Identification of acetyl phosphate as the product of clostridial glycine reductase: Evidence for an acyl enzyme intermediate

It has been reported [Tanaka, H., & Stadtman, T. C. (1979) J. Biol. Chem. 254, 447-452] that glycine reductase from Clostridium sticklandii catalyzes the reaction glycine + ADP + P(i) + 2(e)- - acetate + ATP + NH(4)+. Glycine reductase consists of three proteins, designated A, B, and C. Only A has been purified to homogeneity. A dithiol serves as an electron donor. We find that ADP is not essential for the reaction and that in its absence acetyl phosphate is formed. Upon further purification of components B and C, an acetate kinase activity can be separated from both proteins. This observation establishes that acetate kinase activity is not an intrinsic property of glycine reductase, and therefore the reaction catalyzed by glycine reductase is glycine + P(i) + 2(e)- - acetyl phosphate + NH(4)+. Experiments with [(14)C]glycine and unlabeled acetate show that free acetate is not a precursor of acetyl phosphate. When glycine labeled with l8(O) is converted to product, l8(O) is lost. The l 8 (O) content of unreacted glycine remains unchanged after approximately 50% is converted to product. We propose that an acyl enzyme, most probably an acetyl enzyme,is an intermediate in the reaction and that the acetyl enzyme reacts with P(i) to form acetyl phosphate. A mechanism is proposed for the formation of the acetyl enzyme.     

Purification of protein components of the clostridial glycine reductase system and characterization of protein A as a selenoprotein

A procedure for the isolation in nearly homogeneous form of protein A, a low molecular-weight, acidic, protein component of clostridial glycine reductase, is described. The yield of protein A is high only in early log phase cells of Clostridium sticklandii grown under standard laboratory conditions in a rich tryptone-yeast extract-distilled water medium but, when selenite (1 μm) is added, the levels of protein A remain high throughout the entire log phase of growth. Addition of ⁷⁵Se-labeled selenite to the culture medium results in the highly selective incorporation of radioactive selenium into protein A. The procedure for isolation of protein A results in about a 700-fold enrichment when extracts prepared from cells that actively catalyze glycine reduction are used. However, the catalytic activity of the purified protein varies considerably from preparation to preparation. The molecular weight of protein A, estimated by sucrose density-gradient centrifugation, is approximately 12,000.The other higher molecular-weight components of glycine reductase are associated with the membrane fraction of the cell and are released as soluble proteins by sonic disruption of the membrane. After purification by ion-exchange and molecular sieve chromatography, these components are separated by DEAE-cellulose chromatography into two protein fractions both necessary for glycine reductase activity in protein A-supplemented assays. One of these fractions consists of a major protein component, protein B, also nearly homogeneous as determined by polyacrylamide gel electrophoresis. The other protein fraction still is heterogeneous.     

Purification and immunological studies of selenoprotein A of the clostridial glycine reductase complex

One of the essential catalytic components of the clostridial glycine reductase complex is a selenium-containing protein, selenoprotein A. An improved method for the purification of selenoprotein A has been developed that yields milligram quantities of the protein in a few relatively simple steps. Ferredoxin and rubredoxin can be recovered in pure form as by-products of the procedure. The high resolving capabilities of an anion exchange high pressure liquid chromatography step were exploited in these purification protocols. For effective antibody production, the antigenicity of selenoprotein A was increased by coupling the pure protein via its sulfhydryl/selenol group(s) to the amino groups of bovine serum albumin using m-maleimidobenzoyl-N-hydroxysuccinimide ester. The high titer sheep antisera that were elicited were used to study the mechanisms of selenium incorporation into selenoprotein A. Immunoblot analysis of sodium dodecyl sulfate-polyacrylamide gels was employed to monitor the synthesis of selenoprotein A by Clostridium sticklandii as a function of growth conditions. Cells grown under limiting conditions (1 nM) of selenium contained only 1-2% of normal levels of active selenoprotein A and no precursor forms were detected after DEAE-high pressure liquid chromatography fractionation of extracts. Conversely, cells grown with optimal (1 microM) selenium levels contained maximal amounts of seleno-protein A and expressed full glycine reductase activity.     

Structural characterization of cholylcoenzyme A:glycine-taurine N-acyltransferase and a covalent substrate intermediate

Bile acid-CoA:glycine-taurine N-acyltransferase was found to catalyze a reaction in the absence of glycine or taurine in which the substrate cholyl-CoA is cleaved with the release of CoA and the formation of a covalently bound enzyme-cholate intermediate. This unstable intermediate was trapped by a rapid mixing and denaturation procedure. The denatured protein was digested with trypsin and the cholate-labeled tryptic peptide was isolated. This cholate-peptide is considered to originate from the active site region of the enzyme based on the following criteria: cholyl-CoA does not react with any of the 20 common amino acids, the hydrolysis of cholyl-CoA is known to occur on the enzyme, the lack of reaction of the enzyme with just cholate, and the fact that labeling is extensive even at low (substrate level) concentrations of cholyl-CoA. The isolated cholate-peptide was submitted to amino acid analysis. It contained 32 amino acid residues and was devoid of cysteine, methionine, and tyrosine. Amino acid analysis of the N-acyltransferase was conducted. The enzyme was also shown to possess a blocked N terminus.     

Ubiquitin manipulation by an E2 conjugating enzyme using a novel covalent intermediate

Degradation of misfolded and damaged proteins by the 26 S proteasome requires the substrate to be tagged with a polyubiquitin chain. Assembly of polyubiquitin chains and subsequent substrate labeling potentially involves three enzymes, an E1, E2, and E3. E2 proteins are key enzymes and form a thioester intermediate through their catalytic cysteine with the C-terminal glycine (Gly76) of ubiquitin. This thioester intermediate is easily hydrolyzed in vitro and has eluded structural characterization. To overcome this, we have engineered a novel ubiquitin-E2 disulfide-linked complex by mutating Gly76 to Cys76 in ubiquitin. Reaction of Ubc1, an E2 from Saccharomyces cerevisiae, with this mutant ubiquitin resulted in an ubiquitin-E2 disulfide that could be purified and was stable for several weeks. Chemical shift perturbation analysis of the disulfide ubiquitin-Ubc1 complex by NMR spectroscopy reveals an ubiquitin-Ubc1 interface similar to that for the ubiquitin-E2 thioester. In addition to the typical E2 catalytic domain, Ubc1 contains an ubiquitin-associated (UBA) domain, and we have utilized NMR spectroscopy to demonstrate that in this disulfide complex the UBA domain is freely accessible to non-covalently bind a second molecule of ubiquitin. The ability of the Ubc1 to bind two ubiquitin molecules suggests that the UBA domain does not interact with the thioester-bound ubiquitin during polyubiquitin chain formation. Thus, construction of this novel ubiquitin-E2 disulfide provides a method to characterize structurally the first step in polyubiquitin chain assembly by Ubc1 and its related class II enzymes.     

Bovine intermediate pituitary alpha-amidation enzyme: preliminary characterization

A secretory granule-associated enzymatic activity that converts mono-[125I]-D-Tyr-Val-Gly into mono-[125I]-D-Tyr-Val-NH2 has been studied. The activity is primarily soluble and shows optimal activity at pH 7 to pH 8. Amidation activity was stimulated 9-fold by addition of optimal amounts of copper (3 microM). In the presence of optimal copper, ascorbate stimulated the reaction 7-fold; none of the other reduced or oxidized cofactors tested was as effective. Taking into account the dependence of the reaction on ascorbate and molecular oxygen and the production of glyoxylate [2], it is suggested that the alpha-amidation enzyme is a monooxygenase. Lineweaver Burk plots with D-Tyr-Val-Gly as the varied substrate demonstrated Michelis-Menten type kinetics with the values of Km and Vmax increasing with the addition of ascorbate to the assay. A variety of peptides ending with a COOH-terminal Gly residue act as inhibitors of the reaction. Two synthetic peptides, gamma 2MSH and ACTH(1-14), with carboxyl termini similar to the presumed physiological substrates for the enzyme, act as competitive inhibitors with similar K1 values. It is likely that this secretory granule alpha-amidation activity is involved in the physiological biosynthetic alpha-amidation of a wide range of bioactive peptides.     

The mechanism of action of the fragile histidine triad, Fhit: isolation of a covalent adenylyl enzyme and chemical rescue of H96G-Fhit

The human fragile histidine triad protein Fhit catalyzes the Mg(2+)-dependent hydrolysis of P(1)-5'-O-adenosine-P(3)-5'-O-adenosine triphosphate, Ap(3)A, to AMP and ADP. The reaction is thought to follow a two-step mechanism, in which the complex of Ap(3)A and Mg(2+) reacts in the first step with His96 of the enzyme to form a covalent Fhit-AMP intermediate and release MgADP. In the second step, the intermediate Fhit-AMP undergoes hydrolysis to AMP and Fhit. The mechanism is inspired by the chain-fold similarities of Fhit to galactose-1-phosphate uridylyltransferase, which functions by an analogous mechanism, and the observation of overall retention in configuration at phosphorus in the action of Fhit (Abend, A., Garrison, P. N., Barnes, L. D., and Frey, P. A. (1999) Biochemistry 38, 3668-3676). Direct evidence in support of this mechanism is reported herein. Reaction of Fhit with [8,8'-(3)H]-Ap(3)A and denaturation of the enzyme in the steady state leads to protein-bound tritium corresponding to 11% of the active sites. Similar experiments with the poor substrate MgATP leads to 0.9% labeling. The mutated protein H96G-Fhit is completely inactive against MgAp(3)A. However, it is chemically rescued by free histidine. H96G-Fhit also catalyzes the hydrolysis of adenosine-5'-phosphoimidazolide, AMP-Im, and of adenosine-5'-phospho-N-methylimidazolide, AMP-N-MeIm. The hydrolyses of AMP-Im and of AMP-N-MeIm by H96G-Fhit are thought to represent chemical rescue of the covalent Fhit-AMP intermediate. Wild-type Fhit is also found to catalyze the hydrolyses of AMP-Im and of AMP-N-MeIm nearly as efficiently as the hydrolysis of MgAp(3)A. The results indicate that Mg(2+) in the reaction of Ap(3)A is required for the first step, the formation of the covalent intermediate Fhit-AMP, and not for the hydrolysis of the intermediate in the second step.     

Escherichia coli dihydrofolate reductase: isolation and characterization of two isozymes.

A combination of affinity column chromatography and preparative gel electrophoresis has been used to purify to homogeneity the two isozymes of dihydrofolate reductase from a trimethoprim-resistant strain of Escherichia coli B (RT 500). These enzyme forms are noninterconvertible and are present in crude cell lysates, but other electrophoretic species can be generated durng purification if sulfhydryl-protecting agents, such as dithiothreitol, are not present. The two isozymes, numbered form 1 and form 2 with respect to their decreasing electrophoretic mobilities, have similar molecular weights (18 500), molecular radii (21 A), and apparent Km values for reduced nico inamide adenin- dinucleotide (NADH) and NADH phosphate (NADPH). Both forms contain 2 mol of sulfhydryl/mol of enzyme which can be oxidized to intramolecular disulfide bonds. However, forms 1 and 2 differ physically in their electrophoretic mobility and isoelectric point and kinetically in their pH-activity profile, specific activity, Km for dihydrofolate, and their affinity toward a number of inhibitors.     

Human epithelial cell intermediate filaments: isolation, purification, and characterization

Intermediate filaments (IF) isolated from human epithelial cells (HeLa) can be disassembled in 8 M urea and reassembled in phosphate-buffered solutions containing greater than 0.1 mg/ml IF protein. Eight proteins were associated with HeLa IF after several disassembly-reassembly cycles as determined by sodium dodecyl sulfate gel electrophoresis (SDS PAGE). A rabbit antiserum directed against HeLa IF contained antibodies to most of these proteins. The immunofluorescence pattern that was seen in HeLa cells with this antiserum is complex. It consisted of a juxtanuclear accumulation of IF protein and a weblike array of cytoplasmic fibers extending to the cell border. Following preadsorption with individual HeLa IF proteins, the immunofluorescence pattern in HeLa cells was altered to suggest the presence of at least two distinct IF networks. The amino acid composition and alpha-helix content (approximately 38%) of HeLa IF proteins was similar to the values obtained for other IF proteins. One-dimensional peptide maps show extensive homology between the major HeLa IF protein of 55,000-mol- wt and a similar 55,000-mol-wt protein obtained from hamster fibroblasts (BHK-21). HeLa 55,000-mol-wt homopolymer IF assembled under conditions similar to those required for BHK-21 55,000-mol-wt homopolymers. Several other proteins present in HeLa IF preparations may be keratin-like structural proteins. The results obtained in these studies indicate that the major HeLa IF protein is the same major IF structural protein found in fibroblasts. Ultrastructural studies of HeLa cells revealed two distinct IF organizational stages including bundles and loose arrays. In addition, in vitro reconstituted HeLa IF also exhibited these two organizational states.     

Catalysis by arginine deiminase: Evidence for a covalent intermediate

Arginine deiminase (EC 3.5.3.6) catalyzes the hydrolysis of arginine to ammonia and citrulline. This reaction is postulated to occur in three steps: (1) formation of the Michaelis complex, (2) the formation of an amidino-enzyme intermediate and liberation of ammonia, and (3) the rate-determining step, hydrolysis of the amidino-enzyme. The enzymic reaction is accelerated 5-fold by 0.2 M imidazole. This striking effect is expected for the amidino-enzyme mechanism but otherwise is difficult to explain. The putative amidino-enzyme intermediate can be demonstrated by quenching the [¹⁴C]arginine-arginine deiminase reaction at low pH. Under these conditions, 0.5 equivalents of ¹⁴C label per mol enzyme dimer were covalently bound.     

Mechanism of action of isopentenyl pyrophosphate isomerase: evidence for a carbonium ion intermediate

Isopentenyl pyrophosphate isomerase catalyzes the interconversion of isopentenyl pyrophosphate and dimethylallyl pyrophosphate. The isomerase from yeast has been purified to near homogeneity (purity greater than 90%). The substrate analogue (Z)-3-(trifluoromethyl)-2-butenyl pyrophosphate reacts at less than 1.8 X 10(-6) times the rate of dimethylallyl pyrophosphate. The enzyme is irreversibly inactivated by 2-(dimethyl-amino)ethyl pyrophosphate (I). These observations are consistent with a carbonium ion mechanism for the isomerization. Compound I is an analogue of the intermediate carbonium ion and probably acts as a transition state analogue. For I, kon' = 2.1 X 10(6) M-1 min-1. No off-rate was detected and, therefore, Ki less than 1.4 X 10(-11) M. Upon denaturation of the inactivated enzyme, I is released unchanged. 2-(Trimethylammonio)ethyl pyrophosphate also inhibits with Ki' = 7 X 10(-7) M, kon' = 4.4 X 10(4) M-1 min-1, and koff = 0.03 min-1. Substrate analogues without a positively charged nitrogen were relatively poor inhibitors. The best inhibitor of these is ethyl pyrophosphate, Ki = 10(-4) M. The enzyme is inactivated by sulfhydryl-selective reagents. These reagents also prevent binding of I to the enzyme. The inactivation by iodoacetamide is dependent upon one ionizable group (pK = 9.3). The pH dependence of V and V/K for the isomerase-catalyzed reaction also depends upon a group with pK = 9.3.     

Structure of a trapped endonuclease III-DNA covalent intermediate

Nearly all cells express proteins that confer resistance to the mutagenic effects of oxidative DNA damage. The primary defense against the toxicity of oxidative nucleobase lesions in DNA is the base-excision repair (BER) pathway. Endonuclease III (EndoIII) is a [4Fe-4S] cluster-containing DNA glycosylase with repair activity specific for oxidized pyrimidine lesions in duplex DNA. We have determined the crystal structure of a trapped intermediate that represents EndoIII frozen in the act of repairing DNA. The structure of the protein-DNA complex provides insight into the ability of EndoIII to recognize and repair a diverse array of oxidatively damaged bases. This structure also suggests a rationale for the frequent occurrence in certain human cancers of a specific mutation in the related DNA repair protein MYH.     

Regulation of aldose reductase activity. Mechanism of action of an activated form of the enzyme]

Activation of bovine eye lens aldose reductase during its incubation with NADPH and glucose was studied. The activated form of the enzyme was isolated, and the rate of glucose reduction measured within a broad range of substrate concentrations. Spectrophotometric titration and equilibrium gel-filtration were used to study the interaction of the enzyme active center with substrates. It was found that the reaction kinetics obeys the mechanism of a quasi-equilibrium binding of substrates with isomerization of the enzyme complexes with nicotinamide dinucleotide phosphates. This activation is accompanied by a transition from non-ordered to highly ordered binding of the substrates. The effect of ligands in the catalytic and inhibitory centers of the activated enzyme on the catalytic reaction was examined. It was found that the activated form of aldose reductase is characterized by a lower affinity of the inhibitory center for the flavonoid, morin. Morin binding not only inhibits the reaction but also prevents the activation of the enzyme.     

Trapping of a covalent enzyme intermediate in the reaction of Bacillus macerans cyclomaltodextrin glucanyltransferase with cyclomaltohexaose.

The mechanism of catalysis of Bacillus macerans cyclomaltodextrin glucanyltransferase (CGTase, EC 2.4.1.19) was studied by trapping and isolating a covalent-enzyme intermediate. CGTase catalyzes an acceptor or coupling reaction between cyclomaltohexaose and a carbohydrate acceptor such as D-glucose. CGTase was incubated with 3H-labeled cyclomaltohexaose in the absence of any added acceptor. After 30 s of reaction, the enzyme was rapidly denatured and precipitated by the addition of 10% trifluoroacetic acid (TFA). Extensive washing of the precipitated protein showed retention of radioactivity with the protein. The precipitate was dissolved in 0.1 M TFA, containing 6 M urea and passed over a BioGel P-10 column. The protein fraction retained 95% of its original radioactivity. The reaction with [3H]cyclomaltohexaose was also stopped by the addition of TFA to give an inactive enzyme at pH 2.5. The enzyme was separated from unreacted cyclomaltohexaose on a BioGel P-10 column and was shown to be radioactive. When the radioactive protein fraction was rechromatographed on BioGel P-10, it retained 100% of the label. These results demonstrate the formation of a covalent carbohydrate-enzyme intermediate in the reactions catalyzed by CGTase.     

Spectroscopic and kinetic characterization of nonenzymic and aldose reductase mediated covalent NADP-glycolaldehyde adduct formation

Reaction of glycolaldehyde with the binary E-NADP complex of bovine kidney aldose reductase (ALR2) produces an enzyme-bound chromophore whose absorbance (lambd max 341 nm) and fluorescence (lambda ex max 341 nm; lambda emit max 421 nm) properties are distinct from those of NADPH or E.NADPH yet are consistent with the proposed covalent adduct structure [1,4-dihydro-4-(1-hydroxy-2-oxoethyl)nicotinamide adenine dinucleotide phosphate]. The kinetics of adduct formation, both in solution and at the enzyme active site, support a mechanism involving rate-determining enolization of glycolaldehyde at high [NADP+] or [E.NADP]. At low [NADP+] or [E.NADP] the reaction is second-order overall, but the ALR2-mediated reaction displays saturation by glycolaldehyde due to competition of the aldehyde (plus hydrate) and enol for E.NADP. Measurement of the pre-steady-state burst of E-adduct formation confirms that glycolaldehyde enol is the reactive species and gives a value of 1.3 x 10(-6) for Kenol = [enol]/[( aldehyde] + [hydrate]), similar to that determined by trapping the enol with I3-. At the ALR2 active site, the rate of adduct formation is enhanced 79,000-fold and the adduct is stabilized greater than or equal to 13,000-fold relative to the reaction with NADP+ in solution. A portion of this enhancement is ascribed to specific interaction of NADP+ with the enzyme since the 3-acetylpyridine analogue, (AP)ADP+, gives values that are 15-200-fold lower. Additional evidence for strong interaction of ALR2 with both NADP+ and NADPH is reported. Yet, because dissociation of adduct is slow, catalysis of the overall adduct formation reaction by ALR2 is less than or equal to 67-fold.     

Mechanism of gating and partial agonist action in the glycine receptor

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