Modification of active site histidine in ribulosebisphosphate carboxylase/oxygenase

Identification of essential histidine residues in 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase: analysis by chemical modification with diethyl pyrocarbonate and site-directed mutagenesis

The enzyme 3-deoxy-D-manno-octulosonic acid 8-phosphate (KDO 8-P) synthase from Escherichia coli that catalyzes the aldol-type condensation of D-arabinose 5-phosphate (A 5-P) and phosphoenolpyruvate (PEP) to give KDO 8-P and inorganic phosphate (P(i)) is inactivated by diethyl pyrocarbonate (DEPC). The inactivation is first-order in enzyme and DEPC. A second-order rate constant of 340 M(-1) min(-1) is obtained at pH 7.6 and 4 degrees C. The rate of inactivation is dependent on pH and the pH-inactivation rate data imply the involvement of an amino acid residue with a pK(a) value of 7.3. KDO 8-P synthase activity is not restored to the DEPC-inactivated enzyme following treatment with hydroxylamine. Complete loss of KDO 8-P synthase activity correlates with the ethoxyformylation of three histidine residues by DEPC. KDO 8-P synthase is protected against DEPC inactivation by PEP and partially protected against inactivation by A 5-P. To provide further evidence for the involvement or role of the histidine residues in the aldol-type condensation catalyzed by KDO 8-P synthase, all six histidines were individually mutated to either glycine or alanine. The kinetic constants for the three mutants H40A, H67G, and H246G were unaffected as compared to the wild type enzyme. In contrast, H241G demonstrates a >10-fold increase in K(M) for both PEP and A 5-P and a 4-fold reduction in k(cat), while H97G demonstrates an increase in K(M) for only A 5-P and a 2-fold reduction in k(cat). The activity of the H202G mutant was too low to be measured accurately but the data obtained indicated an approximate 400-fold reduction in k(cat). Circular dichroism measurements of the wild-type and mutant enzymes indicate modest structural changes in only the fully active H67G and H246G mutants. The H241G mutant is protected against DEPC inactivation by PEP and A 5-P to the same extent as the wild-type enzyme, suggesting that the functionally important H241 may not be located in the vicinity of the substrate binding sites. The H97G mutant is protected by PEP against DEPC inactivation to the same degree as the wild-type enzyme but is no longer protected by A 5-P. In the case of the H202G mutant, both A 5-P and PEP protect the mutant against DEPC inactivation but to different extents from those observed for the wild-type enzyme. The catalytic activity of the H97G mutant is partially restored (20% --> 60% of wild-type activity) in the presence of imidazole, while a minor amount of activity is restored to the H202G mutant (<1% --> 4% of wild-type activity) in the presence of imidazole.

Human serum paraoxonase (PON1): identification of essential amino acid residues by group-selective labelling and site-directed mutagenesis

Human serum paraoxonase/arylesterase (PON1, EC 3.1.8.1.) is a calcium-dependent enzyme which hydrolyzes a wide variety of organophosphates, including paraoxon, DFP, sarin and soman. Although the 3-D structure of PON has not yet been determined and its sequence shows no similarity with any other crystallized proteins, we undertook to identify some of its essential amino acid residues by two complementary approaches: group-specific labelling and site-directed mutagenesis. Group-specific labelling studies, performed on the purified native enzyme, indicated that one or more Trp, His and Asp/Glu are potentially important residues for PON activity. Based on these results, we identified some of these residues, conserved in the sequenced mammalian PON1, by site-directed mutagenesis. PON1 mutants were transiently expressed in 293T cells. The catalytic constants k(cat) and Km (relative to k(cat) and Km of the wild-type) determined with four different substrates (phenylacetate, paraoxon, diazoxon, chlorpyrifos oxon), were not significantly changed for the following mutants: W193A, W201A, W253A, H160N, H245N, H250N, H347N, E32A, E48A, D88A, D107A, D121A, D273A. By contrast, k(cat) was less than 1% for eight mutants: W280A, H114N, H133N, H154N, H242N, H284N, E52A and D53A. The essential amino acid residues identified in this work could be part of the PON1 active site, acting either as calcium ligands (E52 and D53?) or as substrate binding (W280?) or nucleophilic (His residues?) sites. However, we cannot rule out that the effects of mutations on catalytic properties resulted from a remote conformational change and/or misfolding of mutant proteins.

Kinetic and mutagenic evidence for the role of histidine residues in the Lycopersicon esculentum 1-aminocyclopropane-1-carboxylic acid oxidase

The ACCO gene from Lycopersicon esculentum (tomato) has been cloned into the expression vector PT7-7. The highly expressed protein was recovered in the form of inclusion bodies. ACCO is inactivated by diethyl pyrocarbonate (DEPC) with a second-order rate constant of 170 M(-1) min(-1). The pH-inactivation rate data imply the involvement of an amino acid residue with a pK value of 6.05. The difference UV spectrum of the the DEPC-inactivated versus native ACCO showed a single peak at 242 nm indicating the modification of histidine residues. The inactivation was reversed by the addition of hydroxylamine to the DEPC-inactivated ACCO. Substrate/cofactor protection studies indicate that both iron and ACC bind near the active site, which contains histidine residues. Four histidines of ACCO were individually mutated to alanine and glycine. H39A is catalytically active, while H177A, H177G, H211A, H211G, H234A, and H234G are basically inactive. The results indicate that histidine residues 177, 211, and 234 may serve as ligands for the active-site iron of ACCO and/or may play some important structural or catalytic role.

Substrate-decreased modification by diethyl pyrocarbonate of two histidines in isocitrate lyase from Escherichia coli

The inactivation of tetrameric 188-kDa isocitrate lyase from Escherichia coli at pH 6.8 (37 degrees C) by diethyl pyrocarbonate, exhibiting saturation kinetics, is accompanied by modification of histidine residues 266 and 306. Substrates isocitrate, glyoxylate, or glyoxylate plus succinate protect the enzyme from inactivation, but succinate alone does not. Removal of the carbethoxy groups from inactivated enzyme by treatment with hydroxylamine restores activity of isocitrate lyase. The present results suggest that the group-specific modifying reagent diethyl pyrocarbonate may be generally useful in determining the position of active site histidine residues in enzymes.

Partial purification of 2,3-oxidosqualene-lanosterol cyclase from hog-liver. Evidence for a functional thiol residue

2,3-Oxidosqualene-lanosterol cyclase is an intrinsic microsomal protein which can be solubilized by ionic (deoxycholate) and nonionic (emulphogene) detergents with good yields. The hog-liver microsomal cyclase was purified approximately 140-fold by chromatography on DEAE-cellulose and hydroxylapatite. The partially purified enzyme was inactivated by N-ethylmaleimide, following pseudo-first order kinetics, indicating that a cysteine residue is essential for activity.

Evidence for catalytic site cysteine and histidine by chemical modification of beta-hydroxy-beta-methylglutaryl-coenzyme A reductase

S-(4-Bromo-2,3-dioxobutyl)-coenzyme A inactivates both yeast and rat liver beta-hydroxy-beta-methylglutaryl-coenzyme A reductase. The inactivation is irreversible, complete in 15 s, and proportional to the concentration of the reagent. beta-Hydroxy-beta-methylglutaryl-CoA provides protection against inactivation, whereas NADPH does not. Inactivation is attributed to reaction with an essential cysteine at the beta-hydroxy-beta-methylglutaryl-CoA binding site. Experiments with other active site-directed reagents confirm the involvement of a cysteine and support the presence of an active-site histidine, but rule out the participation of arginine or serine.

Modification of bovine heart succinate dehydrogenase with ethoxyformic anhydride and rose bengal: evidence for essential histidyl residues protectable by substrates

Purified and membrane-bound succinate dehydrogenase (SDH) from bovine heart mitochondria was inhibited by the histidine-modifying reagents ethoxyformic anhydride (EFA) and Rose Bengal in the presence of light. Succinate and competitive inhibitors protected against inhibition, and decreased the number of histidyl residues modified by EFA. The essential residue modified by EFA was not the essential thiol of SDH, but modification of the essential thiol abolished the protective effect of malonate against inhibition of SDH by EFA. The EFA inhibition was reversed by hydroxylamine nearly completely when the inhibition was less than or equal to 35%, and only partially when the inhibition was more extensive. The uv spectrum of EFA-modified SDH before and after hydroxylamine treatment suggested that extensive inhibition of SDH with EFA may result in ethoxyformylation at both imidazole nitrogens of histidyl residues. Such a modification is not reversed by hydroxylamine. Succinate dehydrogenases and fumarate reductases from several different sources have similar compositions, and the two enzymes from Escherichia coli have considerable homology in the amino acid composition of their respective flavoprotein and iron-sulfur protein subunits. In the former, there is a short stretch containing conserved histidine, cysteine, and arginine residues. These residues, if also conserved in the bovine enzyme, may be the essential active site residues suggested by this work (histidine) and previously (cysteine, arginine).

Inactivation of D-(-)-beta-hydroxybutyrate dehydrogenase by modifiers of carboxyl and histidyl groups

Data presented in this paper suggest that D-(-)-beta-hydroxybutyrate dehydrogenase (BDH) purified from bovine heart mitochondria contains an essential carboxyl group and an essential histidyl residue at or near the active site. Lactate and malate dehydrogenases, which catalyze reactions analogous to that catalyzed by BDH, also contain an aspartyl and a histidyl residue at the active site [Birktoft, J.J., & Banaszak, L.J. (1983) J. Biol. Chem. 258, 472-482]. In addition, all three enzymes contain an essential arginyl residue, apparently concerned with electrostatic interaction with their respective carboxylic acid substrates, and promote ternary adduct formation involving the enzyme, NAD, and sulfite.

Characterization of an active-site peptide modified by glyoxylate and pyridoxal phosphate from spinach ribulosebisphosphate carboxylase/oxygenase

Activated ribulosebisphosphate carboxylase/oxygenase from spinach was treated with glyoxylate plus or minus the transition-state analog, carboxyarabinitol bisphosphate, or the inactive enzyme with pyridoxal phosphate plus or minus the substrate, ribulose bisphosphate. Covalently modified adducts with glyoxylate or pyridoxal phosphate were formed following reduction with sodium borohydride. The derivatized enzymes were carboxymethylated and digested with trypsin; the labeled peptides which were unique to the unprotected samples were purified by ion-exchange chromatography and gel filtration. Both glyoxylate and pyridoxal phosphate were associated with only one major peptide, which in each case was subjected to amino acid analysis and sequencing. The sequence was -Tyr-Gly-Arg-Pro-Leu-Leu-Gly-Cys(Cm)-Thr-Ile-Lys-Lys*-Pro-Lys-, with both reagents exhibiting specificity for the same lysine residue as indicated by the asterisk. This peptide is identical to that previously isolated from spinach carboxylase labeled with either of two different phosphorylated affinity reagents and homologous to one from Rhodospirillum rubrum carboxylase modified by pyridoxal phosphate. The species invariance of this lysine residue, number 175, and the substantial conservation of adjacent sequence support the probability for a functional role in catalysis of the lysyl epsilon-amino group.

Isolation of L8 and L8S8 forms of ribulose bisphosphate carboxylase/oxygenase from Chromatium vinosum

The enzyme ribulose bisphosphate carboxylase/oxygenase has been purified from Chromatium vinosum. When an extract is subjected to centrifugation at 35,000 X g in the presence of polyethylene glycol (PEG)-6000 and the supernatant is treated with 50 mM Mg2+ and the precipitate is then fractionated by vertical centrifugation into a reoriented sucrose gradient followed by chromatography on diethylaminoethyl (DEAE)-Sephadex A50, the resultant enzyme contains large (L) and small (S) subunits. Alternatively, centrifugation of extracts at 175,000 X g in the presence of PEG-6000 followed by fractionation with Mg2+, density gradient centrifugation, and chromatography on DEAE-Sephadex A50 yields an enzyme free of small subunits. The two forms have comparable carboxylase and oxygenase activities and have compositions and molecular weights corresponding to L8 and L8S8 enzymes. The amino acid compositions of L and S subunits are reported. The L8S8 enzyme from spinach cannot be similarly dissociated by centrifugation at 175,000 X g in the presence of PEG-6000.

Modification of carboxyl groups at the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase

Ribulose-1,5-bisphosphate carboxylase/oxygenase from spinach was inactivated by a carboxyl-directed reagent, Woodward's reagent K ( WRK ). The inactivation followed pseudo-first-order kinetics. The reaction order with respect to inactivation by WRK was 1.1, suggesting that inactivation was the consequence of modifying a single residue per active site. The substrate ribulose 1,5-bisphosphate (RBP), two competitive inhibitors, fructose 1,6-bisphosphate (FBP) and sedoheptulose 1,7-bisphosphate (SBP), and a number of sugars-phosphate protected against inactivation by WRK . SBP was a strong protector, displaying a dissociation constant (Kd) of 3 microM with native RBP carboxylase. Pretreatment of RBP carboxylase with diethyl pyrocarbonate prevented WRK incorporation into the enzyme. The enol ester derivative produced by reaction of WRK with RBP carboxylase has a maximal absorbance at 346 nm, and the extinction coefficient was found to be 12300 +/- 700 M-1 cm-1. Spectrophotometric titration of the number of carboxyl groups modified by WRK in RBP carboxylase/oxygenase in the presence and in the absence of SBP suggests that inactivation was associated with the modification of one carboxyl group per active site.

Modification of rat liver iodothyronine 5'-deiodinase activity with diethylpyrocarbonate and rose bengal; evidence for an active site histidine residue

Iodothyronine 5'-deiodinase activity of rat liver microsomes was rapidly and completely lost by treatment with diethylpyrocarbonate (DEP) and by photo-oxidation with Rose Bengal (RB). In both cases inactivation followed pseudo first order reaction kinetics. Inactivation by DEP was diminished in the presence of substrate or competitive inhibitors, and was reversed by hydroxylamine treatment. In addition to photo-oxidation, deiodinase activity was also inhibited by RB in the dark. This inhibition was reversible and competitive with substrate (Ki 60 nM). These results suggest the location of an essential histidine residue at or near the active site of rat liver iodothyronine deiodinase.

Synthesis of the large subunit of ribulose-1,5-bisphosphate carboxylase in anin vitro partially definedE. coli system

Thein vitro DNA- or RNA-directed synthesis of the large subunit (LS) of spinach chloroplast ribulose-1,5-biphosphate carboxylase (RuP2C) has been examined in a highly definedE. coli transcription-translation system. Spinach chloroplast DNA, RNA and recombinant plasmids containing the spinach chloroplast LS gene (rbcL) have been used as templates in thein vitro system and a quantitative assay has been developed to measure LS formation. Thein vitro formed product contains formylmethionine at the N-terminal position and sediments primarily as a monomer. There is no detectable enzymatic activity associated with thein vitro product. To determine where theE. coli RNA polymerase used in these systems initiates, we have examined the transcripts produced by this enzymein vitro. Measurements of run-off transcripts indicate thatE. coli RNA polymerase initiates at the same position on the gene as is seenin vivo. In addition, the complete nucleotide sequence of therbcL gene including previously unsequenced 3' and 5' flanking regions has been determined. The sequence agrees, except at two nucleotide positions, with previously published sequencing data for this gene (Zurawski, G, Perrot, B, Bottomley, W, Whitfeld, PR, 1981. Nucleic Acids Res. 9:3251-3270).

The response to ribulose bisphosphate(4-) (RuBP (4-)) and RuBP-Mg (2-) in catalysis by structurally divergent RuBP carboxylase/oxygenases

Free ribulose bisphosphate (RuBP(4-)) rather than its magnesium complex (RuBP-Mg(2-)) was the apparent substrate for spinach ribulose bisphosphate carboxylase/oxygenase. The apparent Km for total RuBP (pH 8.0 at 30° C) increased with increasing Mg(2+) concentrations from 11.6 μM at 13.33 mM Mg(2+) to 32.6 μM at 40.33 mM Mg(2+). Similarly the apparent Km for RuBP-Mg(2-) complex increased with increasing Mg(2+) from 9.4 μM at 13.33 mM Mg(2+) to 29.7 μM at 40.33 mM Mg(2+). However, the Km values for uncomplexed RuBP(4-) were independent of the (saturating) concentration of Mg(2+) (Km=2.2 μM). The Vmax did not vary with the changing concentrations of Mg(2+).In contrast, the Km for total RuBP remained constant with varying Mg(2+) concentrations (Km=59.5 μM) for the enzyme from R. rubrum. The apparent Km for the RuBP-Mg(2-) complex decreased with increasing Mg(2+) concentrations from 16.0 μM at 7.5 mM Mg(2+) to 5.9 μM at 27.5 mM Mg(2+). The initial velocity for the C. vinosum enzyme was also found to be independent of the (saturating) concentration of Mg(2+) when total RuBP was varied in the assay. Thus the response to total RuBP by these two bacterial enzymes, which markedly differ in structure, was closely similar.

Evidence for a carbanion intermediate in catalysis by spinach ribulose-1,5-bisphosphate carboxylase/oxygenase

Spinach ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (EC 4.1.1.39) showed marked reactivity towards tetranitromethane in the presence of RuBP, when the enzyme was in the fully activated state. The inactivated enzyme did not catalyze substrate-dependent nitroform production. Nitroform production was proportional to the concentration of the enzyme and tetranitromethane at optimal substrate concentrations. The pH optimum for nitroform production was similar to that for carboxylation. The effects of bicarbonate, ribulose-1,5-bisphosphate, and temperature on partition of the intermediate between production of phosphoglycerate and nitroform indicate that both routes share a common intermediate. Data on stoichiometry of the reaction imply that the intermediate is not oxidized by tetranitromethane but instead is nitrated. The data are compatible with a carbanion intermediate in the reaction catalyzed by ribulose-1,5-bisphosphate carboxylase.

Pyridoxal phosphate as a probe in the active site of ribulose bisphosphate carboxylase/oxygenase

Ribulose bisphosphate (RuBP) carboxylase is rapidly and irreversibly inactivated by photooxidation sensitized by pyridoxal phosphate. Both pyridoxal and pyridoxamine phosphate were much less effective in sensitizing the photooxidation even when used at twice the concentration of pyridoxal phosphate. These results imply that pyridoxal phosphate binds at the active site not only through a Schiff base, but also through ionic interaction with the phosphate binding region. Spectral analysis of the photooxidized enzyme showed a new absorption maximum at 325 nm due to reduction of the Schiff base between pyridoxal phosphate and a lysyl residue with concomitant oxidation of a histidine residue. The stoichiometry of photooxidative [3H]pyridoxal phosphate incorporation was 0.87 mol/mol of a 70,000-dalton large subunit-small subunit combination. Studies with 3H-labeled diethyl pyrocarbonate showed that both photooxidation and carbethoxylation occur at the same histidine residue. However, photooxidation by pyridoxal phosphate is very specific for an active site histidine residue due to the high specificity of this affinity label. Several competitive inhibitors with respect to ribulose bisphosphate offered appreciable protection against pyridoxal phosphate-induced photooxidation of the enzyme. The photooxidized enzyme showed an increase in the net negative charge on the protein which was evident from the higher mobility of the photooxidized enzyme toward the anode in polyacrylamide gel electrophoresis.

Interaction of ribulose bisphosphate carboxylase/oxygenase with 2-carboxyhexitol 1,6-bisphosphates

2-C-Carboxy-D-glucitol 1,6-bisphosphate (CGBP) and 2-C-carboxy-D-mannitol 1,6-bisphosphate (CMBP) have been synthesized, isolated, and the structures of these compounds and the derived lactones elucidated by NMR spectroscopy and periodate oxidation. Both carboxyhexitol bisphosphates, which are homologs of the transition state analog 2-C-carboxy-D-arabinitol 1,5-bisphosphate, exhibit competitive inhibiton of ribulose bisphosphate carboxylase/oxygenase (EC 4.1.1.9) isolated from spinach (Spinacia oleracea), with respect to ribulose 1,5-bisphosphate. CMBP was a more potent inhibitor (100-fold) displaying an inhibition constant (Ki at pH 8.0 and 30 degrees C) of 1-2 microM with enzymes from spinach, barley (Hordeum vulgare), and Chromatium vinosum. In contrast the Rhodospirillum rubrum enzyme was inhibited about 40-fold more weakly (Ki = 53 microM at pH 8.0 and 30 degrees C). Both CGBP and CMBP potentiated activation of RuBP carboxylase from spinach and R. rubrum.

The response to ribulose bisphosphate(4-) (RuBP (4-)) and RuBP-Mg (2-) in catalysis by structurally divergent RuBP carboxylase/oxygenases

Free ribulose hisphosphate (RuBP(4-)) rather than its magnesium complex (RuBP-Mg(2-)) was the apparent substrate for spinach ribulose bisphosphate carboxylase/oxygenase. The apparent Km for total RuBP (pH 8.0 at 30° C) increased with increasing Mg(2+) concentrations from 11.6 μM at 13.33 mM Mg(2+) to 32.6 μM at 40.33 mM Mg(2+). Similarly the apparent Km for RuBP-Mg(2-) complex increased with increasing Mg(2+) from 9.4 μM at 13.33 mM Mg(2+) to 29.7 μM at 40.33 mM Mg(2+). However, the Km values for uncomplexed RuBP(4-) were independent of the (saturating) concentration of Mg(2+) (Km=2.2 μM). The Vmax did not vary with the changing concentrations of Mg(2+).In contrast, the Km for total RuBP remained constant with varying Mg(2+) concentrations (Km=59.5 μM) for the enzyme from R. rubrum. The apparent Km for the RuBP-Mg(2-) complex decreased with increasing Mg(2+) concentrations from 16.0 μM at 7.5 mM Mg(2+) to 5.9 μM at 27.5 mM Mg(2+). The initial velocity for the C. vinosum enzyme was also found to be independent of the (saturating) concentration of Mg(2+) when total RuBP was varied in the assay. Thus the response to total RuBP by these two bacterial enzymes, which markedly differ in structure, was closely similar.