Background Pediococcus ssp. are lactic acid bacteria that frequently occur in fermented foods and beverages. In cheese, their role on ripening and flavor development is not well understood. The species Pediococcus acidilactici is of special interest because it degrades threonine and serine and concomitantly forms alanine and α-aminobutyrate. We assume that pyridoxal phosphate (PLP) dependent enzymes are involved in the metabolism of these amino acids. Objectives Identification of PLP-dependent enzymes from P. acidilactici strain FAM18098 that are involved in threonine and serine catabolism. Methods The whole genome of P.acidilactici strain FAM18098 was sequenced using long-read sequencing technology. The assembled and annotated genome was searched for genes encoding PLP-dependent enzymes. Genes of interest were cloned and heterologously expressed in Escherichia coli. The purified proteins were characterized using photometric assays, which detected aminotransferase- and cystathionine lyase activity. Additionally, HPLC analysis was performed to detect and identify the release of organic acids. Results Two genes encoding enzymes with PLP-dependent type-I domains were cloned from P. acidilactici FAM18098. One of the recombinant proteins catalyzed the transamination of methionine, branched chain-amino acids, phenylalanine, and α-aminobutyrate using α-ketoglutarate as cosubstrate. The pH optimum of this reaction was at 7.4. The other recombinant protein was found to be a cystathionine β-lyase that degraded L-cystathionine to L-homocysteine and pyruvate. The pH optimum of this reaction was at 9.2. Both enzymes showed low activity at pH 5.5 , a pH which is usually present in cheese.