structure, a PCR-amplified semi-synthetic gene was constructed and expressed in Escherichia coli JM109. The recombinant Bst. PPase showed the same characteristics and activity as the authentic enzyme, and exhibits higher thermostability than the E. coli enzyme. Furthermore, we prepared tyrosine-substituted variants by site-directed mutagenesis to elucidate the role of two highly conserved tyrosines (Y46 and Y130). As a result, two variants, Y46F and Y130F, lost most of their enzyme activity, whereas their conformations were unaffected. However, the wild-type and two variants exhibited different thermostability behaviors in the presence or absence of Mg2+. Therefore, these tyrosines may contribute to the structural integrity of the active site of the enzyme.

Amino Acid Sequence↗
PubMed1999

Hydrophobic interactions of Val75 are critical for oligomeric thermostability of inorganic pyrophosphatase from Bacillus stearothermophilus.

To determine the role of Val75 in the oligomeric structure of trimeric inorganic pyrophosphatase (PPase) [EC 3.6.1.1] from Bacillus stearothermophilus (Bst.), we used site-directed mutagenesis to prepare variants in which Val75 was replaced by Ala, Phe, Leu, Ile, Lys, Gln, and Asp. As a result, the variants in which valine is replaced by hydrophobic residues such as Ala, Phe, Leu, and Ile (V75A, F, L, and I) show almost the same level of enzyme activity and thermostability as the wild type enzyme, whereas variants with hydrophilic residue replacements such as Lys, Gln, and Asp (V75K, Q, and D) showed gross reductions in enzyme activity and thermostability. The dissociation of V75K and V75D from trimer to monomers occurred rapidly as the temperature rose, while V75F, V75L, and V75I dissociated more slowly than the wild type. There was no particular effect of heat treatment on the dissociation of V75A or V75Q, but these variants were slightly dissociated even in the native state. Thus, we conclude that Val75 may locate at the interface between the monomers and its hydrophobic interactions with its surroundings may play a key role in the thermostability and oligomeric subunit interactions of the enzyme.

Enzyme Stability↗
PubMed1999

Deletion of Ala144-Lys145 in Thermus thermophilus inorganic pyrophosphatase suppresses thermal aggregation.

The regions contributing to the thermostability of inorganic pyrophosphatase (PPase, EC 3.6.1.1) from Thermus thermophilus (Tth) were deduced in our previous study by random chimeragenesis, one of them being estimated to be Ala144-Lys145 [Satoh, T., Takahashi, Y., Oshida, N., Shimizu, A., Shinoda, H., Watanabe, M., and Samejima, T. (1999) Biochemistry 38, 1531-1536]. Therefore, we investigated the contributions of these two residues in Tth by preparing a deletion mutant (del.144-145 mutant) of Tth PPase. We examined its thermostability in terms of the CD and fluorescence spectra, and the thermal change in the enzymatic activity. The thermostability of the enzymatic activity of the del.144-145 mutant was similar to that of the wild type Tth PPase, whereas this mutant was more stable against heating. Furthermore, we compared the thermal aggregation of the wild type with that of the del.144-145 mutant. We found that the thermal aggregation of the mutant was reduced relative to that of the wild type. Moreover, the molecular weight of the mutant after heating at 90 degrees C was higher than that of the unheated one, whereas the wild type aggregated under the same conditions. Therefore, we can conclude that although the Ala144-Lys145 residues in Tth PPase may partly cause thermal aggregation, the deletion of these residues may stabilize the Tth PPase molecule structurally against heating and suppress thermal aggregation.

Alanine↗
PubMed1988

Chemical modifications of histidyl and tyrosyl residues of inorganic pyrophosphatase from Escherichia coli.

Chemical modifications by photooxidation in the presence of rose bengal (RB) and with tetranitromethane (TNM) were carried out to elucidate the amino acid residues involved in the active site of inorganic pyrophosphatase (pyrophosphate phosphohydrolase) [EC 3.6.1.1] from Escherichia coli Q13. The photooxidation caused almost complete inactivation, which followed pseudo-first-order kinetics depending on pH and concentration of RB. The presence of Mg2+ or complex between Mg2+ and substrate or substrate analogues, imidodiphosphate and sodium methylenediphosphate, gave partial protection against the photoinactivation, whereas the substrate alone showed no protective effect. The enzyme was almost completely inactivated by chemical modification with TNM, depending upon the concentration of TNM. The amino acid analyses and enzyme activity measurements revealed that 2 histidyl residues among 5 photooxidized residues and 2 tyrosyl residues per subunit were essential for the enzyme activity. The circular dichroism (CD) spectra in the far ultraviolet region showed no significant alteration during these two modifications, indicating that the polypeptide chain backbone of the enzyme remained unaltered. However, the modifications altered considerably the CD bands in the near ultraviolet region and the fluorescence spectra, indicating that subtle change in conformation had occurred in the vicinity of the active site in the enzyme molecule. These results strongly suggest that histidyl and tyrosyl residues may be involved in the active site or be located in the vicinity of the active site and seem to participate in the mechanism of stability against heat inactivation.

Binding Sites↗
PubMed1983

Purification and properties of inorganic pyrophosphatase from porcine brain.

Inorganic pyrophosphatase [EC 3.6.1.1] was purified from porcine brain to an electrophoretically homogeneous state. The molecular weight of the enzyme was estimated to be 62,000 by gel filtration and that of the subunit to be 33,000 by gel electrophoresis in the presence of sodium dodecyl sulfate, suggesting that the enzyme consists of two identical subunits. The stability of the purified enzyme was dependent on its protein concentration. The enzyme was stable above 50 micrograms/ml at 20 degrees C, but it was gradually inactivated below this concentration, even at 0 degree C unless other proteins such as bovine serum albumin, calmodulin, etc. were present. Those added proteins not only protected the enzyme from inactivation, but also completely reactivated the enzyme after it had been once inactivated. The enzyme catalyzed the hydrolysis of inorganic pyrophosphate but not that of other phosphate esters. Only Mg2+ was required as an activating cation, and other divalent cations inhibited the activity to some degree. The addition of sulfhydryl reagents prevented the inhibition of activity by divalent cations.

Animals↗
PubMed1997

Rapid reconstitution of tonoplast H(+)-translocating pyrophosphatase from cultured rice cells into liposomes.

We report the rapid and functional reconstitution of H(+)-pyrophosphatase (H(+)-PPase) from the tonoplast of cultured rice (Oryza sativa L.) cells to proteoliposomes. The CHAPS-solubilized H(+)-PPase was incorporated into liposomes by gel-filtration. Both the activities of PPi-hydrolysis and H(+)-pumping were influenced by the lipid-protein ratio and cholesterol.

Blotting, Western↗
PubMed1998

Structural studies of the vacuolar H(+)-pyrophosphatase: sequence analysis and identification of the residues modified by fluorescent cyclohexylcarbodiimide and maleimide.

We determined the amino acid residues of the H(+)-translocating inorganic pyrophosphatase (H(+)-PPase) of pumpkin which are covalently labeled by two fluorescent labeling reagents; N-cyclohexyl-N'-[4-(dimethyl amino)-alpha-naphthyl] carbodiimide (NCD) and N-pyrenylmaleimide (NPM). NCD and NPM are fluorescent analogues of N,N-dicycrohexylcarbodiimide and N-ethylmaleimide, respectively, and inactivate H(+)-PPase activity. Excess Mg2+ protected the H(+)-PPase from the inactivation by these reagents. Furthermore, we identified the cDNA clone encoding the pumpkin H(+)-PPase in order to determine the position of labeled residues. The nucleotide sequence of the cDNA clone contains a 2,304 bp open reading frame encoding a polypeptide with 768 amino acids. Chemical sequence analysis of fluorescent peptide fragments revealed that Glu749 located in the C-terminal putative transmembrane alpha-helix was a NCD-labeled residue, and Cys632 was a NPM-labeled residue located in a putative cytosolic domain. The amino acid sequence of the region that includes Glu749 is highly conserved in H(+)-PPases from other plants and it also shows some sequence similarity with the region of the carbodiimide-reactive Glu (or Asp) of F0F1-ATPase c-subunit. The reactive glutamic acids in these proteins are located at the last C-terminal transmembrane alpha-helix. We also found that the H(+)-PPase shows significant amino acid sequence similarity to Kdp-ATPase A chain of E. coli. This similarity between the two different proteins suggest that they have evolved from a common ancestor and may utilize a common basic mechanism for ion transport.

Amino Acid Sequence↗
PubMed1991

Characterization of the 5' flanking region of the Escherichia coli ppa gene encoding inorganic pyrophosphatase: mutations in the ribosome-binding site decrease the level of ppa mRNA.

We have previously cloned and sequenced the ppa gene, encoding inorganic pyrophosphatase (PPase), of Escherichia coli K12 [Lahti, R., Pitkäranta, T., Valve, E., Ilta, I., Kukko-Kalske, E. & Heinonen, J. (1988) Journal of Bacteriology 170, 5901-5907]. In this work mutations were constructed in the 5' flanking region of E. coli ppa and the effect on expression was determined. The minimum length of the fully active ppa5' flanking region was shown to be 117 bp. Further deletion decreased the activity, and upon deletion to nucleotide -37 the promoter activity was totally lost. A clear point of inflection was observed in the inactivation upon deletion over the nucleotide -50. This is consistent with the fact that by binding to promoters RNA polymerase holoenzyme generally covers the -50 to +20 region in E. coli genes. When the -35 sequence of ppa, AAGACA, was mutated to AAAACA, ppa expression, as measured by PPase production, decreased to 20% of the wild-type, whereas by the change of the -10 sequence, TATAAT, to TTTAAT or TATAAA, the ppa gene was totally inactivated. Furthermore, when the ribosome-binding site (RBS) sequence, AGGAAA, was altered to AAGAAA, PPase production decreased to 19% of the wild-type. Surprisingly, when the RBS sequence was mutated to the consensus RBS sequence, AGGAGG, the intracellular levels of both ppa mRNA and PPase decreased drastically. The implications of these results are discussed.

Base Sequence↗
PubMed1994

Isolation and characterization of cDNAs encoding the vacuolar H(+)-pyrophosphatase of Beta vulgaris.

The H(+)-pyrophosphatase (V-PPase) of plant vacuolar membranes catalyzes the electrogenic translocation of H+ from the cytosol to vacuole lumen and, in parallel with the vacuolar H(+)-ATPase located in the same membrane, establishes the inside-acid, inside-positive H(+)-electrochemical potential difference responsible for energizing the H(+)-coupled transport of solutes into the vacuole. The results of previous investigations suggest that the gene encoding the substrate-binding subunit of the V-PPase is present in a single copy in the genome of Arabidopsis thaliana (V. Sarafian, Y. Kim, R.J. Poole, P.A. Rea [1992] Proc Natl Acad Sci USA 89: 1775-1779), but it is not known whether the situation in Arabidopsis is typical of most vascular plants. With the objective of assessing the general applicability of this finding and acquiring sequence data for structure-function analyses of the enzyme from Beta vulgaris, we have sought to isolate cDNAs encoding the V-PPase from this organism by screening a Beta cDNA library constructed in lambda ZAP with the Arabidopsis cDNA insert (AVP) encoding the V-PPase. The results of these investigations demonstrate that at least two genes encode the V-PPase in Beta. Restriction and sequence analyses of the cDNAs from Beta reveal two classes, designated BVP1 and BVP2. BVP1 and BVP2 encode closely related but distinct polypeptides with computed masses of 80,550 and 80,000 D, respectively, exhibiting 88% identity with each other and 89% identity with the corresponding polypeptide from Arabidopsis. The nucleotide sequences of BVP1 and BVP2, on the other hand, are 70% identical within their coding regions but less than 28 and 53% identical within their respective 5' and 3' noncoding regions. Southern analyses of Beta genomic DNA confirm that two genes encode the V-PPase, and northern analyses of polyadenylated RNA isolated from a range of tissue types and probed with RNAs transcribed from the 3' noncoding sequences of BVP1 or BVP2 indicate that both genes are expressed in the intact plant. On the basis of these findings and the recent demonstration of then sufficiency of the substrate-binding polypeptide, alone, for all of the known catalytic functions of the V-PPase (E.J. Kim, R.-G. Zhen, P.A. Rea [1994] Proc Natl Acad Sci USA [91:6128-6132]), the two cDNA species isolated from Beta are concluded to encode variant, possibly isoforms, of the enzyme.

Amino Acid Sequence↗
PubMed1995

Vacuolar H(+)-translocating pyrophosphatase is induced by anoxia or chilling in seedlings of rice.

The present study was undertaken to determine whether vacuolar H(+)-pyrophosphatase (V-PPase) might replace vacuolar H(+)-ATPase under energy stress due to anoxia or chilling in anoxia-tolerant species such as rice (Oryza sativa L.) and corn (Zea mays L.). The relative transcript level of V-PPase in rice seedlings, like that of alcohol dehydrogenase 1, increased greatly under anoxia and declined again when the seedlings were returned to air. However, the distribution of transcripts in root, shoot, and seed differed somewhat from that of alcohol dehydrogenase 1. Immunoreactive V-PPase protein and V-PPase enzyme specific activity in a tonoplast fraction from rice seedlings increased progressively with time of anoxia or chilling at 10 degrees C, showing a 75-fold increase after 6 d of anoxia, compared with a 2-fold increase of vacuolar H(+)-ATPase activity. When the seedlings were returned to air, the specific activity returned to its initial level within 2 d. After 6 d of chilling at 10 degrees C, V-PPase specific activity reached a level 20-fold of that at 25 degrees C. In microsomes of corn roots, V-PPase specific activity did not respond to anoxia but was constitutively high. It is proposed that V-PPase can be an important element in the survival strategies of plants under hypoxic or chilling stress.

Anaerobiosis↗
PubMed1991

Genetic engineering of Escherichia coli inorganic pyrophosphatase. Tyr55 and Tyr141 are important for the structural integrity.

Two tyrosines are supposed to be essential for the activity and to participate in the stabilization of Escherichia coli inorganic pyrophosphatase (PPiase) against heat denaturation [Samejima, T., Tamagawa, Y., Kondo, Y., Hachimori, A., Kaji, H., Takeda, A. and Shiroya, Y. (1988) J. Biochem. (Tokyo) 103, 766-772]. To locate these two tyrosines in the amino acid sequence, we substituted all the eight tyrosines of E. coli PPiase with phenylalanine and studied the properties of these YF mutant PPiases. Interestingly, substitution of the tyrosines (Tyr51, Tyr55 and Tyr141) conserved with the amino acid sequence of yeast PPiase [Lahti, R., Kolakowski, L. F., Heinonen, J., Vihinen, M., Pohjanoksa, K. and Cooperman, B. (1990) Biochim. Biophys. Acta 1038, 338-345] exerted the most drastic effects on the structure and activity of E. coli PPiase. PPiase variants YF51, YF55 and YF141 had 64%, 7% and 22% of the wild-type PPiase activity, respectively. Furthermore, PPiase variant YF141 had an increased sensitivity to heat denaturation, whereas mutant PPiase YF55 displayed a profound conformational change, as demonstrated by the binding of the fluorescent dye 9-(diethylamino)-5H-benzo(alpha) phenoxazine-5-one (Nile red) that monitors the hydrophobicity of protein surfaces. None of the tyrosines of E. coli PPiase seem to be essential for catalysis, but Tyr55 and Tyr141 are important for the structural integrity of E. coli PPiase.

Amino Acid Sequence↗
PubMed1993

Steady-state kinetics of substrate hydrolysis by vacuolar H(+)-pyrophosphatase. A simple three-state model.

The results of analyses of the steady-state kinetics of the vacuolar H(+)-translocating pyrophosphatase (V-PPase) of native tonoplast vesicles isolated from etiolated hypocotyls of Vigna radiata (mung bean) and purified enzyme from the same source under a wide range of Mg2+, pyrophosphate (PPi) and K+ concentrations are consistent with a minimal reaction scheme in which dimagnesium pyrophosphate is the active substrate species and catalysis is mediated by preformed enzyme-Mg2+ complex. When account is taken of the sensitivity of the V-PPase to ionic strength, additional kinetic interactions are not required to describe the behavior of the enzyme. N-Ethylmaleimide-protection assays show that the dissociation constant for Mg2+ binding in the absence of PPi is an order of magnitude smaller than that estimated from the steady-state kinetics of PPi hydrolysis. Two distinct Mg(2+)-binding sites are therefore invoked. Since the protective action of Mg2+ is independent of the nature of the monovalent cations and Mg2+ and K+ do not compete during substrate hydrolysis, divalent and monovalent cations are concluded to bind at separate sites. The pH dependencies of the kinetic parameters are consistent with the participation of groups of pKa 5.7 and 8.6 in substrate binding and groups of pKa 6.1 and 9.0 in the substrate-conversion step, indicating that at least four ionizable groups are essential for catalysis. These findings are discussed with respect to the reaction mechanism of the V-PPase and the potential regulatory significance of cytosolic free Mg2+ and K+ in vivo.

Binding Sites↗
PubMed1996

Kinetic characterization of the hydrolytic activity of the H+-pyrophosphatase of Rhodospirillum rubrum in membrane-bound and isolated states.

Substrate hydrolysis by the H+-pyrophosphatase (pyrophosphate phosphohydrolase, H+-PPase) of the photosynthetic bacterium Rhodospirillum rubrum follows a two-pathway reaction scheme in which preformed 1:1 and 1:2 . enzyme . Mg2+ complexes (EMg and EMg2) convert dimagnesium pyrophosphate (the substrate). This scheme is applicable to isolated enzyme, uncoupled chromatophores and chromatophores energized by a K+/valinomycin diffusion potential. Tris and other amine buffers exert a specific effect on the bacterial H+-PPase by increasing the Michaelis constant for substrate binding to EMg by a factor of 26-32, while having only small effect on substrate binding to EMg2. Formation of EMg requires a basic group with pKa of 7.2-7.7 and confers resistance against inactivation by mersalyl and N-ethylmaleimide to H+-PPase. The dissociation constants governing EMg and EMg2 formation, as estimated from the mersalyl-protection assays and steady-state kinetics of PPi hydrolysis, respectively, differ by an order of magnitude. Comparison with the data on soluble PPases suggests that, in spite of gross structural differences between H+-PPase and soluble PPases and the added ability of H+-PPase to act as a proton pump, the two classes of enzyme utilize the same reaction mechanism in PPi hydrolysis.

Bacterial Proteins↗
PubMed1996

X-ray structure of yeast inorganic pyrophosphatase complexed with manganese and phosphate.

The three-dimensional structure of the manganese-phosphate complex of inorganic pyrophosphatase from Saccharomyces cerevisiae has been refined to an R factor of 19.0% at 2.4-A resolution. X-ray data were collected from a single crystal using an imaging plate scanner and synchrotron radiation. There is one dimeric molecule in the asymmetric unit. The upper estimate of the root-mean-square coordinate error is 0.4 A using either the delta A plot or the superposition of the two crystallographically independent subunits. The good agreement between the coordinates of the two subunits, which were not subjected to non-crystallographic symmetry restraints, provides independent validation of the structure analysis. The active site in each subunit contains four manganese ions and two phosphates. The manganese ions are coordinated by the side chains of aspartate and glutamate residues. The phosphate groups, which were identified on the basis of their local stereochemistry, interact either directly or via water molecules with manganese ions and lysine, arginine, and tyrosine side chains. The phosphates are bridged by two of the manganese ions. The outer phosphate is exposed to solvent. The inner phosphate is surrounded by all four manganese ions. The ion-binding sites are related to the order of binding previously established from kinetic studies. A hypothesis for the transition state of the catalytic reaction is put forward.

Crystallography, X-Ray↗
PubMed1987

Cytochemical localization of thiamine pyrophosphatase and nicotinamide adenine dinucleotide phosphatase activities in rat epiphyseal chondrocytes.

Two phosphatase activities, which have been reported to be associated with the Golgi apparatus in several cellular types, have been cytochemically demonstrated in rat epiphyseal cartilage. This was the case for thiamine pyrophosphatase (TPPase) which was detected in Golgi trans face cisternae and also in nascent or immature secretory granules of chondrocytes. beta-Nicotinamide adenine dinucleotide phosphatase (beta-NADPase), on the other hand, was localized mainly in the endoplasmic reticulum region of both proliferative and hypertrophic chondrocytes. Most of the beta-NADPase reaction was shown to be associated with the cytoplasmic side of the rough endoplasmic reticulum membranes and also partially dispersed throughout the cytosol background. We suggest that beta NADPase in chondrocytes could be an enzyme with different properties from that described in other secretory cells.

Animals↗