Biomedical subjects

R G Kemp

Publications and source records attributed to R G Kemp.

At least 37 records · Page 2Linked to original sources

PubMed1995

Cloning and sequencing a putative pyrophosphate-dependent phosphofructokinase gene from Entamoeba histolytica.

Pyrophosphate-dependent phosphofructokinase (PPi-PFK) gene from Entamoeba histolytica was cloned from its genomic library and sequenced. The open reading frame has 1149 bp and codes for a protein of 41.5 kDa. The deduced amino acid sequence of E. histolytica PPi-PFK has 25 to 28% identity to the PPi-PFKs from Propionibacterium freudenreichii, Naegleria fowleri and potato. The amino acid residues known to contribute to the active site of PPi-PFK from P. freudenreichii are conserved.

Amino Acid Sequence↗

PubMed1994

Identification of interactions that stabilize the transition state in Escherichia coli phosphofructo-1-kinase.

The activity of Escherichia coli phosphofructo-1-kinase depends upon the dissociation of a group with a pK of approximately 6.6. Mutation of the 2 active site residues most likely to be titrated in this range, Asp-127 and Asp-129, lowered activity but produced little change in the pH dependence, suggesting that these residues while important to activity were not responsible for the pH dependence of the enzyme. Alternatively, the pH dependence was thought to correspond to the negative charge on the phosphoryl group being transferred in the reaction. Mutation of Arg-72 to histidine, while lowering the activity substantially, shifted the pH optimum to approximately 6.2 with a secondary plateau on the alkaline limb that was eliminated in the double mutant R72H/R171H. Mutation of Arg-171 alone produced only a small decrease in maximal activity and little change in pH dependence from the wild type enzyme. The data support an associative mechanism with a transition state stabilized by the interaction between the negative charge on the phosphoryl group being transferred and the arginyl residue at position 72 on the enzyme.

Amino Acid Sequence↗

PubMed1994

Identification of basic residues involved in substrate binding and catalysis by pyrophosphate-dependent phosphofructokinase from Propionibacterium freudenreichii.

Despite overall low identity of sequence between ATP- and PPi-dependent phosphofructo-1-kinases (PFK), an alignment permits the tentative identification of catalytically important residues in PPi-dependent PFK. Seven basic residues of the PPi-dependent PFK of Propionibacterium freudenreichii, Arg-310, Lys-315, Arg-326, Arg-186, Arg-78, Arg-90, and Lys-148 were chosen on the basis of this alignment for site-directed mutagenesis to neutral residues. Mutants R186A, K315A, and R326A had substantial increases of 43-, 389- and 678-fold, respectively, in Km for fructose 6-phosphate relative to wild-type enzyme and relatively small effects on kcat. The modest kinetic effects of mutations at Arg-78, Arg-90, and Arg-310 were not considered to indicate important roles for these residues. On the other hand, mutant K148M had a Km for PPi that was increased by 132-fold and kcat lowered by a factor of 490. Cho and Cook (Cho, Y.-K., and Cook, P.F. (1988) Biochemistry 28, 4155-4160) concluded on the basis of kinetic and chemical modification data that the enzyme utilizes a proton shuttle mechanism and that two lysines are involved in substrate binding. The present data along with our previous data on mutant D151A support a double proton shuttle mechanism involving Asp-151 and Lys-148 with Lys-148, Arg-326, Lys-315, and perhaps Arg-186 being important for substrate binding.

Amino Acid Sequence↗

PubMed1994

Site-directed mutagenesis of two highly conserved residues near the active site of phosphofructo-1-kinase.

Mutations of either of two highly conserved residues near the active site of Escherichia coli phosphofructokinase, Ile-126 or Asn-128, produce no changes in the Km for ATP, relatively small changes in kcat, and a large increase in the Km for fructose 6-P, despite the fact that these residues are not directly involved in substrate binding. A computer graphics analysis of the three-dimensional structure suggests that the mutations effect the orientation of Arg-252, a residue important both for fructose 6-P binding and for catalysis.

Amino Acid Sequence↗

PubMed1994

Structure and expression of the cDNA for the C isozyme of phosphofructo-1-kinase from rabbit brain.

Rabbit brain contains three phosphofructo-1-kinase (PFK) isozymic subunits designated A, B, and C. The primary structures of the first of these two isozyme types have been determined previously. The isozyme C of rabbit brain was isolated by immunoaffinity chromatography and subjected to proteolytic and chemical digestion. A large number of peptides were sequenced, the total number of amino acids identified being equal to about 80% of the total structure. The sequence of the cDNA derived from brain mRNA for C isozyme was determined from polymerase chain reaction fragments synthesized using oligonucleotides designed on the basis of the peptide sequences. The deduced size of the C isozyme was 86,371 Da, slightly larger than PFKs described previously. The amino acid sequence identity with the rabbit A isozyme was 68.9% and a range of identity to other sequenced mammalian PFKs was 67-69%. Using these data plus previously published data on chemical modification, assignments of the 6 organic ligand binding sites of PFK were inferred. The full-length cDNA was cloned into and expressed in Escherichia coli. Phosphofructokinase C was purified to homogeneity from the bacterial extracts.

Amino Acid Sequence↗

PubMed1993

Identification of reactive vicinal cysteines in Saccharomyces cerevisiae (ATP) and cytosolic rat liver (GTP) phospho enol pyruvate carboxykinases.

Saccharomyces cerevisiae (ATP) and cytosolic rat liver (GTP) phospho enol pyruvate carboxykinases (EC 4.1.1.49/32) have been labeled with N-(1-pyrenyl)-iodoacetamide. Reagent incorporation was completely prevented by the presence of the respective nucleoside diphosphate plus MnCl2. Under appropriate conditions, 2 mol of reagent per mol of enzyme subunit were incorporated. The fluorescence spectra of the labeled proteins showed the pyrene excimer emission band. The pyrenyl-derivatized enzymes were digested with trypsin after carboxymethylation, and two labeled peptides were isolated for each carboxykinase upon reverse-phase high-performance liquid chromatography. Automated Edman degradation of the labeled peptides indicated that cysteines 364 and 457 (yeast enzyme), and cysteines 288 and 413 (rat enzyme) were labeled with the fluorescence SH-specific reagent. The relative reactivity of these residues was characterized. Labeling experiments utilizing the 5,5'-dithiobis(2-nitrobenzoate)-oxidized enzymes suggested that the reactive SH-groups occupy a vicinal position in the tertiary structure of the proteins, probably in the nucleotide-binding region.

Adenosine Triphosphate↗

PubMed1993

Identification of active site residues in pyrophosphate-dependent phosphofructo-1-kinase by site-directed mutagenesis.

The primary structure of pyrophosphate-dependent phosphofructokinase (PFK) from Propionibacterium freudenreichii exhibits a low but significant level of sequence identity with Escherichia coli ATP-dependent PFK, permitting the tentative assignment of residues that may be involved in catalysis. Based on these assignments, the roles in catalysis of 2 aspartyl residues (Asp151 and Asp153) and 2 lysyl residues (Lys80 and Lys85) were examined. Mutagenesis of the Asp151 to alanine and serine reduced kcat by a factors of 2 x 10(4) and 4 x 10(5), respectively, while showing no change in Km for either substrate in the forward reaction or for metal ion in the back reaction. The kcat for Asp153 was decreased by a factor of 700 with no change in Km for pyrophosphate and an increase of about 20-fold in Km for fructose 6-P and close to 4-fold for magnesium ion. That these changes in the mutants were not the result of global conformational changes was indicated by their identical behavior during substrate-specific elution chromatography, ion-exchange chromatography, and limited proteolysis by trypsin and subtilisin. Mutations of Lys80 and Lys85 showed no significant changes in kinetic parameters, suggesting no involvement in mechanism or substrate binding. These and other results permit preliminary modeling of the active site of pyrophosphate-dependent PFK.

Aspartic Acid↗

PubMed1993

Pyrophosphate-dependent phosphofructo-1-kinase complements fructose 1,6-bisphosphatase but not phosphofructokinase deficiency in Escherichia coli.

The gene from Propionibacterium freudenreichii for PPi-dependent phosphofructo-1-kinase, an enzyme that is found in some bacteria, in a number of anaerobic protists, and in plants, complements the absence of fructose 1,6-bisphosphatase in Escherichia coli but does not complement the deficiency of the ATP-dependent phosphofructokinase.

Adenosine Triphosphate↗

PubMed1992

The mechanism of ATP inhibition of wild type and mutant phosphofructo-1-kinase from Escherichia coli.

Escherichia coli 6-phosphofructo-1-kinase was inhibited by high concentrations of ATP at alkaline pH. The mechanism of the inhibition was studied with two mutants generated by site-directed mutagenesis; I126A, with a Km for fructose-6-P that was more than two orders of magnitude higher than that of wild type but with minimal changes in kcat and Km for ATP, and R72H, with little change in substrate half-saturation concentrations but with a kcat that was 300-fold lower that of wild type enzyme. ATP and fructose-6-P interacted in a mutually antagonistic manner; that is ATP decreased the apparent affinity for fructose-6-P and vice versa. The half-saturation concentrations for both substrates, most strikingly fructose-6-P, increased with increasing pH while the kcat increased. Studies with I126A suggested that ATP inhibition was not dependent on a dissociable group with a pK in the alkaline range and that the inhibition was not caused by abortive binding of substrate to the wrong substrate site. Inhibition was not the result of differential affinity of ATP for the R and T states of the enzyme. The low kcat mutant, R72H, did not display ATP inhibition. These data indicate that ATP inhibition results from substrate antagonism coupled with a steady state random mechanism wherein the high rate of catalysis does not permit equilibration of substrates.

Adenosine Triphosphate↗

PubMed1992

Identification of critical lysyl residues in the pyrophosphate-dependent phosphofructo-1-kinase of Propionibacterium freudenreichii.

Pyrophosphate-dependent 6-phosphofructo-1-kinase (PPi-PFK) from Propionibacterium freudenreichii was inactivated by low concentrations of the lysine-specific reagent pyridoxal phosphate (PLP) after sodium borohydride reduction. The substrates fructose 6-phosphate and fructose 1,6-bisphosphate protected against inactivation whereas inorganic pyrophosphate had little effect. An HPLC profile of a tryptic digest of PPi-PFK modified at low concentrations of PLP showed a single major peak with only a small number of minor peaks. The major peak peptide was isolated and sequenced to obtain IGAGXTMVQK, where X represents a modified lysine residue, corresponding to Lys-315. Lys-315 was protected from reaction with PLP by fructose 1,6-bisphosphate. As indicated by HPLC maps of PPi-PFK modified with varying concentrations of PLP, a direct correlation was observed between activity loss and the modification of Lys-315. Two of the minor peptide peaks were shown to contain Lys-80 and Lys-85, which were modified in a mutually exclusive manner. Partial protection against modification of these two residues was provided by MgPPi. The data were used to adjust the sequence alignment of the Propionibacterium enzyme with that of ATP-dependent PFK of Escherichia coli to identify homologous residues in the substrate binding site. It is suggested that Lys-315 interacts with the 6-phosphate of fructose 6-phosphate and that Lys-80 and -85 may be located near the pyrophosphate binding site.

Amino Acid Sequence↗

PubMed1992

ATP-dependent Saccharomyces cerevisiae phospho enol pyruvate carboxykinase: isolation and sequence of a peptide containing a highly reactive cysteine.

Saccharomyces cerevisiae phospho enol pyruvate carboxykinase (EC 4.1.1.49), inactivated by N-(iodoacetyl)-N'-(5-sulfo-1-naphthyl)ethylenediamine, incorporated 0.95 mol of the fluorescent moiety per mol of enzyme subunit. Reagent incorporation was completely protected by the presence of ADP plus MnCl2. The labeled protein was digested with trypsin after carboxymethylation. Two labeled peptides were isolated by reverse-phase high-performance liquid chromatography and were sequenced by gas-phase automatic Edman degradation. Both peptides contained overlapping amino acid sequences from Asn-358 to Lys-375, thus identifying Cys-364 as the reactive amino acid residue. The position of the target amino acid residue is immediately preceding a putative phosphoryl-binding sequence proposed for some nucleotide-binding proteins.

Adenosine Triphosphate↗

PubMed1991

Cloning, sequencing, and expression of pyrophosphate-dependent phosphofructokinase from Propionibacterium freudenreichii.

Pyrophosphate-dependent 6-phosphofructo-1-kinase (PPi-PFK) from Propionibacterium freudenreichii is a non-allosteric enzyme with properties dissimilar to those of other described phosphofructokinases. The enzyme was cloned into pBluescript, sequenced, and expressed in Escherichia coli at levels 15 times higher than those observed in Propionibacterium. The gene consists of 1215 bases which code for a protein of 404 amino acids and a mass of 43,243 daltons. High G + C in the codon usage (66%) of the gene is consistent with the classification of Propionibacterium in the High-G + C subdivision of the Gram-positive bacteria. While showing no sequence identity to the non-allosteric ATP-dependent phosphofructokinase of E. coli, alignments of the amino acid sequence with other PFKs reveal degrees of identities among the amino halves of the proteins, from 26% between the Propionibacterium and potato PPi-PFKs, and 29% between Propionibacterium and E. coli ATP-PFKs. These levels of identities indicate that the amino halves of these proteins are homologous. Identities between the carboxyl half of Propionibacterium PFK and carboxyl halves of other sequences are below 20%, suggesting that the carboxyl half is not homologous. Despite the poor conservation, most of the residues that take part in the binding of fructose-6-P or Mg-PPi could be readily identified by analogy to the structure of the E. coli PFK. Both the fructose-6-P and ATP-binding sites are conserved, indicating that PPi binds to the homologous site of the E. coli ATP-binding site.

Adenosine Triphosphate↗

PubMed1990

Resistance of brain phosphofructo-1-kinase to pH-dependent inhibition.

The kinetic regulatory properties of rabbit brain phosphofructo-1-kinase (PFK), which consists of a mixture of heterotetramers containing A, B, and C isozymic subunits, were found to be much less responsive to pH than the properties of skeletal muscle PFK, the A4 isozyme. The muscle enzyme was strongly inhibited at low pH as a result of a striking increase in the allosteric interaction coefficient or Hill coefficient at pH values below 7.3. This phenomenon was not seen with the brain enzyme. This property of brain PFK may protect this organ, which is exclusively dependent on glucose metabolism, by permitting continued glycolysis despite decreases in intracellular pH.

Allosteric Regulation↗

PubMed1989

Aurintricarboxylic acid is a potent inhibitor of phosphofructokinase.

Aurintricarboxylic acid (ATA) was found to be a very potent inhibitor of purified rabbit liver phosphofructokinase (PFK), giving 50% inhibition at 0.2 microM. The inhibition was in a manner consistent with interaction at the citrate-inhibitory site of the enzyme. The data suggest that inhibition of PFK by ATA was not due to denaturation of the enzyme or the irreversible binding of inhibitor, since the inhibition could be reversed by addition of allosteric activators of PFK, i.e. fructose 2,6-bisphosphate or AMP. Two other tricarboxylic acids, agaric acid and (-)-hydroxycitrate, were found to inhibit PFK. ATA at much higher concentrations (500 microM) was shown to inhibit fatty acid synthesis from endogenous glycogen in rat hepatocytes; however, protein synthesis was not altered.

Animals↗

PubMed1989

The sites of phosphorylation of rabbit brain phosphofructo-1-kinase by cyclic AMP-dependent protein kinase.

The three isozymic subunits of phosphofructo-1-kinase present in rabbit brain and designated A, B and C were phosphorylated in vitro by cyclic AMP-dependent protein kinase with 32P-labeled ATP. Limited digestion of the labeled enzymes with trypsin or with Staphylococcus aureus V8 proteinase led to the solubilization of radiolabeled peptides derived from the three isozymic subunits. Limited digestion by V8 proteinase was accompanied by a slight reduction in the apparent sizes of the subunits, indicating that the phosphorylated sites are located near either the amino or carboxyl termini of the protein. V8 proteinase digestion led to no change in the maximal activity of the enzyme but did abolish sensitivity to ATP inhibition. The phosphopeptides of the tryptic and the V8 digests were purified by chromatography and their amino acid sequences were determined and compared to the previously established sequence from rabbit muscle isozyme A. PFK-A E H I S R K R S G E A T V PFK-B H V T R R S L S M A K G F PFK-C V S A S P R G S Y R K F L In each instance, the phosphorylated serine, underlined in the above sequences, was found to be one or two residues toward the C-terminus of one or more basic residues. No other similarities in structure were noted.

Adenosine Triphosphate↗

PubMed1988

Reactivity of the thiol groups of Escherichia coli phosphofructo-1-kinase.

Modification of Escherichia coli phosphofructo-1-kinase (6-phosphofructokinase; EC 2.7.1.11) with several thiol modifying reagents led to a pseudo-first-order loss of activity that was associated with the modification of a single cysteine residue, identified as the cysteine at position 119 in the protein sequence. This cysteine was protected from reaction with vinyl pyridine, bromopyruvate, and dithionitrobenzoic acid by the substrate, fructose-6-P. In the crystal structure of the highly homologous phosphofructokinase from Bacillus stearothermophilus, cysteine 119 is sufficiently distant from the catalytic site to exclude a direct steric inhibition of the binding of substrate as a mechanism of inactivation for the modification. Thus, the inhibition is unlikely to be a direct one but to be the result of interference with the conformational change that is associated with fructose-6-P binding. A second thiol, position 283, was shown to be protected from reaction when the enzyme was in its native conformation. In contrast to the previously published sequence for the E. coli enzyme six cysteines as opposed to seven have been found both in enzyme from strain LE392 and in enzyme produced by a plasmid that was derived from pLC 16-4. The position in question, 75, was identified as phenylalanine.

Chemical Phenomena↗

PubMed1988

Identification of the AMP binding sites of rabbit phosphofructo-1-kinase isozymes B and C.

Rabbit liver phosphofructo-1-kinase, designated isozyme B, and rabbit brain phosphofructokinase, which contains all three isozymes as heteropolymers, have been modified by [14C]fluorosulfonylbenzoyladenosine (FSBAdo). Several lines of evidence supported modification at the binding site for AMP. The modification proceeded to the extent of 2 to 4 mol of reagent incorporated per mol of tetramer, and AMP protected against the reaction. The kinetic properties of modified isozymes A and B and of modified brain phosphofructokinase were examined and compared to their unmodified forms. It was observed that modification greatly diminished ATP inhibition of all of the isozymes. Furthermore, equilibrium binding studies of modified phosphofructokinase B showed a greatly diminished capacity and affinity for cyclic AMP. Cyclic AMP had little or no influence on the properties of modified A isozyme or brain phosphofructokinase, but was capable of further deinhibiting modified B isozyme, apparently at sites remaining unmodified by FSBAdo. Phosphofructokinase B, modified by radiolabeled FSBAdo, was digested by trypsin, and the digest separated by high-pressure liquid chromatography. The labeled peptide was isolated and sequenced to provide the sequence: Asn-Tyr-Gly-Thr-Lys-Leu-Gly-Val-Lys, with the lysine in the fifth position being the site of modification. To isolate isozyme C, a monoclonal antibody to this isozyme was produced by injecting purified rabbit brain phosphofructokinase into mice, and subsequently selecting for those clones that recognized brain phosphofructokinase but not purified phosphofructokinases A and B. The selected monoclonal was specific for native rabbit isozyme C and would not recognize mouse or rat brain phosphofructokinases. Linking the antibody to an inert phase provided an efficient means of purifying rabbit isozyme C from rabbit brain. The enzyme so recovered retained little of its original activity, but the method provided a simple technique for the preparation of enzyme for protein chemistry studies. The modified C isozyme was isolated on the immuno-affinity column and digested with trypsin. A tryptic peptide bearing the label was isolated and sequenced to provide the structure: Asn-Phe-Gly-Thr-Lys-Ile-Ser-Ala-Arg, with position 5 being the site of modification. The sequences of isozymes B and C are homologous to the site of modification of the A isozyme by FSBAdo.

Adenosine↗

PubMed1988

Inorganic pyrophosphate: fructose-6-phosphate 1-phosphotransferase of the potato tuber is related to the major ATP-dependent phosphofructokinase of E. coli.

A procedure was developed for the purification of inorganic pyrophosphate: fructose-6-phosphate 1-phospho-transferase (PPi-PFK) from potato tubers. The enzyme has the structure alpha 4 beta 4 with a subunit of 68 kDa and a beta subunit of 60 kDa. The structural relationship of this enzyme to other PFKs and to fructose bisphosphatase was examined by immunoprecipitation and immunoblotting. Antibodies to the plant enzyme did not react with E. coli PFK. No cross-reaction was seen among the following enzymes or their antibodies: yeast fructose bisphosphatase; rabbit PFKs A, B, or the enzyme from brain; and the two subunits of the potato PPi-PFK. On the other hand, antibody to E. coli PFK-1 strongly cross-reacts with the 60 kDa polypeptide but not 68 kDa peptide.

Escherichia coli↗