Stereochemistry of proton abstraction catalyzed by lysine and ornithine omega-aminotransferases

Comparative genomic analysis of hyper-ammonia producing Acetoanaerobium sticklandii DSM 519 with purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630

Acetoanaerobium sticklandii DSM519 (CST) is a hype-ammonia producing non-pathogenic anaerobe that can use amino acids as important carbon and energy sources through the Stickland reactions. Biochemical aspects of this organism have been extensively studied, but systematic studies addressing its metabolic discrepancy remain scant. In this perspective, we have intensively analyzed its genomic and metabolic characteristics to comprehend the evolutionary conservation of amino acid catabolism by a comparative genomic approach. The whole-genome data indicated that CST has shown a phylogenomic similarity with hyper-ammonia producing, purinolytic, and proteolytic pathogenic Clostridia. CST has shown to common genomic context sharing across the purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630. Genome syntenic analysis described that syntenic orthologs might be originated from the recent ancestor at a slow evolution rate and syntenic-out paralogs evolved from either CDF or CAC via α-event and β-event. Collinearity of either gene orders or gene families was adjusted with syntenic out-paralogs across these genomes. The genome-wide metabolic analysis predicted 11 unique putative metabolic subsystems from the CST genome for amino acid catabolism and hydrogen production. The in silico analysis of our study revealed that a characteristic system for amino acid catabolism-directed biofuel synthesis might have slowly evolved and established as a core genomic content of CST.

Kenji Soda--researching enzymes with the spirit of an alpinist

Like an alpinist continuously seeking virgin peaks to climb, Kenji Soda has investigated a variety of unique enzymes for which there was little or no information available; and by doing so he opened up a variety of new fields in enzyme science and technology. In particular, he has promoted the study of enzymes requiring vitamin B-derived cofactors such as FAD, NAD(P) and pyridoxal 5'-phosphate, shedding light on their reaction mechanisms, enzymological properties, crystal structures and potential practical applications. Highlighted in this review are the studies of enzymes acting on d-amino acids and sulphur/selenium-containing amino acids and those from thermophilic and psychrophilic bacteria.

Lysine is catabolized to 2-aminoadipic acid in Penicillium chrysogenum by an omega-aminotransferase and to saccharopine by a lysine 2-ketoglutarate reductase. Characterization of the omega-aminotransferase

The biosynthesis and catabolism of lysine in Penicillium chrysogenum is of great interest because these pathways provide 2-aminoadipic acid, a precursor of the tripeptide delta-L-2-aminoadipyl-L-cysteinyl-D-valine that is an intermediate in penicillin biosynthesis. In vivo conversion of labelled L-lysine into two different intermediates was demonstrated by HPLC analysis of the intracellular amino acid pool. L-lysine is catabolized to 2-aminoadipic acid by an omega-aminotransferase and to saccharopine by a lysine-2-ketoglutarate reductase. In lysine-containing medium both activities were expressed at high levels, but the omega-aminotransferase activity, in particular, decreased sharply when ammonium was used as the nitrogen source. The omega-aminotransferase was partially purified, and found to accept L-lysine, L-ornithine and, to a lesser extent, N-acetyl-L-lysine as amino-group donors. 2-Ketoglutarate, 2-ketoadipate and, to a lesser extent, pyruvate served as amino group acceptors. This pattern suggests that this enzyme, previously designated as a lysine-6-aminotransferase, is actually an omega-aminotransferase. When 2-ketoadipate is used as substrate, the reaction product is 2-aminoadipic acid, which contributes to the pool of this intermediate available for penicillin biosynthesis. The N-terminal end of the purified 45-kDa omega-aminotransferase was sequenced and was found to be similar to the corresponding segment of the OAT1 protein of Emericella (Aspergillus) nidulans. This information was used to clone the gene encoding this enzyme.

Crystal structure of human ornithine aminotransferase complexed with the highly specific and potent inhibitor 5-fluoromethylornithine

Ornithine aminotransferase (l-ornithine:2-oxoacid delta-aminotransferase; EC 2.6.1.13), a pyridoxal-5'-phosphate-dependent mitochondrial enzyme controls the l-ornithine level in tissues by catalyzing the transfer of the delta-amino group of l-ornithine to 2-oxoglutarate, producing l-glutamate- gamma-semialdehyde and l-glutamate. (2S, 5S)-5-Fluoromethylornithine is the only inhibitor exclusively specific for ornithine aminotransferase known to date. Both in vitro and in vivo, it blocks the enzyme by a suicide reaction leading to a covalent adduct with the cofactor. The crystal structure of the enzyme-inhibitor complex was solved at a resolution of 1.95 A. No significant conformational changes compared with the native enzyme structure were observed. The structure reveals the atomic details of the cofactor-inhibitor adduct and its interactions with the active site of the enzyme. The main residues responsible for specific binding of the inhibitor are Arg180, which forms a strong salt bridge with the alpha-carboxylate and Tyr55, which is involved in a short hydrogen bond with the alpha-amino group. The experimental observation that in the racemic mixture, (2S, 5S)-5-fluoromethylornithine is exclusively responsible for the enzyme inhibition can be explained on the basis of the active site topology. Model building studies strongly suggest that the natural substrate l-ornithine, in its external aldimine adduct with the enzyme, makes use of the same recognition site as the inhibitor. It is proposed that the neutralization of the active site Arg413 by a salt bridge with Glu235 also plays an important role in productive binding of both 5-fluoromethylornithine and l-ornithine. Arg180 and Arg413 are believed to be instrumental in recognition of l-glutamate, by binding its gamma and alpha-carboxylate groups, respectively. This requires a different side-chain conformation of Glu235. Lys292 is the only obvious candidate for catalyzing the rate-limiting proton transfer steps in the transamination reaction.

Stereochemistry of the reaction catalysed by 2-aminoethylphosphonate aminotransferase. A 1H-NMR study

(R)- and (S)-2-amino[2-D1]ethylphosphonic acids ([2-D1]AEP) were synthesised to investigate the stereochemistry of the reaction catalysed by 2-aminoethlphosphonate aminotransferase from Pseudomonas aeruginosa. This enzyme catalyses the transfer of the amino group of AEP to pyruvate to produce 2-phosphonoacetaldehyde and alanine. The enzymic reaction proceeding through the abstraction of a proton from the Schiff-base complex formed between the enzyme-bound pyridoxal 5'-phosphate, and the substrate, was carried out in an aqueous buffer at pH 8.5; it was followed by high-field 1H-NMR measurements (500 MHz, H2O) on an AMX 500 Bruker spectrometer. The spectra, recorded with chiral (R)- or (S)-[2-D1]AEP, both showed the methylenic signal (3.0 ppm), whereas (S)-[2-D1]AEP gave the additional aldehydic signal (CHO, 9.6 ppm). These data clearly show that AEP-aminotransferase catalyses the abstraction of the pro-S hydrogen atom at the prochiral C2 carbon of AEP. Furthermore, careful timing of NMR measurements over a 2-hour period allows us to show the occurrence of an isotopic effect.

A comparison of pyridoxal 5'-phosphate dependent decarboxylase and transaminase enzymes at a molecular level

Pyridoxal 5'-phosphate is a coenzyme for a number of enzymes which catalyse reactions at C alpha of amino acid substrates including transaminases, decarboxylases and serine hydroxymethyltransferase. Using the X-ray coordinates for a transaminase, aspartate aminotransferase, and the results of stereochemical and mechanistic studies for decarboxylases and serine hydroxymethyltransferase, an active-site structure for the decarboxylase group is constructed. The structure of the active-site is further refined through active-site pyridoxyllysine peptide sequence comparison and a 3-D catalytic mechanism for the L-alpha-amino acid decarboxylases is proposed. The chemistry of serine hydroxymethyltransferase is re-examined in the light of the proposed decarboxylase mechanism.

Stereochemistry of the inactivation of 4-aminobutyrate: 2-oxoglutarate aminotransferase and L-glutamate 1-carboxylase by 4-aminohex-5-ynoic acid enantiomers

Incubation of rat brain or bacterial 4-aminobutyrate aminotransferase (EC 2.6.1.19) with both (S)-(+)- and (R)-(-)-enantiomers of 4- aminohex -5- ynoic acid results in a time-dependent irreversible loss of enzymatic activity. Rat brain glutamate decarboxylase (EC 4.1.1.15) is inactivated by the (S)-(+)-enantiomer while the bacterial glutamate decarboxylase is inactivated by the (R)-(-)-enantiomer. In addition, we demonstrate that (R)-(-)-4- aminohex -5- ynoic acid is a selective and effective inhibitor of rat brain 4-aminobutyrate aminotransferase in vivo.