Defining Sequence Space and Reaction Products within the Cyanuric Acid Hydrolase (AtzD)/Barbiturase Protein Family

• Published in: Journal of Bacteriology 2012-09, Vol.194 (17), p.4579-4588
• Main Authors: Seffernick, Jennifer L, Erickson, Jasmine S, Cameron, Stephan M, Cho, Seunghee, Dodge, Anthony G, Richman, Jack E, Sadowsky, Michael J, Wackett, Lawrence P
• Format: Article
• Language: English
• Subjects: Amidohydrolases - chemistry; Amidohydrolases - genetics; Amidohydrolases - metabolism; Amino Acid Sequence; atrazine; Azorhizobium caulinodans - enzymology; Bacteria; Bacteria - enzymology; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Bacteriology; Bioinformatics; Biological and medical sciences; biuret; Biuret - metabolism; Bradyrhizobium - enzymology; carbon dioxide; Cloning; enzymatic reactions; Fundamental and applied biological sciences. Psychology; genome; hydrolases; Mass spectrometry; melamine; metals; Microbiology; Miscellaneous; molecular cloning; Molecular Sequence Data; Moorella - enzymology; NMR; Nuclear magnetic resonance; nuclear magnetic resonance spectroscopy; Phylogeny; Proteins; Rhizobium leguminosarum - enzymology; Sequence Alignment; Sequence Analysis, Protein; Substrate Specificity; Triazines - metabolism; X-radiation
• ISSN: 0021-9193; 1098-5530; 1067-8832
• DOI: 10.1128/JB.00791-12

Cyanuric acid hydrolases (AtzD) and barbiturases are homologous, found almost exclusively in bacteria, and comprise a rare protein family with no discernible linkage to other protein families or an X-ray structural class. There has been confusion in the literature and in genome projects regarding the reaction products, the assignment of individual sequences as either cyanuric acid hydrolases or barbiturases, and spurious connection of this family to another protein family. The present study has addressed those issues. First, the published enzyme reaction products of cyanuric acid hydrolase are incorrectly identified as biuret and carbon dioxide. The current study employed 13C nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry to show that cyanuric acid hydrolase releases carboxybiuret, which spontaneously decarboxylates to biuret. This is significant because it revealed that homologous cyanuric acid hydrolases and barbiturases catalyze completely analogous reactions. Second, enzymes that had been annotated incorrectly in genome projects have been reassigned here by bioinformatics, gene cloning, and protein characterization studies. Third, the AtzD/barbiturase family has previously been suggested to consist of members of the amidohydrolase superfamily, a large class of metallohydrolases. Bioinformatics and the lack of bound metals both argue against a connection to the amidohydrolase superfamily. Lastly, steady-state kinetic measurements and observations of protein stability suggested that the AtzD/barbiturase family might be an undistinguished protein family that has undergone some resurgence with the recent introduction of industrial s-triazine compounds such as atrazine and melamine into the environment.