Cloning, molecular characterization and chromosome localization of the inorganic pyropbosphatase (PPA) gene from S.cerevisiae

Kolakowski, Lee F.; Schloesser, Manfred; Cooperman, Barry S.

doi:10.1093/nar/16.22.10441

Cited by 62 publications

(44 citation statements)

References 42 publications

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“…Tyr 139, which forms a hydrogen bond to the anion in the present structure, can serve as a proton donor for this Pi. It is difficult to be certain Amino acid sequences have been determined for soluble PPases from Saccharomyces cerevisiae (cytoplasmic, Kolakowski et al, 1988; mitochondrial, Lundin et al, IWI), Schizosaccharomyces pombe (Kawasaki et al, 1990), Kluyveromyces lactis (Stark & Milner, 1989), bovine retina (Yang & Wensel, 1992), Arabidopsk thaliana (Kieber & Signer, 1991), E. coli (Lahti et al, 1988), Thermoplasma acidophilum (Richter & Schafer, 1992), thermophilic bacterium PS-3 (Ichiba et al, 1990), Bacillusstearothermophilus and 7: thermophilus (Ishii K, Shibuya K, Kaji H, Satoh T, Teplyakov A, Obmolova G , Kuranova I, Samejima T, manuscript in prep.). Their alignment clearly shows 2 distinct groups with much higher similarity inside the groups than between them.…”

Section: Active Center and Catalytic Mechanismmentioning

confidence: 99%

“…Extensive chemical modification studies indicated residues that might be essential for catalytic activity and substrate binding (Cooperman, 1982). The genes encoding these PPases have been cloned (Kolakowski et al, 1988;Lahti et al, 1988) and site-directed mutagenesis studies of the catalytic mechanism are now under way (Lahti et al, 1990b(Lahti et al, , 1991. Thus, detailed 3-dimensional information on PPases is urgently required.…”

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confidence: 99%

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Crystal structure of inorganic pyrophosphatase from Thermus thermophilus

et al. 1994

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The 3-dimensional structure of inorganic pyrophosphatase from Therrnus thermophilus (T-PPase) has been determined by X-ray diffraction at 2.0 A resolution and refined to R = 15.3%. The structure consists of an antiparallel closed @sheet and 2 a-helices and resembles that of the yeast enzyme in spite of the large difference in size (174 and 286 residues, respectively), little sequence similarity beyond the active center (about 20%), and different oligomeric organization (hexameric and dimeric, respectively). The similarity of the polypeptide folding in the 2 PPases provides a very strong argument in favor of an evolutionary relationship between the yeast and bacterial enzymes. The same Greek-key topology of the 5-stranded 0-barrel was found in the OB-fold proteins, the bacteriophage gene-5 DNA-binding protein, toxic-shock syndrome toxin-1, and the major cold-shock protein of Bacillus subtilis. Moreover, all known nucleotide-binding sites in these proteins are located on the same side of the 0-barrel as the active center in T-PPase. Analysis of the active center of T-PPase revealed 17 residues of potential functional importance, 16 of which are strictly conserved in all sequences of soluble PPases. Their possible role in the catalytic mechanism is discussed on the basis of the present crystal structure and with respect to site-directed mutagenesis studies on the Escherichia coli enzyme. The observed oligomeric organization of T-PPase allows us to suggest a possible mechanism for the allosteric regulation of hexameric PPases.

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Section: Active Center and Catalytic Mechanismmentioning

confidence: 99%

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confidence: 99%

Crystal structure of inorganic pyrophosphatase from Thermus thermophilus

et al. 1994

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“…Their genes have been recently cloned, and experiments involving site-directed mutagenesis are now under way [3,4].…”

Section: Introductionmentioning

confidence: 99%

Tightly bound pyrophosphate inEscherichia coliinorganic pyrophosphatase

1990

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Hexameric inorganic pyrophosphatase of Escherichiu coil contains about I mol/mol of 'structural' pyrophosphate, which survives gel filtration and prolonged incubation with Me;"', does not exchange with medium phosphate and pyrophosphate but is removed with 0.8 M perchloric acid. The site of pyrophosphate binding seems to be another than the active site. An additional 0.9 mol of enzyme-bound pyrophosphate is formed in the presence of phosphate and M$' but this pyrophosphate is in fast equilibrium with medium phosphate and appears to be bound to the active site.

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“…Inorganic pyrophosphatase (EC 3.6.1.1; PPase) 1 catalyzes reversible phosphoryl transfer from pyrophosphate (PP i ) to water, a metabolically important reaction chemically similar to that catalyzed by numerous ATPases and GTPases. Yeast PPase is a homodimer containing 286 amino acid residues/ monomer (1) and requiring three or four divalent metal ions for catalysis, with Mg 2ϩ conferring the highest activity (2)(3)(4)(5).…”

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confidence: 99%

Probing Essential Water in Yeast Pyrophosphatase by Directed Mutagenesis and Fluoride Inhibition Measurements

Pohjanjoki¹,

Fabrichniy²,

Kasho³

et al. 2001

Journal of Biological Chemistry

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Inorganic pyrophosphatase (EC 3.6.1.1; PPase) 1 catalyzes reversible phosphoryl transfer from pyrophosphate (PP i ) to water, a metabolically important reaction chemically similar to that catalyzed by numerous ATPases and GTPases. Yeast PPase is a homodimer containing 286 amino acid residues/ monomer (1) and requiring three or four divalent metal ions for catalysis, with Mg 2ϩ conferring the highest activity (2-5). Two divalent metal ions (M1 and M2) per active site have been identified in the "resting" enzyme by x-ray crystallography and four metal ions (M1-M4) and two phosphates (P1 and P2) in the product complex of Y-PPase (6, 7).PP i hydrolysis by PPase occurs via direct attack of water without formation of a phosphorylated enzyme intermediate (8). Modeling the transition state of the chemical step from the structure of the enzyme-product complex Y-PPase⅐Mn 2 (MnP i ) 2 has led to two models that differ in the identity of the water nucleophile placed between metal ions M1 and M2 in the model of Heikinheimo et al. (6) or in the vicinity of Tyr 93 in the model of Harutyunyan et al. (7,9). Although the former model requires an additional "relaxation" step, in which a new water molecule displaces P i oxygen from the position between M1 and M2, it has an advantage of providing an efficient mechanism for nucleophile activation through combined action of the two metal ions and an adjacent Asp 117 residue (see Fig. 1). In aqueous solution and even in crystalline state, proteins are surrounded with water shells, making identification of function-related water molecules a difficult task. Use of fluoride, a potent and most specific inhibitor of cytoplasmic pyrophosphatase, provides a convenient approach to detect such water molecules because molecules of HF and H 2 O are isoelectronic and of similar size, as are the anions derived therefrom.

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Cloning, molecular characterization and chromosome localization of the inorganic pyropbosphatase (PPA) gene from S.cerevisiae

Cited by 62 publications

References 42 publications

Crystal structure of inorganic pyrophosphatase from Thermus thermophilus

Crystal structure of inorganic pyrophosphatase from Thermus thermophilus

Tightly bound pyrophosphate inEscherichia coliinorganic pyrophosphatase

Probing Essential Water in Yeast Pyrophosphatase by Directed Mutagenesis and Fluoride Inhibition Measurements

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