Amino acid activation of 3-phosphoglycerate dehydrogenase from peas

When l-methionine was added to an extract of etiolated pea epicotyls activation of 3-phosphoglycerate dehydrogenase occurred and was complete in 20–30 min. Storage of extracts at 5° led to a loss in the ability of l-methionine to activate the enzyme and after 24 hr storage almost no activation was observed. On the basis of tests with 16 compounds the ability to activate 3-phosphoglycerate dehydrogenase was restricted to l-amino acids with intermediate-length side chains. There appears to be no requirement for a reactive group in the side chain. Gel-filtration showed that the higher levels of 3-phosphoglycerate dehydrogenase activity obtained after treatment with l-methionine are relatively stable.     

The isolation and characterization of 3-phosphoglycerate dehydrogenase from peas

1. 3-Phosphoglycerate dehydrogenase was purified 400-fold from crude extracts of etiolated pea epicotyls. 2. Michaelis constants were determined for all four substrates. 3. Loss of sensitivity to inhibition by l-serine occurs on purification. 4. The purified enzyme is inhibited by thiol-group reagents and, with N-ethyl-maleimide, protection is afforded by 3-phosphoglycerate though not by NAD(+).     

A model for the regulation of D-3-phosphoglycerate dehydrogenase,a Vmax-type allosteric enzyme.

Escherichia coli D-3-phosphoglycerate dehydrogenase (ePGDH) is a tetramer of identical subunits that is allosterically inhibited by L-serine, the end product of its metabolic pathway. Because serine binding affects the velocity of the reaction and not the binding of substrate or cofactor, the enzyme is classified as of the Vmax type. Inhibition by a variety of amino acids and analogues of L-serine indicate that all three functional groups of serine are required for optimal interaction. Removing or altering any one functional group results in an increase in inhibitory concentration from micromolar to millimolar, and removal or alteration of any two functional groups removes all inhibitory ability. Kinetic studies indicate at least two serine-binding sites, but the crystal structure solved in the presence of bound serine and direct serine-binding studies show that there are a total of four serine-binding sites on the enzyme. However, approximately 85% inhibition is attained when only two sites are occupied. The three-dimensional structure of ePGDH shows that the serine-binding sites reside at the interface between regulatory domains of adjacent subunits. Two serine molecules bind at each of the two regulatory domain interfaces in the enzyme. When all four of the serines are bound, 100% inhibition of activity is seen. However, because the domain contacts are symmetrical, the binding of only one serine at each interface is sufficient to produce approximately 85% inhibition. The tethering of the regulatory domains to each other through multiple hydrogen bonds from serine to each subunit apparently prevents the body of these domains from undergoing the reorientation that must accompany a catalytic cycle. It is suggested that part of the conformational change may involve a hinge formed in the vicinity of the union of two antiparallel beta-sheets in the regulatory domains. The tethering function of serine, in turn, appears to prevent the substrate-binding domain from closing the cleft between it and the nucleotide-binding domain, which may be necessary to form a productive hydrophobic environment for hydride transfer. Thus, the structure provides a plausible model that is consistent with the binding and inhibition data and that suggests that catalysis and inhibition in this rare Vmax-type allosteric enzyme is based on the movement of rigid domains about flexible hinges.     

Regulatory properties of purified 3-phosphoglycerate dehydrogenase from Bacillus subtilis.

3-Phosphoglycerate dehydrogenase (3-phosphoglycerate:NAD oxidoreductase, EC. 1.1.1.95) was purified from Bacillus subtilis by conventional methods. The final preparation was homogeneous by electrophoretic analysis and had a sedimentation constant of 6.3 S. On the basis of gel filtration data the enzyme had a molecular weight of about 166000. The plot of velocity versus phosphoglycerate concentration was biphasic while similar plots for hydroxypyruvate phosphate and NADH were the conventional hyperbolic type. The enzyme was specifically inhibited by serine. The inhibition was time dependent, requiring several minutes incubation before a constant level of inhibition was achieved. Serine inhibition was of the "mixed type" with respect to 3-phosphoglycerate and Hill plots of these data had slopes that approached 2. Desensitization of the enzyme to serine inhibition was achieved by incubation in the absence of dithiothreitol. The desensitized enzyme was different from the native enzyme in fluoresence properties, sedimentation characteristics and in the absence of the biphasic phosphoglycerate saturation curve. Evidence was obtained for the participation of sulphydryl groups in the changes in protein structure responsible for serine inhibition as well as the dehydrogenase activity of the enzyme.     

Inhibition of 3-phosphoglycerate dehydrogenase by l-serine

1. l-Serine was shown to be a highly specific inhibitor of 3-phosphoglycerate dehydrogenase. 2. 3-Phosphoglycerate dehydrogenase is cold-labile with respect to its catalytic activity and to sensitivity to serine. 3. l-Serine protects the catalytic site as well as the inhibitor site. 4. Glycerol protects the catalytic site as well as the inhibitor site. 5. Serine acts as a ;classical' non-competitive inhibitor of fresh preparations of 3-phosphoglycerate dehydrogenase. 6. ;Aged' preparations when assayed at pH6.5 show sigmoid inhibition curves at saturating substrate concentrations. 7. A generalized model is advanced to account for the variation of the catalytic activity and the inhibitory effect of l-serine with time and conditions. 8. The possibility that the sigmoid kinetics of inhibition observed are an artifact of isolation is discussed.     

De-regulation of D-3-phosphoglycerate dehydrogenase by domain removal.

Escherichia coli 3-phosphoglycerate dehydrogenase (PGDH) catalyzes the first step in serine biosynthesis, and is allosterically inhibited by serine. Structural studies revealed a homotetramer in which the quaternary arrangement of subunits formed an elongated ellipsoid. Each subunit consisted of three domains: nucleotide, substrate and regulatory. In PGDH, extensive interactions are formed between nucleotide binding domains. A second subunit-subunit interaction occurs between regulatory domains creating an extended beta sheet. The serine-binding sites overlap this interface. In these studies, the nucleotide and substrate domains (NSDs) were subcloned to identify changes in both catalytic and physical properties upon removal of a subunit-subunit interface. The NSDs did not vary significantly from PGDH with respect to kinetic parameters with the exception that serine no longer had an effect on catalysis. Temperature dependent dynamic light scattering (DLS) revealed the NSDs aggregated > 5 degrees C before PGDH, indicating decreased stability. DLS and gel filtration studies showed that the truncated enzyme formed a tetramer. This result negated the hypothesis that the removal of the regulatory domain would create an enzyme mimic of the unregulated, closely related dimeric enzymes. Expression of the regulatory domain, to study conformational changes induced by serine binding, yielded a product that by CD spectra contained stable secondary structure. DLS and pulsed field gradient NMR studies of the regulatory domain showed the presence of higher oligomers instead of the predicted dimer. We have concluded that the removal of the regulatory domain is sufficient to eliminate serine inhibition but does not have the expected effect on the quaternary structure.     

The D-glyceraldehyde-3-phosphate dehydrogenase and 3-phosphoglycerate kinase complex from rabbit skeletal muscles

The experimental conditions favouring the association of Sepharose-bound D-glyceraldehyde-3-phosphate dehydrogenase with soluble 3-phosphoglycerate kinase were studied. Acylation of D-glyceraldehyde-3-phosphate dehydrogenase by 1.3-bisphosphoglycerate was found to be a prerequisite for the complex formation.     

Inactivation of chicken liver d-3-phosphoglycerate dehydrogenase by N-alkylmaleimides

Chicken liver d-3-phosphoglycerate dehydrogenase was effectively inhibited at 25 °C by micromolar concentrations of N-ethyl-, N-butyl-, N-pentyl-, N-heptyl-, and N-phenylmaleimide. The rates of inactivation of the enzyme did not vary with chain length of the N-alkylmaleimide derivative. Saturation kinetics in the same concentration range was observed with each maleimide derivative studied. A maximum pseudo-first-order rate constant of 0.1 min^?1 was determined for all of the maleimide inactivation reactions. Compounds shown to bind at the coenzyme binding site such as NAD, 3-aminopyridine adenine dinucleotide, adenosine diphosphoribose, and adenosine diphosphate did not protect the enzyme against N-ethylmaleimide inactivation. AMP was demonstrated to be a substrate-competitive inhibitor of the enzyme. AMP and 3-phosphoglycerate both effectively protected the enzyme against N-ethylmaleimide inactivation. Diazotized 3-aminopyridine adenine dinucleotide, a sulfhydryl modifying, site-labeling reagent for several pyridine nucleotide-dependent enzymes, did not inactivate the phosphoglycerate dehydrogenase but functioned rather as a reversible coenzyme-competitive inhibitor.     

Yeast 3-phosphoglycerate kinase. Essential arginyl residues at the 3-phosphoglycerate binding site.

Yeast 3-phosphoglycerate kinase (ATP:3-phospho-D-glycerate 1-phospho-transferase, EC 2.7.2.3) is inactivated by phenylglyoxal. Loss of activity correlates with the modification of two arginyl residues, both of which are protected by all of the substrates. The modification is not accompanied by any significant conformational change as determined by optical rotatory dispersion. Ultraviolet difference spectrophotometry indicates that the inactivated enzyme retains its capacity for binding the nucleotide substrates whereas the spectral perturbation characteristic of 3-phosphoglycerate binding is abolished in the modified enzyme. The data suggest that at least one of the two essential arginyl residues is located at or near the 3-phosphoglycerate binding site. A likely role of this residue could be its interaction with the negatively charged phosphate or carboxylate groups of 3-phosphoglycerate.     

Interaction between D-glyceraldehyde-3-phosphate dehydrogenase and 3-phosphoglycerate kinase and its functional consequences.

E. coli D-glyceraldehyde-3-phosphate dehydrogenase covalently bound to Sepharose was shown to form a complex with soluble E. coli 3-phosphoglycerate kinase with a stoichiometry of 1.77 +/- 0.61 kinase molecules per tetramer of the dehydrogenase and an apparent Kd of 1.03 +/- 0.68 microM (10 mM sodium phosphate, 0.15 M NaCl). No interaction was detected between E. coli D-glyceraldehyde-3-phosphate dehydrogenase and rabbit muscle 3-phosphoglycerate kinase. The species-specificity of the bienzyme association made it possible to develop a kinetic approach to demonstrate the functionally significant interaction between E. coli D-glyceraldehyde-3-phosphate dehydrogenase and E. coli 3-phosphoglycerate kinase, which consists of an increase in steady-state rate of the coupled reaction.     

Crystal structures of type IIIH NAD-dependent D-3-phosphoglycerate dehydrogenase from two thermophiles

In the l-Serine biosynthesis, D-3-phosphoglycerate dehydrogenase (PGDH) catalyzes the inter-conversion of D-3-phosphoglycerate to phosphohydroxypyruvate. PGDH belongs to 2-hydroxyacid dehydrogenases family. We have determined the crystal structures of PGDH from Sulfolobus tokodaii (StPGDH) and Pyrococcus horikoshii (PhPGDH) using X-ray diffraction to resolution of 1.77 Å and 1.95 Å, respectively. The PGDH protomer from both species exhibits identical structures, consisting of substrate binding domain and nucleotide binding domain. The residues and water molecules interacting with the NAD are identified. The catalytic triad residues Glu-His-Arg are highly conserved. The residues involved in the dimer interface and the structural features responsible for thermostability are evaluated. Overall, structures of PGDHs with two domains and histidine at the active site are categorized as type III_H and such PGDHs structures having this type are reported for the first time.     

Inhibition of 3-phosphoglycerate dehydrogenase from Pisum sativum by purine nucleotides (Short Communication)

The inhibition of 3-phosphoglycerate dehydrogenase from etiolated pea epicotyls by purine nucleoside di- and tri-phosphates is linear, competitive with regard to NADH, and the nucleotides are mutually exclusive in their binding. Free ATP and ADP are more effective inhibitors than are the respective magnesium complexes.