Steady-state kinetic mechanism of the proline:ubiquinone oxidoreductase activity of proline utilization A (PutA) from Escherichia coli

The multifunctional proline utilization A (PutA) flavoenzyme from Escherichia coli performs the oxidation of proline to glutamate in two catalytic steps using separate proline dehydrogenase (PRODH) and Δ¹-pyrroline-5-carboxylate (P5C) dehydrogenase domains. In the first reaction, the oxidation of proline is coupled to the reduction of ubiquinone (CoQ) by the PRODH domain, which has a β₈α₈-barrel structure that is conserved in bacterial and eukaryotic PRODH enzymes. The structural requirements of the benzoquinone moiety were examined by steady-state kinetics using CoQ analogs. PutA displayed activity with all the analogs tested; the highest k_cat/K_m was obtained with CoQ₂. The kinetic mechanism of the PRODH reaction was investigated use a variety of steady-state approaches. Initial velocity patterns measured using proline and CoQ₁, combined with dead-end and product inhibition studies, suggested a two-site ping-pong mechanism for PutA. The kinetic parameters for PutA were not strongly influenced by solvent viscosity suggesting that diffusive steps do not significantly limit the overall reaction rate. In summary, the kinetic data reported here, along with analysis of the crystal structure data for the PRODH domain, suggest that the proline:ubiquinone oxidoreductase reaction of PutA occurs via a rapid equilibrium ping-pong mechanism with proline and ubiquinone binding at two distinct sites.     

The phosphoenolpyruvate: methyl-α-D-glucoside phosphotransferase system in Bacillus subtilis Marburg: kinetic studies of enzyme II and evidence for a phosphoryl enzyme II intermediate

The Enzyme II complex catalyzing the phosphoryl transfer from P-HPr to sugar in the inducible methyl-α-D-glucoside: phosphotransferase system in Bacillus subtilis acts according to a ping-pong mechanism, implying a phosphorylated Enzyme II intermediate. This result is supported by the demonstration of a specific transphosphorylation between [¹⁴C] αMG and glucose-6-phosphate in the presence of an induced Enzyme II preparation.     

Putative ACP phosphodiesterase gene (acpD) encodes an azoreductase

An FMN-dependent NADH-azoreductase of Escherichia coli was purified and analyzed for identification of the gene responsible for azo reduction by microorganisms. The N-terminal sequence of the azoreductase conformed to that of the acpD gene product, acyl carrier protein phosphodiesterase. Overexpression of the acpD gene provided the E. coli with a large amount of the 23-kDa protein and more than 800 times higher azoreductase activity. The purified gene product exhibited activity corresponding to that of the native azoreductase. The reaction followed a ping-pong mechanism requiring 2 mol of NADH to reduce 1 mol of methyl red (4'-dimethylaminoazobenzene-2-carboxylic acid) into 2-aminobenzoic acid and N,N'-dimethyl-p-phenylenediamine. On the other hand, the gene product could not convert holo-acyl carrier protein into the apo form under either in vitro or in vivo conditions. These data indicate that the acpD gene product is not acyl carrier protein phosphodiesterase but an azoreductase.     

Characterization of NMCR-2, a new non-mobile colistin resistance enzyme: implications for an MCR-8 ancestor

MCR-4 and MCR-8 are two recently identified members of an ongoing MCR family of colistin resistance. Although that aquatic reservoir for MCR-4 is proposed, the origin and mechanism of MCR-8 is poorly understood. Here we report a previously unrecognized non-mobile colistin resistance enzyme, termed NMCR-2, originating from the plant pathogen Kosakonia pseudosacchari. NMCR-2 (551aa) gives 67.3% identity to MCR-8 (565aa). NMCR-2 is placed as a progenitor/ancestor for MCR-8 in phylogeny of MCR members. Genetic study reveals that nmcr-2 is comparable to mcr-8 in the ability of producing phenotypic colistin resistance. Biochemical analyses determine that these two enzymes catalyse the transfer of PEA from the donor PE lipid substrate to the recipient lipid A molecule by a putative ‘ping-pong’ trade-off. Further experiment of protein engineering demonstrates that the two motifs (TM region and catalytic domain) of NMCR-2 are functionally exchangeable with that of MCR-8, rather than MCR-1. Physiological impacts of nmcr-2 and/or mcr-8 are detected in Escherichia coli, featuring with fitness cost. Evidently, the action and mechanism of NMCR-2 is analogous to that of MCR-8. Therefore, our finding underlines that NMCR-2 might be a possible progenitor of MCR-8.     

Kinetic characterization of GABA-transaminase from cultured neurons and astrocytes

The enzymatic mechanism and the kinetic parameters of GABA-transaminase extracted from cultured mouse cerebral cortex neurons and astrocytes were studied. Neuronal as well as astrocytic GABA-transaminase obeyed a bi bi ping-pong reaction mechanism. The estimated K_m-values for -ketoglutarate and GABA were significantly lower for astroglial GABA-transaminase compared to the neuronal enzyme suggesting a possible existence of cell specific isozymes of GABA-transaminase. The observed enzymatic mechanism and the magnitude of the estimated kinetic parameters imply that GABA-transaminase synthesized in the two types of cultured neural cells is mechanistically and kinetically equivalent to the enzyme synthesized in the brainin vivo.     

Fatty acid synthetase. A steady state kinetic analysis of the reaction catalyzed by the enzyme from pigeon liver.

The kinetic mechanism of pigeon liver fatty acid synthetase action has been studied using steady state kinetic analysis. Initial velocity studies are consistent with an earlier suggestion that the enzyme catalyzes this reaction by a seven-site ping-pong mechanism. Although the range of substrate concentrations that could be used was limited by several factors, the initial velocity patterns showing the relationship between the substrates acetyl coenzyme CoA, malonyl-CoA, and NADPH appear to be a series of parallel lines, regardless of which substrate is varied at fixed levels of a second substrate. However, two of the substrates, acetyl-CoA and malonly-CoA, apparently exhibit a competitive substrate inhibition with respect to each other, but NADPH shows no inhibition of any kind. Product inhibition patterns suggest that free CoA is competitive versus acetyl-CoA and malonyl-CoA and is uncompetitive versus NADPH, and that NADP+ is competitive versus NADPH and uncompetitive versus acetyl-CoA or malonyl-CoA. These results are consistent with a seven-site ping-pong mechanism with intermediates covalently bound to 4'-phosphopantetheine (part of acyl carrier protein). Double competitive substrate inhibition by acetyl-CoA and malonyl-CoA is consistent with the rate equation derived for the over-all mechanism. The kinetic mechanism developed from these results is capable of explaining the formation of fatty acids from malonyl-CoA and NADPH alone (Katiyar, S. S., Briedis, A. V., and Porter, J. W. (1974) Arch. Biochem. Biophys. 162, 412-420) and also the formation of triacetic acid lactone from either malonyl-CoA alone or acetyl-CoA plus malonyl-CoA.     

Purification and Properties of Beef Liver Phosphoglucomutase

A procedure is described for purification of phosphoglucomutase [EC 2.7.5.1] from beef liver. The purified enzyme preparation was homogeneous on the analysis of ultracentrifugation and zone electrophoresis. The molecular weight was determined to be 64,000 by the meniscus depletion method.

The amino acid composition of liver phosphoglucomutase was very similar to that of the rabbit muscle enzyme.

The reaction mechanism of liver phosphoglucomutase was examined kinetically. The results of kinetical experiments strongly suggested that the reaction of liver phosphoglucomutase proceeds via “ping-pong” mechanism.

Liver phosphoglucomutase activity was remarkably inhibited by Fru-1,6-P₂, glycerate-2,3-P₂ and glycerate-1,3-P₂. Role of the bisphosphate compounds on the control of carbohydrate metabolism is discussed.     

Diamine Transamination Catalyzed by ω-Amino Acid : Pyruvate Aminotransferase of Pseudomonas sp. F–126

ω-Amino acid: pyruvate aminotransferase of Pseudomonas sp. F–126 catalyzes a transamination between various diamines and pyruvate, an exclusive amino acceptor. Based on a stoichiometric studies it was shown that one of the two amino groups of 1,2-diaminoethane, putrescine and cadaverine transaminated to pyruvate. The transamination between putrescine and pyruvate seemed to proceed by a ping-pong bi bi mechanism. Michaelis constants for putrescine and pyruvate were calculated to be 76.9 and 6.25 mm, respectively.     

piRNA biogenesis during adult spermatogenesis in mice is independent of the ping-pong mechanism

piRNAs, a class of small non-coding RNAs associated with PIWI proteins, have broad functions in germline development, transposon silencing, and epigenetic regulation. In diverse organisms, a subset of piRNAs derived from repeat sequences are produced via the interplay between two PIWI proteins. This mechanism, termed “ping-pong” cycle, operates among the PIWI proteins of the primordial mouse testis; however, its involvement in postnatal testes remains elusive. Here we show that adult testicular piRNAs are produced independent of the ping-pong mechanism. We identified and characterized large populations of piRNAs in the adult and postnatal developing testes associated with MILI and MIWI, the only PIWI proteins detectable in these testes. No interaction between MILI and MIWI or sequence feature for the ping-pong mechanism among their piRNAs was detected in the adult testis. The majority of MILI- and MIWI-associated piRNAs originate from the same DNA strands within the same loci. Both populations of piRNAs are biased for 5′ Uracil but not for Adenine on the 10th nucleotide position, and display no complementarity. Furthermore, in Miwi mutants, MILI-associated piRNAs are not downregulated, but instead upregulated. These results indicate that the adult testicular piRNAs are predominantly, if not exclusively, produced by a primary processing mechanism instead of the ping-pong mechanism. In this primary pathway, biogenesis of MILI- and MIWI-associated piRNAs may compete for the same precursors; the types of piRNAs produced tend to be non-selectively dictated by the available precursors in the cell; and precursors with introns tend to be spliced before processed into piRNAs.     

Programs simulating a I lost eric and other enzyme kinetics for computer-aided teaching

Two programs have been written in BASIC as a teaching aid for instruction of HNC, HND, and degree students in a strategy of experimentation, taking enzyme kinetics as a particular example. Little prior knowledge is required to use the programs. One of the programs (ENZY) simulates the action of a non-allosteric enzyme as (a) a simple case with or without inhibitors including substrate inhibition (b) a two-substrate case with either random-order or ping-pong kinetics. The other program (ALLO) simulates the action of an allosteric enzyme with or without activators or inhibitors or both. A detailed example of an investigation using ALLO is given.     

Purification and Characterization of NfrA1, a Bacillus subtilis Nitro/flavin Reductase Capable of Interacting with the Bacterial Luciferase

ipa-43d is a hypothetical gene identified by the Bacillus subtilis genome project (Mol. Microbiol. 10, 371-384 1993; Nature 390, 249-256 1997). The ipa-43d protein overexpressed in E. coli was purified to homogeneity and its properties were analyzed biochemically. The ipa-43d protein was found to be tightly associated with FMN and to be capable of reducing both nitrofurazone and FMN effectively. Although the ipa-43d protein catalysis obeys the ping-pong Bi-Bi mechanism, catalysis mode was changed to the sequential mechanism upon coupling with the bioluminescent reaction. Database search showed that B. subtilis possessed four genes (ipa-44d, ytmO, yddN, and yvbT), encoding proteins similar in amino acid sequence to LuxA and LuxB of Photobacterium fischeri, and, in particular, ipa-44d is immediately adjacent to the ipa-43d gene on the chromosome.     

Acetyl-coenzyme A carboxylase from the developing endosperm of Ricinus communis: II. A two-site kinetic mechanism

The reaction kinetics of acetyl-coenzyme A carboxylase purified from developing castor oil seeds have been examined. On the basis of the substrate interaction and product inhibition results, a hybrid ping-pong mechanism is proposed. This type of mechanism demands that the active site of the enzyme be separated into two functionally distinct catalytic sites. The carboxybiotin intermediate formed at one site by the hydrolysis of ATP swings to the second site where acetyl-CoA is carboxylated to form malonyl-CoA. This hybrid rapid-equilibrium random bi bi uni uni ping-pong mechanism which includes the formation of three abortive complexes, E · HCO₃^? · ADP, E · HCO₃^? · P_i and E · P_i · P_i, is analogous to the hybrid ping-pong mechanism previously described for methylmalonyl-CoA transcarboxylase (D. B. Northrop (1969) J. Biol. Chem., 244, 5808) and pyruvate carboxylase (R. E. Barden, C-H. Fung, M. F. Utter, and M. C. Scrutton (1972) J. Biol. Chem., 247, 1323).     

Functional properties of purified and reconstituted mitochondrial metabolite carriers

Eight mitochondrial carrier proteins were solubilized and purified in the authors' laboratories using variations of a general procedure based on hydroxyapatite and Celite chromatography. The molecular mass of all the carriers ranges between 28 and 34 kDa on SDS-PAGE. The purified carrier proteins were reconstituted into liposomes mainly by using a method of detergent removal by hydrophobic chromatography on polystyrene beads. The various carriers were identified in the reconstituted state by their kinetic properties. A complete set of basic kinetic data including substrate specificity, affinity, interaction with inhibitors, and activation energy was obtained. These data closely resemble those of intact mitochondria, as far as they are available from the intact organelle. Mainly on the basis of kinetic data, the asymmetric orientation of most of the reconstituted carrier proteins were established. Several of their functional properties are significantly affected by the type of phospholipids used for reconstitution. All carriers which have been investigated in proteoliposomes function according to a simultaneous (sequential) mechanism of transport; i.e., a ternary complex, made up of two substrates and the carrier protein, is involved in the catalytic cycle. The only exception was the carnitine carrier, where a ping-pong mechanism of transport was found. By reaction of particular cysteine residues with mercurial reagents, several carriers could be reversibly converted to a functional state different from the various physiological transport modes. This unphysiological transport mode is characterized by a combination of channel-type and carrier-type properties.     

Plant pyruvate dehydrogenase complex: analysis of the kinetic properties and metabolite regulation

The pyruvate dehydrogenase complex was isolated from the mitochondria of broccoli florets and shown to be similar in its reaction mechanism to the complexes from other sources. Three families of parallel lines were obtained for the initial velocity patterns, indicating a multisite ping-pong mechanism. The apparent K_m values obtained were 321 ± 18, 148 ± 13, and 7.2 ± 0.51 μm for pyruvate, NAD⁺, and CoA, respectively. Product inhibition studies using acetyl-CoA and NADH yielded results which were in agreement with those predicted by the multisite ping-pong mechanism. Acetyl-CoA and NADH were found to be competitive inhibitors versus CoA and NAD⁺, respectively. All other substrate-product combinations showed uncompetitive inhibition patterns, except for acetyl-CoA versus NAD⁺. Among various metabolites tested, only hydroxypyruvate (K_i = 0.11 mM) and glyoxylate (K_i = 3.27 mM) were found to be capable of inhibiting the broccoli enzyme to a significant degree. Initial velocity patterns using Mg²⁺? or Ca²⁺-thiamine pyrophosphate and pyruvate as the variable substrate were found to be consistent with an equilibrium ordered mechanism where Mg? or Ca-thiamine pyrophosphate bind first, with dissociation constants of 33.8 and 3 μm, respectively. The Mg- or Ca-thiamine pyrophosphate complexes also dissociated rapidly from the enzyme complex.     

Decolorization of azo dyes by Rhodobacter sphaeroides

Rhodobacter sphaeroides AS1.1737 decolorized more than 90% of several azo dyes (200 mg dyes l^–1) in 24 h. The optimal culture conditions were: anaerobic illumination (1990 lx), peptone as carbon source, temperature 35–40 °C and pH 7–8. Intracellular crude enzyme from this strain had azoreductase activity, optimized temperature as 45–50 °C, and decolorization kinetics which were consistent with a ping-pong mechanism.     

Hindered migration of amino acids toward their isoelectric positions in gel electrofocusing, and facilitation of the migration at high ionic strength

Amino acids with a largepI -pK_p difference are known to be poor carrier ampholytes in electrofocusing, exhibiting isoelectric zones with poor conductivity across as many as 4 pH units. Accordingly, radioactive amino acids of this type, e.g., glycine, are found to be distributed over the entire pH gradient formed by Ampholine in electrofocusing gels, while radioactive amino acids like histidine or glutamic acid with small pI - pK_p differences form single peaks at or near their pI's. When poor carrier ampholyte amino acids are subjected to gel electrofocusing in 0.1 KCl, their distribution sharpens into single peaks, at or near the pI, indistinguishable from those of the good carrier ampholyte amino acids. At an intermediate stage of peak coalescence of the original broad distributions of poor carrier ampholyte amino acids, in 0.01 KCl, acidic and basic peaks of amino acid can be observed, possibly analogous to acidie and basic distributions previously observed with labeled Ampholine. The rate of peak coalescence of anionic amino acids seems higher than that of the cationic species. The mechanism by which high ionic strength facilitates the condensation of poor carrier ampholyte amino acids at their pI remains unknown. Possibly, the current within zones of poor carrier ampholyte amino acids is insufficient, or poor carrier ampholyte amino acids are not sufficiently charged, to allow for electrophoretic migration of the bulk of loaded amino acid to its isoelectric position, unless the current density is increased by electrofocusing at high ionic strength. Alternatively, 0.1 KCl may interfere with electrovalent interactions between amino acids and isoelectric carrier ampholyte zones, analogous to the action of urea in preventing the interaction between polyanions and carrier ampholytes.     

Kinetic properties of aspartate transport in rat heart mitochondrial inner membranes.

The mitochondrial glutamate-aspartate exchange carrier catalyzes the electrogenic exchange of intramitochondrial aspartate for extramitochondrial glutamate. Protons are cotransported with glutamate in a 1:1 ratio. In the present study, the effects of pH and glutamate concentration on glutamate entry into intact mitochondria were determined. Hydrogen ions were found to decrease the K_m for glutamate entry. In addition, using glutamate-loaded submitochondrial particles, aspartate transport into the particles was measured as a function of internal and external glutamate concentrations, pH, and electrical potential across the membrane. Glutamate, was a competitive inhibitor of aspartate transport when both amino acids were present on the same side of the membrane, while H⁺ was a noncompetitive inhibitor of aspartate entry into the particles. A decrease in glutamate concentration on the inside of the particles brought about a parallel decrease in V and K_m for aspartate outside of the particles, thus suggesting a ping-pong mechanism for the carrier. The uncoupling agent, carbonyl cyanide p-trifluoromethoxy-phenylhydrazone (FCCP), lowered both the K_m and V of aspartate transport, while the effect on V was somewhat larger. Data obtained in the presence of KSCN was similar to that obtained with FCCP, and therefore it is concluded that both K_m and V changes are dependent on a change of electrical potential across the membrane. A model for the carrier is proposed, which is consistent with the data presented. The model includes a single binding site specific for either glutamate or aspartate, and a separate binding site for the cotransported proton. The affinity of the binding site for protons is increased by simultaneous glutamate binding, but decreased by aspartate binding. The data suggest that an increase in the membrane potential increases the mobility of the charged carrier-aspartate complex, but also facilitates some additional step in the exchange cycle involving subsequent return of the carrier to the matrix side of the membrane. The additional membrane-potential-dependent step could be proton binding on the cytosolic side of the carrier.     

Characterisation of the flavin-free oxygen-tolerant azoreductase from Xenophilus azovorans KF46F in comparison to flavin-containing azoreductases

The flavin-free azoreductase from Xenophilus azovorans KF46F (AzoB), which has been the very first characterized oxygen-tolerant azoreductase, was analyzed in comparison to various recently described flavin-containing azoreductases from different bacterial sources. Sequence comparisons demonstrated that the azoreductase from X. azovorans KF46F is a member of the NmrA family of proteins and demonstrates 30% sequence identity with a NADPH-dependent quinone oxidoreductase from Escherichia coli (encoded by ytfG). In contrast, it was found that the flavin-containing azoreductases from E. coli OY1-2 (AZR), Bacillus sp. OY1-2 (AZR) and related azoreductases all belong to the FMN_red superfamily of enzymes. The substrate specificity of AzoB was reanalyzed in respect to the recently characterized flavin-containing azoreductases, and it was found that purified AzoB converted in addition to different ortho-hydroxy azo compounds [such as Orange II = 1-(4′-sulfophenylazo)-2-naphthol] also the simple non-hydroxylated non-sulfonated azo dye Methyl Red (4′-dimethylaminoazobenzene-2-carboxylic acid), but no indications for the conversion of quinones were obtained. Significant differences were observed in the substrate specificities between AzoB and the flavin-containing azoreductases. The kinetic analysis of the turn-over of Orange II by AzoB suggested an ordered bireactant reaction mechanism which was different from the ping-pong mechanism suggested for the flavin-containing azoreductases.