Modeling of the spatial structure of eukaryotic ornithine decarboxylases

Abstract

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 fi/a-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 @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.

Identification of a novel amino acid racemase from a hyperthermophilic archaeon Pyrococcus horikoshii OT-3 induced by d-amino acids

“…Like the P. horikoshii BAR, the gene encoding the Ile 2-epimerase was originally annotated as a GABA-AT. The primary structure of Lactobacillus Ile 2-epimerase (450 residues) showed 40, 37, 36 and 44 % homology with those of P. horikoshii BAR (466 residues), PH0782 (474 residues), PH1423 (454 residues) and PH1501 (438 residues), respectively, all of which are classified as fold type I PLP-dependent enzymes (Grishin et al 1995;Mutaguchi et al 2013). These observations prompted us to speculate that the three other GABA-AT homologs may also function as racemases or epimerases.…”

Tryptophan synthase: a mine for enzymologists

“…1) are: (1) the a and b subunits are arranged in an abba linear mode (Fig. 1a) [12]; (2) the a-subunit exhibits a TIM barrel conformation, with the a-active site crystallographically localized by the presence of allosteric ligands; (3) within the superfamily of PLP-dependent enzymes, the b-subunit of TS belongs to fold type II [17], and is composed of two domains, with the active site located at their interface; (4) an intramolecular tunnel connects the a-and b-sites, channeling the product of the a-site, indole, to the b-site [12]; (5) monovalent cations bind to a specific site adjacent to the b-active site [12,18]; (6) a flexible domain of the b-subunit composed of residues bGly102-bGly189, and including b-helix6 (COMM domain), preferentially interacts with the flexible structural elements a-loop2 and a-loop6 of the a-subunit (Fig. 1b) [13,19]; and (7) both the a- (Fig.…”

A subfamily of PLP-dependent enzymes specialized in handling terminal amines

“…However it is essential to note that just a couple of years after the first study by Mehta et al [10], Grishin and coworkers renamed the very same subfamily of enzymes 'class III aminotransferases' [6]. The change arose due to those authors splitting subgroup I (identified by Mehta et al) into two smaller subfamilies.…”

“…Building on this shared mechanistic feature, PLP-dependent enzymes comprise, among others, transaminases, decarboxylases, racemases, aldolases, lyases, and enzymes that catalyze β-or γ-replacement reactions [1][2][3][4][5]. In spite of such functional diversity, all PLP-dependent enzymes structurally characterized to date can be grouped in just seven distinct structural families, or 'fold-types' [6][7][8][9], presumably corresponding to different evolutionary lineages. Of these, the so-called fold-type I is the most populated, functionally and structurally diverse and possibly the most evolutionarily ancient.…”

“…5 Two phylogenetically distinct groups of LAT enzymes have been described, one from Gram-positive [29] and the other from Gram-negative bacteria [31]; one representative sequence per group is given. 6 The listed PUAT enzyme (from Escherichia coli) can transaminate efficiently both putrescine and cadaverine [58], and can be legitimately assigned to two different EC numbers. 7 COA-β-AT is an AT recently discovered based on a bacterial metagenome analysis [93].…”