Computational Studies of the Nudix Hydrolase Superfamily and Nitrophenyl Phosphatase Subfamily of the Had Superfamily

The Protein Structure Initiative (PSI) was an effort by consortiums to solve as many unique protein structures as possible; the Protein Data Bank contains a number of enzymes whose structures have been solved, but for which no enzymatic activity has been determined. The Enzyme Function Initiative (EFI) is an effort to determine as many unique enzyme functions as possible. There are a number of putative NUDIX Hydrolase and Haloacid Dehalogenase (HAD) superfamily members whose structures have been solved, but for which no enzymatic activity has been determined. We have catalogued the structurally‐determined enzymes within the NUDIX Hydrolase superfamily and the nitrophenyl phosphatase subfamily of the HAD superfamily using BLAST, Dali, and SCOP. We are now beginning to characterize these enzymes in the biochemistry teaching laboratory. Computational programs, such as ProMOL, aid in annotating uncharacterized enzymes. ProMOL works by aligning the relative spatial arrangement of the catalytic residues of a reference enzyme with query searches. We have used ProMOL to design catalytic motifs for the NUDIX hydrolase superfamily and the nitrophenyl phosphatase subfamily of the HAD superfamily, which then can be used to uncover family members whose structures have been solved. Likewise, we have used the docking program PyRx to predict substrate specificity. Through this process, we have discovered the strengths and limitations of these programs. Bioinformatics tools, including databases and computational programs, are good starting points for determining protein function; however, the only way to definitively determine protein function is through experimentally determining activity. Support or Funding Information NSF DUE‐IUSE 1503811