Identification of a novel class in the α/β hydrolase fold superfamily: The N‐myc differentiation‐related proteins

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Abstract
The α/β hydrolases constitute a large protein superfamily that mainly consists of enzymes that catalyze a diverse range of reactions. These proteins exhibit the α/β hydrolase fold, the essential features of which have recently been delineated: the presence of at least five parallel β-strands, a catalytic triad in a specific order (nucleophile-acid-histidine), and a nucleophilic elbow. Because of the difficulties experimentally in identifying protein structures, we have used a Bayesian computational algorithm (PROBE) to identify the members of this superfamily based on distant sequence relationships. We found that the presence of five sequence motifs, which contain residues important for substrate binding and stabilization of the fold, are required for membership in this superfamily. The superfamily consists of at least 909 members, including the N-myc downstream regulated proteins, which are believed to be involved in cell differentiation. Unlike most of the other superfamily members, the N-myc downstream regulated proteins have never been proposed to possess the α/β hydrolase fold and do not appear to be hydrolases. Proteins 2002;47:163–168.
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