The crystal structure of the formiminotransferase domain of formiminotransferase-cyclodeaminase: implications for substrate channeling in a bifunctional enzyme. (1/224)

BACKGROUND: The bifunctional enzyme formiminotransferase-cyclodeaminase (FTCD) contains two active sites at different positions on the protein structure. The enzyme binds a gamma-linked polyglutamylated form of the tetrahydrofolate substrate and channels the product of the transferase reaction from the transferase active site to the cyclodeaminase active site. Structural studies of this bifunctional enzyme and its monofunctional domains will provide insight into the mechanism of substrate channeling and the two catalytic reactions. RESULTS: The crystal structure of the formiminotransferase (FT) domain of FTCD has been determined in the presence of a product analog, folinic acid. The overall structure shows that the FT domain comprises two subdomains that adopt a novel alpha/beta fold. Inspection of the folinic acid binding site reveals an electrostatic tunnel traversing the width of the molecule. The distribution of charged residues in the tunnel provides insight into the possible mode of substrate binding and channeling. The electron density reveals that the non-natural stereoisomer, (6R)-folinic acid, binds to the protein; this observation suggests a mechanism for product release. In addition, a single molecule of glycerol is bound to the enzyme and indicates a putative binding site for formiminoglutamate. CONCLUSIONS: The structure of the FT domain in the presence of folinic acid reveals a possible novel mechanism for substrate channeling. The position of the folinic acid and a bound glycerol molecule near to the sidechain of His82 suggests that this residue may act as the catalytic base required for the formiminotransferase mechanism.  (+info)

Mechanism of action of ethanolamine ammonia-lyase, an adenosylcobalamin-dependent enzyme. Proton nuclear magnetic resonance studies of the binding of adenine nucleosides and substrate to ethanolamine ammonia-lyase. (2/224)

Proton NMR spectroscopy was used to study the binding of adenosine, 5'-deoxyadenosine, adenine, and ethanolamine to the adenosylcobalamin-dependent enzyme ethanolamine ammonia-lyase. Broadening of ligand resonances in the presence of ethanolamine ammonia-lyase indicated that adenosine, 5'-deoxyadenosine, and ethanolamine all formed complexes with the enzyme (KD(mM) = 3.5, 3.0, and 2.5 respectively). The methyl group of enzyme-bound 5'-deoxyadenosine rotated at a rate exceeding 10(7) revolutions/s. Adenine did not appear to bind to the enzyme. Rates of dissociation of nucleosides from the enzyme were fast on the NMR time scale, precluding measurements of rate constants for the binding reaction. The departure of ethanolamine was slow, however, permitting their determination. The values for these rate constants were: k1 = 4.4 times 10(5) M-1 S-1; k-1 = 1.1 times 10(3) S-1. Addition of 1 mol of cyanocobalamin/mol of active sites led to narrowing of the enzyme-broadened ligand resonances. With 5'-deoxyadenosine, linewidths still exceeded those of the free ligand, indicating that binding to enzyme was weakened but not abolished. The KD for this nucleoside in the presence of CNCbl was 8.0 mM. With ethanolamine and adenosine, however, linewidths reverted to values characteristic of the unbound ligand, indicating either that CNCbl greatly lowered the rate of dissociation of the ligand or displaced the ligand from the enzyme. A decision between these two possibilities could not be made from the data at hand, although analogy with the situation obtaining with 5'-deoxyadenosine suggests that adenosine is displaced from the enzyme by CNCbl. 5'-Deoxyadenosine inhibited catalytic activity of the enzyme, competing with adenosylcobalamin (Ki = 2.7 mM). Adenosine had no effect, despite NMR evidence indicating that it formed a complex with free enzyme. These experiments showed that ethanolamine ammonia-lyase possesses binding sites for adenine nucleosides, a class of compounds chemically related to the Cobeta-ligand of the cofactor, as well as for ethanolamine. Binding to the enzyme has now been demonstrated for all three categories of low molecular weight compounds thought to be involved in the reaction; namely, substrate (ethanolamine), corrin, and adenine nucleoside.  (+info)

Interaction between ethanolamine ammonia-lyase and methylcobalamin. Half-site reactivity with an adenosylcobalamin-dependent enzyme. (3/224)

The adenosylcobalamin-dependent enzyme ethanolamine ammonia-lyase contains two active sites per molecule. The effects of methylcobalamin on the properties of this enzyme differ qualitatively depending on whether one or both of these sites is occupied by the cobamide. At 0.5 mol of methylcobalamin/mol of active sites, catalytic activity fell rapidly to approximately 30% of control levels, thereafter remaining constant for an hour. With the partially inhibited enzyme, Km values for ethanolamine and adenosylcobalamin were 5.5 muM and 1.6 muM, respectively, values that do not differ significantly from those of uninhibited enzyme. When the methylcobalamin per active site ratio was increased to 1, the decline in activity became progressive with time, eventually falling to levels much lower than seen at a cobamide per active site ratio of 0.5. Methylcobalamin also promotes the formation of a complex stable to gel filtration between ethanolamine and enzyme. Complex formation increased with increasing methylcobalamin per active site ratios up to a ratio of 0.7/1, at which point 0.5 mol of ethanol/mol of active sites was taken up. Ethanolamine uptake did not increase at higher methylcobalamin to active sites ratios. Methylcobalamin itself was taken up by enzyme, forming a complex containing 0.5 mol of methylcobalamin/mol of active sites that was stable to gel filtration. Measurement by the technique of Hummel and Dreyer ((1962) Biochim. Biophys. Acta 63, 530-532), however, showed one methylcobalamin binding site per active site. The formation of enzyme-ligand complexes stable to gel filtration was not affected by 5'-deoxyadenosine nor did 5'-deoxyadenosine by itself promote the formation of a stable complex between enzyme and ethanolamine. These observations were interpreted as evidence indicating half-site reactivity of ethanolamine ammonia-lyase with methylcobalamin. Comparison with previous results suggested that this half-site reactivity was an epiphenomenon not related to catalysis.  (+info)

The mechanism of action of ethanolamine ammonia-lyase, an adenosylcobalamin-dependent enzyme. The source of the third methyl hydrogen in the 5'-deoxyadenosine generated from the cofactor during catalysis. (4/224)

Ethanolamine ammonia-lyase is an adenosylcobalamin-dependent enzyme which catalyzes the conversion of ethanolamine and propanolamine to ammonia and the corresponding aldehydes. A mechanism has been proposed for this and other adenosylcobalamin-dependent reactions which involves cleavage of the carbon-cobalt bond of the cofactor followed by abstraction of a substrate hydrogen atom by the adenosyl fragment to form 5'-deoxyadenosine. In support of this proposal, a previous study demonstrated that the deamination of propanolamine by ethanolamine ammonia-lyase is accompanied by the reversible cleavage of the carbon-cobalt bond of the cofactor, with the production of 5'-deoxyadenosine (Babior, B.M., Carty, T.J., and Abeles, R.H. (1974) J. Biol. Chem. 249, 1689-1695). The present study is concerned with the origin of the third hydrogen atom on the methyl group of the 5'-deoxyadenosine produced in that reaction. The 5'-deoxyadenosine isolated from an incubation mixture initially containing enzyme, [5',5'-D2]adenosylcobalamin, and [1,1-D2]propanolamine was chemically degraded so that the 4' and 5' carbon atoms were, respectively, converted to the carbonyl and methyl carbons of acetaldehyde. Analysis of the p-nitrophenylhydrazone of the acetaldehyde by gas-liquid chromatography-mass spectroscopy revealed 3 deuterium atoms/molecule, indicating that two of the methyl hydrogens originated from adenosylcobalamin and the third was donated by substrate. This observation provides further support for the participation of 5'-deoxyadenosine in the mechanism of adenosylcobalamin-dependent reactions.  (+info)

Cloning and characterization of the pnb genes, encoding enzymes for 4-nitrobenzoate catabolism in Pseudomonas putida TW3. (5/224)

Pseudomonas putida strain TW3 is able to metabolize 4-nitrotoluene via 4-nitrobenzoate (4NBen) and 3, 4-dihydroxybenzoic acid (protocatechuate [PCA]) to central metabolites. We have cloned, sequenced, and characterized a 6-kbp fragment of TW3 DNA which contains five genes, two of which encode the enzymes involved in the catabolism of 4NBen to PCA. In order, they encode a 4NBen reductase (PnbA) which is responsible for catalyzing the direct reduction of 4NBen to 4-hydroxylaminobenzoate with the oxidation of 2 mol of NADH per mol of 4NBen, a reductase-like enzyme (Orf1) which appears to have no function in the pathway, a regulator protein (PnbR) of the LysR family, a 4-hydroxylaminobenzoate lyase (PnbB) which catalyzes the conversion of 4-hydroxylaminobenzoate to PCA and ammonium, and a second lyase-like enzyme (Orf2) which is closely associated with pnbB but appears to have no function in the pathway. The central pnbR gene is transcribed in the opposite direction to the other four genes. These genes complete the characterization of the whole pathway of 4-nitrotoluene catabolism to the ring cleavage substrate PCA in P. putida strain TW3.  (+info)

A novel interaction of the Golgi complex with the vimentin intermediate filament cytoskeleton. (6/224)

The integration of the vimentin intermediate filament (IF) cytoskeleton and cellular organelles in vivo is an incompletely understood process, and the identities of proteins participating in such events are largely unknown. Here, we show that the Golgi complex interacts with the vimentin IF cytoskeleton, and that the Golgi protein formiminotransferase cyclodeaminase (FTCD) participates in this interaction. We show that the peripherally associated Golgi protein FTCD binds directly to vimentin subunits and to polymerized vimentin filaments in vivo and in vitro. Expression of FTCD in cultured cells results in the formation of extensive FTCD-containing fibers originating from the Golgi region, and is paralleled by a dramatic rearrangements of the vimentin IF cytoskeleton in a coordinate process in which vimentin filaments and FTCD integrate into chimeric fibers. Formation of the FTCD fibers is obligatorily coupled to vimentin assembly and does not occur in vim(-/-) cells. The FTCD-mediated regulation of vimentin IF is not a secondary effect of changes in the microtubule or the actin cytoskeletons, since those cytoskeletal systems appear unaffected by FTCD expression. The assembly of the FTCD/vimentin fibers causes a coordinate change in the structure of the Golgi complex and results in Golgi fragmentation into individual elements that are tethered to the FTCD/vimentin fibers. The observed interaction of Golgi elements with vimentin filaments and the ability of FTCD to specifically interacts with both Golgi membrane and vimentin filaments and promote their association suggest that FTCD might be a candidate protein integrating the Golgi compartment with the IF cytoskeleton.  (+info)

Quantitative measurement of the course of bean callus differentiation. (7/224)

Two strains of callus have been isolated from bean hypocotyl and grown on a defined maintenance medium supplemented with 2 mg/l. 2:4-dichlorophenoxyacetic acid (2:4D) and 2% sucrose. Root initiation was observed in one strain and formation of nodules containing xylem and phloem in both strains after transfer to an induction medium supplemented with 1 mg/l. naphthyleneacetic acid, 0-2 mg/l. kinetin and 3% sucrose, after 3 transfers to maintenance medium. The number of nodules per gramme increased 10-fold between 6 and 12 days after transfer, and thereafter remained constant. Phenylalanine ammonia lyase (PAL) activity rose to a maximum value when the rate of nodule formation was greatest, and decreased after the maximum nodule concentration was reached. The final constant value for PAL activity was above that of callus grown on maintenance medium. Beta I leads to 3 glucan synthetase activity rose to a maximum 15 days after transfer, and then fell gradually to a level above that measured in callus on maintenance medium. Callus was transferred from maintenance medium after 3, 4, 5 and 6 transfers. The concentration of nodules after 21 days on induction medium decreased as the callus was kept in culture. No further differentiation could be induced after 6 transfers. The fall in nodule formation was paralleled by a decrease in PAL and betaI leads to 3 glucan synthetase activities measured 21 days after transfer.  (+info)

Methanococcus jannaschii generates L-proline by cyclization of L-ornithine. (8/224)

Cell extracts of Methanococcus jannaschii have been shown to readily convert L-ornithine to L-proline. This cyclization reaction proceeds with the loss of only the C-2 nitrogen, as has been documented for ornithine cyclodeaminase (EC 4.3.1.12). Since no gene homologous to that coding for ornithine cyclodeaminase is present in the genome of M. jannaschii, these results indicate that proline biosynthesis in M. jannaschii is accomplished by a previously unrecognized enzyme.  (+info)

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