Predicted distribution of NAD domain among glycolytic enzymes

Abstract

X-RAY crystallographic studies have indicated that four dehydrogenases^1–4, including lactate¹ and glyceraldehyde phosphate⁴ dehydrogenase, contain a central parallel β sheet consisting of six strands flanked by four α helices. This super-secondary structure⁵ is called the dinucleotide fold or nicotinamide adenine dinucleotide (NAD) domain since it forms an NAD-binding site at the C terminus of the β sheet. The dinucleotide fold can be considered as two roughly identical mononucleotide domains each containing about 60 residues arranged in an alternating βαβαβ sequence and related by an approximate twofold axis⁵. The aromatic specificity site of subtilisin^6,7 and the flavin-binding site of flavodoxin^8,9 seem⁵ to be formed by a secondary structure very similar to a mononucleotide domain of the dehydrogenases. Crystallographic studies have shown that the structures of phosphoglycerate kinase^10,11, hexokinase¹², adenylate kinase¹³, phosphoglycerate mutase¹⁴ and triosephosphate isomerase¹⁵ also contain β sheets containing at least five strands flanked by at least three α helices. The nucleoside phosphate or, in the case of the mutase and isomerase, the sugar phosphate-binding site for each of these enzymes is either known^10–12, or strongly suspected^13–15 to be located at the C terminus of the β sheet. Differences occur, however, in some of these supersecondary structures relative to the NAD domain of the dehydrogenase family as regards the direction of the β strands¹², the location of the binding site relative to the plane of the β sheet¹², and most significantly, the sequential order or connectivity of the individual strands in the β sheet^12–14. Whether these related supersecondary structures represent convergent^5,12 or divergent evolutionary processes^4,16, or both¹⁷, is a topic of active debate.