Multiple evolutionary origin of pyridoxal-5'-phosphate-dependent amino acid decarboxylases

The roles of His-167 and His-275 in the reaction catalyzed by glutamate decarboxylase from Escherichia coli

Two histidine residues in glutamate decarboxylase from Escherichia coli, potential participants in catalysis because they are conserved among amino acid decarboxylases and because they are at the active site in the homologous enzyme ornithine decarboxylase, were mutated. His-275 is shown to bind the cofactor pyridoxal 5'-phosphate but not to contribute directly to catalysis. The H275N enzyme was unable to bind the cofactor whereas the H275Q mutant contained 50% of the normal complement of cofactor and its specific activity (expressed per mole of cofactor) was 70% of that of the wild-type enzyme. The H167N mutant bound the cofactor tightly, its specific activity was approximately half that of the wild-type enzyme and experiments in D2O showed that it catalyzed replacement of the carboxyl group with retention of configuration as does the wild-type enzyme. Comparison of reaction profiles by observing changes in the absorbance of the cofactor after stopped-flow mixing, revealed that a slow reaction, in which approximately one-third of the wild-type enzyme is converted to an unreactive complex during catalysis, does not occur with the H167N mutant enzyme. This reaction is attributed to a substrate-induced conformational change, a proposal that is supported by differential scanning calorimetry.

The GTP effector site of ornithine decarboxylase from Lactobacillus 30a: kinetic and structural characterization

A nucleotide effector site of the biodegradative form of ornithine decarboxylase from Lactobacillus 30a (OrnDC L30a) has been identified. OrnDC L30a activity at pH 8.0, where the enzyme is normally inactive, is stimulated by GTP and dGTP and to a lesser extent by GDP but not by ATP, CTP, or UTP. The pH profile indicates that activation by GTP is reflected by an increase in kcat/KM,orn (above pH 6.8), while Vmax remains constant over the pH range 4.0-9. 0. Scatchard plot analysis shows that GTP binds to OrnDC L30a at both pH 5.8 (KD = 0.11 microM) and pH 8.0 (KD = 1.6 microM), but unexpectedly, half-site binding is observed at the higher pH. The OrnDC L30a dodecamer dissociates into dimers at high pH in the presence or absence of GTP. The GTP binding site was located in difference electron density maps using low-resolution X-ray data. This represents a new type of GTP binding site. A model explaining the activation of OrnDC L30a by GTP is presented.

Mutation of cysteine 111 in Dopa decarboxylase leads to active site perturbation

Cysteine 111 in Dopa decarboxylase (DDC) has been replaced by alanine or serine by site-directed mutagenesis. Compared to the wild-type enzyme, the resultant C111A and C111S mutant enzymes exhibit Kcat values of about 50% and 15%, respectively, at pH 6.8, while the K(m) values remain relatively unaltered for L-3,4-dihydroxyphenylalanine (L-Dopa) and L-5-hydroxytryptophan (L-5-HTP). While a significant decrease of the 280 nm optically active band present in the wild type is observed in mutant DDCs, their visible co-enzyme absorption and CD spectra are similar to those of the wild type. With respect to the wild type, the Cys-111-->Ala mutant displays a reduced affinity for pyridoxal 5'-phosphate (PLP), slower kinetics of reconstitution to holoenzyme, a decreased ability to anchor the external aldimine formed between D-Dopa and the bound co-enzyme, and a decreased efficiency of energy transfer between tryptophan residue(s) and reduced PLP. Values of pKa and pKb for the groups involved in catalysis were determined for the wild-type and the C111A mutant enzymes. The mutant showed a decrease in both pK values by about 1 pH unit, resulting in a shift of the pH of the maximum velocity from 7.2 (wild-type) to 6.2 (mutant). This change in maximum velocity is mirrored by a similar shift in the spectrophotometrically determined pK value of the 420-->390 nm transition of the external aldimine. These results demonstrate that the sulfhydryl group of Cys-111 is catalytically nonessential and provide strong support for previous suggestion that this residue is located at or near the PLP binding site (Dominici P, Maras B, Mei G, Borri Voltattorni C. 1991. Eur J Biochem 201:393-397). Moreover, our findings provide evidence that Cys-111 has a structural role in PLP binding and suggest that this residue is required for maintenance of proper active-site conformation.

Overexpression of arginine decarboxylase in transgenic plants

The activity of arginine decarboxylase (ADC), a key enzyme in plant polyamine biosynthesis, was manipulated in two generations of transgenic tobacco plants. Second-generation transgenic plants overexpressing an oat ADC cDNA contained high levels of oat ADC transcript relative to tobacco ADC, possessed elevated ADC enzyme activity and accumulated 10-20-fold more agmatine, the direct product of ADC. In the presence of high levels of the precursor agmatine, no increase in the levels of the polyamines putrescine, spermidine and spermine was detected in the transgenic plants. Similarly, the activities of ornithine decarboxylase and S-adenosylmethionine decarboxylase were unchanged. No diversion of polyamine metabolism into the hydroxycinnamic acid-polyamine conjugate pool or into the tobacco alkaloid nicotine was detected. Activity of the catabolic enzyme diamine oxidase was the same in transgenic and control plants. The elevated ADC activity and agmatine production were subjected to a metabolic/physical block preventing increased, i.e. deregulated, polyamine accumulation. Overaccumulation of agmatine in the transgenic plants did not affect morphological development.

The Escherichia coli ldcC gene encodes another lysine decarboxylase, probably a constitutive enzyme

A gene (designated ldcC) mapped at 4.6 min on the Escherichia coli chromosome codes for a protein of 713 amino acids (aa) that shows strong similarities in both size and amino-acid sequence (69% identical residues and 85% conserved residues) to lysine decarboxylase (LDC) from E. coli (CadA, acid-inducible LDC, 715 aa) or from Hafnia alvei (739 aa). A pUC18 derivative carrying the ldcC gene conferred high LDC activities on an E. coli strain devoid of the functional cadA gene, even when the bacteria were grown under non-inducing conditions at physiological pH. Thus, the gene encodes another lysine decarboxylase, probably a constitutively expressed enzyme, the presence of which was suggested from the previous observations that low LDC activities were detectable in cadA- mutant and non-induced wild-type cells.

Monoclonal antibodies against Nalpha-(5'-phosphopyridoxyl)-L-lysine. Screening and spectrum of pyridoxal 5'-phosphate-dependent activities toward amino acids

Cofactors may be expected to expand the range of reactions amenable to antibody-assisted catalysis. The biological importance of pyridoxal 5'-phosphate (PLP) as enzymic cofactor in amino acid metabolism and its catalytic versatility make it an attractive candidate for the generation of cofactor-dependent abzymes. Here we report an efficient procedure to screen antibodies for PLP-dependent catalytic activity and detail the spectrum of catalytic activities found in monoclonal antibodies elicited against Nalpha-(5'-phosphopyridoxyl)-L-lysine. This hapten is a nonplanar analog of the planar, resonance-stabilized coenzyme-substrate adducts formed in the PLP-dependent reactions of amino acids. The hapten-binding antibodies were screened for binding of the planar Schiff base formed from PLP and D- or L-norleucine by competition enzyme-linked immunosorbent assay. The Schiff base (external aldimine) is an obligatory intermediate in all PLP-dependent reactions of amino acids. This simple, yet highly discriminating screening step eliminated most of the total 24 hapten-binding antibodies. Three positive clones bound the Schiff base with L-norleucine, two preferred that with the D-enantiomer. The positive clones were assayed for catalysis of Schiff base formation and of the alpha,beta-elimination reaction with the D- and L-enantiomers of beta-chloroalanine. Three antibodies were found to accelerate aldimine formation, and two of these catalyzed the PLP-dependent alpha,beta-elimination reaction. One of the alpha, beta-elimination-positive antibodies catalyzed the transamination reaction with hydrophobic D-amino acids and oxoacids (Gramatikova, S. I., and Christen, P. (1996) J. Biol. Chem. 271, 30583-30586). All catalytically active antibodies displayed continuous turnover. No PLP-dependent reactions other than aldimine formation, alpha, beta-elimination of beta-chloroalanine and transamination were detected. The successive screening steps plausibly simulate the functional selection pressures having been operative in the molecular evolution of primordial PLP-dependent protein catalysts to reaction- and substrate-specific enzymes.

Experimental evidence for structure-activity features in common between mammalian histidine decarboxylase and ornithine decarboxylase

Common protein motifs between histidine decarboxylase (HDC) and ornithine decarboxylase (ODC) were detected by computational analysis. Mutants were generated and expressed in vitro. In both enzymes, terminal PEST-region-containing fragments are not essential for decarboxylation (PEST regions are sequence fragments enriched in proline, glutamic acid, serine and threonine residues in a hydrophilic fragment flanked by cationic amino acids). The substitution of a very well conserved histidine residue by alanine causes a severalfold increase of the apparent K(m) values for the respective substrates.

Stereochemical constraint in the evolution of pyridoxal-5'-phosphate-dependent enzymes. A hypothesis

In the transamination reactions undergone by pyridoxal-5'-phosphate-dependent enzymes that act on L-amino acids, the C4' atom of the cofactor is without exception protonated from the si side. This invariant absolute stereochemistry of enzymes not all of which are evolutionarily related to each other and the inverse stereochemistry in the case of D-alanine aminotransferase might reflect a stereochemical constraint in the evolution of these enzymes rather than an accidental historical trait passed on from a common ancestor enzyme. Conceivably, the coenzyme and substrate binding sites of primordial pyridoxal-5'-phosphate-dependent enzymes had to fulfil the following prerequisites in order to allow their development toward effective catalysts: (i) the negatively charged alpha-carboxylate group of the amino acid substrate had to be positioned as far as possible away from the negatively charged phosphate group of the cofactor, and (ii) the C alpha-H bond had to be oriented toward the protein. Compliance with these two criteria implies, under the assumption that C4' is protonated by an acid-base group of the protein, the observed stereochemical feature.

Molecular cloning and functional identification of a plant ornithine decarboxylase cDNA

A cDNA for a plant ornithine decarboxylase (ODC), a key enzyme in putrescine and polyamine biosynthesis, has been isolated from root cultures of the solanaceous plant Datura stramonium. Reverse transcription-PCR employing degenerate oligonucleotide primers representing conserved motifs from other eukaryotic ODCs was used to isolate the cDNA. The longest open reading frame potentially encodes a peptide of 431 amino acids and exhibits similarity to other eukaryotic ODCs, prokaryotic and eukaryotic arginine decarboxylases (ADCs), prokaryotic meso-diaminopimelate decarboxylases and the product of the tabA gene of Pseudomonas syringae cv. tabaci. Residues involved at the active site of the mouse ODC are conserved in the plant enzyme. The plant ODC does not possess the C-terminal extension found in the mammalian enzyme, implicated in rapid turnover of the protein, suggesting that the plant ODC may have a longer half-life. Expression of the plant ODC in Escherichia coli and demonstration of ODC activity confirmed that the cDNA encodes an active ODC enzyme. This is the first description of the primary structure of a eukaryotic ODC isolated from an organism where the alternative ADC routine to putrescine is present.

Crystallization of a mammalian ornithine decarboxylase

Crystals of truncated (delta425-461) pyridoxal-5'-phosphate (PLP)-dependent mouse ornithine decarboxylase (mOrnDC') have been obtained that diffract to 2.2 angstroms resolution (P2(1)2(1)2, a = 119.5 angstroms, b = 74.3 angstroms, c = 46.1 angstroms). OrnDC produces putrescine, which is the precursor for the synthesis of polyamines in eukaryotes. Regulation of activity and understanding of the mechanism of action of this enzyme may aid in the development of compounds against cancer. mOrnDC is a member of group IV PLP-dependent decarboxylases, for which there are no known representative structures.

Comparative studies of human recombinant 74- and 54-kDa L-histidine decarboxylases

We have expressed and characterized human recombinant 74-kDa (rHDC74) and 54-kDa (rHDC54) L-histidine decarboxylases (HDCs) in Sf9 cells. By immunoblot analysis, rHDC74 and rHDC54 were shown to be localized predominantly in the particulate and soluble fractions, respectively. rHDC74 exhibited histamine-synthesizing activity equivalent to that of rHDC54. The existence of 74- and 54-kDa HDCs was also confirmed in the particulate and supernatant fractions of the cell lysate, respectively, from the human basophilic leukemia cell line KU-812-F. The ratio of HDC activity to immunoreactivity was similar for the two forms of the enzyme. The specific activity of purified rHDC54 (1.12 mumol/mg/min) was comparable to those of HDCs from other mammalian tissues or cells. The purified rHDC54 was eluted as a monomer form from a Superdex-200 column; the molecular mass of the enzyme was approximately 54 kDa on SDS-polyacrylamide gel electrophoresis without 2-mercaptoethanol. The HDC activity of rHDC54 significantly decreased on dialysis against buffer without pyridoxal 5'-phosphate; addition of pyridoxal 5'-phosphate to the dialysate readily increased in the enzyme activity to the original activity. Taken together, these results suggest that human HDC functions as both 74- and 54-kDa forms having equivalent HDC activity, which are localized in the particulate and soluble fractions, respectively, and that the latter form exhibits its activity as a monomer form.

Modeling of the spatial structure of eukaryotic ornithine decarboxylases

We used sequence and structural comparisons to determine the fold for eukaryotic ornithine decarboxylase, which we found is related to alanine racemase. These enzymes have no detectable sequence identity with any protein of known structure, including three pyridoxal phosphate-utilizing enzymes. Our studies suggest that the N-terminal domain of ornithine decarboxylase folds into a beta/alpha-barrel. Through the analysis of known barrel structures we developed a topographic model of the pyridoxal phosphate-binding domain of ornithine decarboxylase, which predicts that the Schiff base lysine and a conserved glycine-rich sequence both map to the C-termini of the beta-strands. Other residues in this domain that are likely to have essential roles in catalysis, substrate, and cofactor binding were also identified, suggesting that this model will be a suitable guide to mutagenic analysis of the enzyme mechanism.

Acidic residues important for substrate binding and cofactor reactivity in eukaryotic ornithine decarboxylase identified by alanine scanning mutagenesis

Ornithine decarboxylases from Trypanosoma brucei, mouse, and Leishmania donovani share strict specificity for three basic amino acids, ornithine, lysine, and arginine. To identify residues involved in this substrate specificity and/or in the reaction chemistry, six conserved acidic resides (Asp-88, Glu-94, Asp-233, Glu-274, Asp-361, and Asp-364) were mutated to alanine in the T. brucei enzyme. Each mutation causes a substantial loss in enzyme efficiency. Most notably, mutation of Asp-361 increases the Km for ornithine by 2000-fold, with little effect on kcat, suggesting that this residue is an important substrate binding determinant. Mutation of the only strictly conserved acidic residue, Glu-274, decreases kcat 50-fold; however, substitution of N-methylpyridoxal-5'-phosphate for pyridoxal-5'-phosphate as the cofactor in the reaction restores the kcat of E274A to wild-type levels. These data demonstrate that Glu-274 interacts with the protonated pyridine nitrogen of the cofactor to enhance the electron withdrawing capability of the ring, analogous to Asp-222 in aspartate aminotransferase (Onuffer, J. J., and Kirsch, J. F. (1994) Protein Eng. 7, 413-424). Eukaryotic ornithine decarboxylase is a homodimer with two shared active sites. Residues 88, 94, 233, and 274 are contributed to each active site from the same subunit as Lys-69, while residues 361 and 364 are part of the Cys-360 subunit.

Structural motifs for pyridoxal-5'-phosphate binding in decarboxylases: an analysis based on the crystal structure of the Lactobacillus 30a ornithine decarboxylase

Two of the five domains in the structure of the ornithine decarboxylase (OrnDC) from Lactobacillus 30a share similar structural folds around the pyridoxal-5'-phosphate (PLP)-binding pocket with the aspartate aminotransferases (AspATs). Sequence comparisons focusing on conserved residues of the aligned structures reveal that this structural motif is also present in a number of other PLP-dependent enzymes including the histidine, dopa, tryptophan, glutamate, and glycine decarboxylases as well as tryptophanase and serine-hydroxymethyl transferase. However, this motif is not present in eukaryotic OrnDCs, the diaminopimelate decarboxylases, nor the Escherichia coli or oat arginine decarboxylases. The identification and comparison of residues involved in defining the different classes are discussed.

Sequence of ornithine decarboxylase from Lactobacillus sp. strain 30a

A gene encoding biodegradative ornithine decarboxylase from Lactobacillus sp. strain 30a was isolated from a genomic DNA library and sequenced. Primer extension analysis revealed two transcription initiation sites. The deduced amino acid sequence is compared with the amino acid sequences of five previously reported bacterial decarboxylases, and conserved pyridoxal phosphate motif residues are identified.