Vitamin B(6) salvage enzymes: mechanism, structure and regulation

Vitamin B(6) is a generic term referring to pyridoxine, pyridoxamine, pyridoxal and their related phosphorylated forms. Pyridoxal 5'-phosphate is the catalytically active form of vitamin B(6), and acts as cofactor in more than 140 different enzyme reactions. In animals, pyridoxal 5'-phosphate is recycled from food and from degraded B(6)-enzymes in a "salvage pathway", which essentially involves two ubiquitous enzymes: an ATP-dependent pyridoxal kinase and an FMN-dependent pyridoxine 5'-phosphate oxidase. Once it is made, pyridoxal 5'-phosphate is targeted to the dozens of different apo-B(6) enzymes that are being synthesized in the cell. The mechanism and regulation of the salvage pathway and the mechanism of addition of pyridoxal 5'-phosphate to the apo-B(6)-enzymes are poorly understood and represent a very challenging research field. Pyridoxal kinase and pyridoxine 5'-phosphate oxidase play kinetic roles in regulating the level of pyridoxal 5'-phosphate formation. Deficiency of pyridoxal 5'-phosphate due to inborn defects of these enzymes seems to be involved in several neurological pathologies. In addition, inhibition of pyridoxal kinase activity by several pharmaceutical and natural compounds is known to lead to pyridoxal 5'-phosphate deficiency. Understanding the exact role of vitamin B(6) in these pathologies requires a better knowledge on the metabolism and homeostasis of the vitamin. This article summarizes the current knowledge on structural, kinetic and regulation features of the two enzymes involved in the PLP salvage pathway. We also discuss the proposal that newly formed PLP may be transferred from either enzyme to apo-B(6)-enzymes by direct channeling, an efficient, exclusive, and protected means of delivery of the highly reactive PLP. This new perspective may lead to novel and interesting findings, as well as serve as a model system for the study of macromolecular channeling. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.     

The structure and mechanism of action of cellulolytic enzymes

The modern structural classification of polysaccharases comprising cellulase–hemicellulase enzyme systems is dis cussed. Their catalytic domains are currently grouped into 15 of more than 80 known glycosyl hydrolase families, whereas substrate binding domains fall into 13 families. The structures of catalytic and substrate binding domains, as well as linker sequences, are briefly considered. A hypothetical mechanism of concerted action of catalytic and substrate binding domains of cellobiohydrolases on the surface of highly ordered cellulose is suggested.     

Conservation of structure and mechanism by Trm5 enzymes

Enzymes of the Trm5 family catalyze methyl transfer from S-adenosyl methionine (AdoMet) to the N¹ of G37 to synthesize m¹G37-tRNA as a critical determinant to prevent ribosome frameshift errors. Trm5 is specific to eukaryotes and archaea, and it is unrelated in evolution from the bacterial counterpart TrmD, which is a leading anti-bacterial target. The successful targeting of TrmD requires detailed information on Trm5 to avoid cross-species inhibition. However, most information on Trm5 is derived from studies of the archaeal enzyme Methanococcus jannaschii (MjTrm5), whereas little information is available for eukaryotic enzymes. Here we use human Trm5 (Homo sapiens; HsTrm5) as an example of eukaryotic enzymes and demonstrate that it has retained key features of catalytic properties of the archaeal MjTrm5, including the involvement of a general base to mediate one proton transfer. We also address the protease sensitivity of the human enzyme upon expression in bacteria. Using the tRNA-bound crystal structure of the archaeal enzyme as a model, we have identified a single substitution in the human enzyme that improves resistance to proteolysis. These results establish conservation in both the catalytic mechanism and overall structure of Trm5 between evolutionarily distant eukaryotic and archaeal species and validate the crystal structure of the archaeal enzyme as a useful model for studies of the human enzyme.     

Characterization of Escherichia coli B glycogen synthase enzymatic reactions and products.

Previous reports implicate UDPglucose as an active glucosyl donor for the unprimed reaction and “glucoprotein” formation in glycogen biosynthesis in Escherichia coli. Results presented here indicate that UDPglucose and GDPglucose are glucosyl donors in the primed and unprimed reactions catalyzed by purified E. coli B glycogen synthase at less than 5% the rate observed when ADPglucose is the donor. The unprimed reaction is stimulated by 0.25 m citrate and a high molecular weight product is formed similar to that produced when ADPglucose is the glucosyl donor. Physiological amounts of branching enzyme and high concentrations of glycogen inhibit transfer from UDPglucose and GDPglucose. In addition, transfer from UDPglucose is inhibited by ADPglucose. These results strongly suggest that ADPglucose is the physiological donor in both the primed and unprimed reactions. Furthermore, these and previously reported results suggest that one enzyme is involved in the catalysis of the primed, unprimed, and TCA-insoluble product formation reactions. Antiserum prepared against purified E. coli B glycogen synthase inactivates transfer of glucose from either ADPglucose or UDPglucose in the above reactions catalyzed by E. coli B crude extracts. Purified E. coli B glycogen synthase preparations contain significant amounts of α-glucan primer. Evidence shows that this glucan is not covalently attached to the enzyme. Results presented show that formation of material insoluble in TCA and previously considered to be due to “glucoprotein” formation, is in fact due to the generation of long chain length glucan molecules intrinsically acid insoluble. The data suggest that previous results purported to be de novo synthesis of glycogen are due to glucan associated with the glycogen synthase and not to formation of a “glucoprotein” intermediate which then acts as primer for further oligosaccharide synthesis.     

Bacterial enzymatic resistance: beta-lactamases and aminoglycoside-modifying enzymes

Numerous novel beta-lactamases and aminoglycoside-modifying enzymes with altered substrate profiles continue to be identified. Plasmid-mediated transmission of many of these enzymes readily occurs due to inclusion of the encoding genes in mobile gene cassettes. Recent crystallographic determinations of the structures of metallo-beta-lactamases and aminoglycoside-modifying enzymes provide the opportunity for the rational design of inhibitors.     

Effect of molecular mobility on coupled enzymatic reactions involving cofactor regeneration using nanoparticle-attached enzymes

Cofactor-dependent multi-step enzymatic reactions generally require dynamic interactions among cofactor, enzyme and substrate molecules. Maintaining such molecular interactions can be quite challenging especially when the catalysts are tethered to solid state supports for heterogeneous catalysis for either biosynthesis or biosensing. The current work examines the effects of the pattern of immobilization, which presumably impacts molecular interactions on the surface of solid supports, on the reaction kinetics of a multienzymic system including glutamate dehydrogenase, glucose dehydrogenase and cofactor NAD(H). Interestingly, particle collision due to Brownian motion of nanoparticles successfully enabled the coupled reactions involving a regeneration cycle of NAD(H) even when the enzymes and cofactor were immobilized separately onto superparamagnetic nanoparticles (124 nm). The impact of particle motion and collision was evident in that the overall reaction rate was increased by over 100% by applying a moderate alternating magnetic field (500 Hz, 17 Gs), or using additional spacers, both of which could improve the mobility of the immobilized catalysts. We further observed that integrated immobilization, which allowed the cofactor to be placed in the molecular vicinity of enzymes on the same nanoparticles, could enhance the reaction rate by 1.8 fold. These results demonstrated the feasibility in manipulating molecular interactions among immobilized catalyst components by using nanoscale fabrication for efficient multienzymic biosynthesis.     

On the structure of flavin-oxygen intermediates involved in enzymatic reactions.

During the catalytic reactions of flavoprotein hydroxylases and bacterial luciferase, flavin peroxides are formed as intermediates [see Massey, V. and Hemmerich, P. (1976) in The Enzymes, 3rd edn (P. Boyer, ed.) pp. 421--505, Academic Press, New York]. These intermediates have been postulated to be C(4a) derivatives of the flavin coenzyme. To test this hypothesis, modified flavin coenzymes carrying an oxygen substituent at position C(4a) of the isoalloxazine ring were synthesized. They are tightly bound by the apoenzymes of D-amino acid oxidase, p-hydroxybenzoate hydroxylase and lactate oxidase; the resulting complexes show spectral properties closely similar to those of the transient oxygen adducts of the hydroxylases. The optical spectra of the lumiflavin model compounds were found to be highly dependent on the solvent environment and nature of the subsituents. Under appropriate conditions they simulate satisfactorily the spectra of the transient enzymatic oxygen adducts. The results support the proposal that the primary oxygen adducts formed with these flavoproteins on reaction of the reduced enzymes with oxygen are flavin C(4a) peroxides.     

Integrated enzymatic reactions and analysis

Summary Enzymatic reactions were performed in a modified auto-injector unit of a Shimadzu HPLC system. The reactions were analyzed by automated injections directly into the HPLC separation system. Two reactions were studied, and the enzymes mandelonitrile lyase and α-chymotrypsin were immobilized by adsorption onto a solid support, e.g., Celite and Chromosorb. The reactions were performed in various organic solvents e.g., diisopropyl ether, heptane/ethyl acetate mixtures and acetonitrile.     

Determinants of enzymatic specificity in the Cys-Met-metabolism PLP-dependent enzymes family: crystal structure of cystathionine gamma-lyase from yeast and intrafamiliar structure comparison

The crystal structure of cystathionine gamma-lyase (CGL) from yeast has been solved by molecular replacement at a resolution of 2.6 A. The molecule consists of 393 amino acid residues and one PLP moiety and is arranged in the crystal as a tetramer with D2 symmetry as in other related enzymes of the Cys-Met-metabolism PLP-dependent family like cystathionine beta-lyase (CBL). A structure comparison with other family members revealed surprising insights into the tuning of enzymatic specificity between the different family members. CGLs from yeast or human are virtually identical at their active sites to cystathionine gamma-synthase (CGS) from E. coli. Both CGLs and bacterial CGSs exhibit gamma-synthase and gamma-lyase activities depending on their position in the metabolic pathway and the available substrates. This group of enzymes has a glutamate (E333 in yeast CGL) which binds to the distal group of cystathionine (CTT) or the amino group of cysteine. Plant CGSs use homoserine phosphate instead of O-succinyl-homoserine as one substrate. This is reflected by a partially different active site structure in plant CGSs. In CGL and CBL the pseudosymmetric substrate must dock at the active site in different orientations, with S in gamma-position (CBL) or in delta-position (CGL). The conserved glutamate steers the substrate as seen in other CGLs. In CBLs this position is occupied by either tyrosine or hydrophobic residues directing binding of CTT such that S is in the in gamma-position. In methionine gamma-lyase a hydrophic patch operates as recognition site for the methyl group of the methionine substrate.     

Effective activation energy of enzymatic and nonenzymatic reactions. Evolution-imposed requirements to enzyme structure

The difference of the activation energies in a protein globule and water has been treated in terms of the theory of an elementary act of charge transfer reaction with regards to the energy spent on the transfer of charged reactants from water into the protein. The protein was treated as a structureless dielectric with a given optical and static dielectric constants surrounded by the aqueous phase. Reactions of different types (charge exchange between reactants, charge separation, neutralization, etc.) have been analyzed both under prevalence of purely electrostatic effects and under considerable nonelectrostatic contributions to the activation energies. It is shown that for all one-electron and most multi-electron reactions involving two reaction centres the energy spent for charged reactant transfer from water into protein is greater than the concomitant activation energy gain. The same effect takes place in a number of cases for multi-centre processes as well. To overcome the entropy hindrances, the reactants and catalysts must combine into multiparticle complexes, i.e. form microscopic regions of low dielectric constant. This results in increased effective activation energy as compared to reactions in water. It has been hypothesized that in order to make up for this loss the evolution has selected the proteins which are characterized by considerable intraglobular permanent electric fields. The presence in proteins of high concentrations of strongly polar peptide groups renders them advantageous in this respect over other polymers that are less polar.     

Relations between enzymatic and association reactions in the development of bovine fibrin clot structure

Development of fibrin clot structure was examined at pH 7.0, Γ/2 0.15, and 29 °C as a function of thrombin and fibrinogen concentrations. Parameters for the release of Apeptides, to give $\text{?}{}_{\mathrm{<mtext>A</mtext>}}$ were evaluated. Characteristics of time dependencies of development of turbidity, 90 ° light scattering, network, and compactible network were established. Mean mass/length ratios of fibrin in developing and mature networks were determined. Relationships between results combined with an inferred dependence of lateral interaction on release of B-peptides are used to disclose a model in which a protofibril network is formed first and the intrinsic length of this network (i.e., length exclusive of overlap or loose ends) determines network length, thus mean mass/length ratio, at maturity. Statements regarding initial protofibril network are: (i) A dominant group of $\text{?}{}_{\mathrm{<mtext>A</mtext>}}$-protofibrils appears first. With decreasing rate of production of $\text{?}{}_{\mathrm{<mtext>A</mtext>}}$ their average length increases and number decreases. (ii) Slower release of B-peptides produces $\text{?}{}_{\mathrm{<mtext>AB</mtext>}}$ whose fraction $\text{θ}{}_{\mathrm{<mtext>AB</mtext>}}\text{=}\text{?}{}_{\mathrm{<mtext>AB</mtext>}}\text{(?}{}_{\mathrm{A}}\text{+?}{}_{\mathrm{AB}}$) determines the occurrence of protofibril regions capable of contributing to a lateral interaction sufficiently stable for the formation of network. (iii) When dominant protofibrils attain a minimum combination of average length, number concentration, and frequency of occurrence of capable regions, an initial protofibril network is rapidly generated. (iv) Capable regions near protofibril ends are preferentially involved in initial network formation. (v) The initial network mesh size is large compared to average concomitant free protofibril length. (vi) With B-peptide release dependent on prior A-peptide release, protofibrils in the initial network have the highest capable region frequency, and this is maintained as lateral interaction progresses. Then, fibrin which is free at initial network formation and fibrin which is produced subsequently interact mainly to increase the mean mass/length ratio of initial network elements.     

Primary structure,unique enzymatic properties,and molecular evolution of pepsinogen B and pepsin B

Purification of pepsinogen B from dog stomach was achieved. Activation of pepsinogen B to pepsin B is likely to proceed through a one-step pathway although the rate is very slow. Pepsin B hydrolyzes various peptides including beta-endorphin, insulin B chain, dynorphin A, and neurokinin A, with high specificity for the cleavage of the Phe-X bonds. The stability of pepsin B in alkaline pH is noteworthy, presumably due to its less acidic character. The complete primary structure of pepsinogen B was clarified for the first time through the molecular cloning of the respective cDNA. Molecular evolutional analyses show that pepsinogen B is not included in other known pepsinogen groups and constitutes an independent cluster in the consensus tree. Pepsinogen B might be a sister group of pepsinogen C and the divergence of these two zymogens seems to be the latest event of pepsinogen evolution.