Identification and characterization of novel broad-spectrum amino acid racemases from Escherichia coli and Bacillus subtilis

• Published in: Amino acids 2017-11, Vol.49 (11), p.1885-1894
• Main Authors: Miyamoto, Tetsuya, Katane, Masumi, Saitoh, Yasuaki, Sekine, Masae, Homma, Hiroshi
• Format: Article
• Language: English
• Subjects: Alanine; Amino Acid Isomerases - analysis; Amino Acid Isomerases - chemistry; Amino Acid Isomerases - isolation & purification; Amino Acid Isomerases - metabolism; Amino acids; Amino Acids - chemistry; Amino Acids - metabolism; Analytical Chemistry; Arginine; Bacillus subtilis; Bacillus subtilis - enzymology; Bacteria; Bacterial Proteins - analysis; Bacterial Proteins - chemistry; Bacterial Proteins - isolation & purification; Bacterial Proteins - metabolism; Biochemical Engineering; Biochemistry; Biofilms; Biomedical and Life Sciences; Catalysis; Catalytic activity; Catalytic Domain; Cell walls; D-Alanine; D-Amino acids; Dismantling; E coli; Environmental changes; Escherichia coli; Escherichia coli - enzymology; Glutamic acid; Isomerism; Kinetics; Life Sciences; Lysine; Models, Molecular; Neurobiology; Original Article; Ornithine; Peptidoglycans; Protein Conformation; Protein Structure, Quaternary; Proteomics; Racemization; Substrate Specificity
• ISSN: 0939-4451; 1438-2199
• DOI: 10.1007/s00726-017-2486-2

The peptidoglycan layer of the bacterial cell wall typically contains d -alanine ( d -Ala) and d -glutamic acid ( d -Glu), and also various non-canonical d -amino acids that have been linked to peptidoglycan remodeling, inhibition of biofilm formation, and triggering of biofilm disassembly. Bacteria produce d -amino acids when adapting to environmental changes as a common survival strategy. In our previous study, we detected non-canonical d -amino acids in Escherichia coli grown in minimal medium. However, the biosynthetic pathways of non-canonical d -amino acids remain poorly understood. In the present study, we identified amino acid racemases in E. coli MG1655 (YgeA) and Bacillus subtilis (RacX) that produce non-canonical d -amino acids other than d -Ala and d -Glu. We characterized their enzymatic properties, and both displayed broad substrate specificity but low catalytic activity. YgeA preferentially catalyzes the racemization of homoserine, while RacX preferentially racemizes arginine, lysine, and ornithine. RacX is dimeric, and appears not to require pyridoxal 5′-phosphate (PLP) as a coenzyme as is the case with YgeA. To our knowledge, this is the first report on PLP-independent amino acid racemases possessing broad substrate specificity in E. coli and B. subtilis .