New sequence motifs in flavoproteins: Evidence for common ancestry and tools to predict structure

We describe two new sequence motifs, present in several families of flavoproteins. The “GG motif” (RxGGRxxS/T) is found shortly after the βαβdinucleotide‐binding motif (DBM) in L‐amino acid oxidases, achacin and aplysianin‐A, monoamine oxidases, corticosteroid‐binding proteins, and tryptophan 2‐monooxygenases. Other disperse sequence similarities between these families suggest a common origin. A GG motif is also found in protoporphyrinogen oxidase and carotenoid desaturases and, reduced to the central GG doublet, in the THI4 protein, dTDP‐4‐dehydrorhamnose reductase, soluble fumarate reductase, steroid dehydrogenases, Rab GDP‐dissociation inhibitor, and in most flavoproteins with two dinucleotide‐binding domains (glutathione reductase, glutamate synthase, flavin‐containing monooxygenase, trimethylamine dehydrogenase . . . ). In the latter families, an “ATG motif” (oxhhhATG) is found in both the FAD‐ and NAD(P)H‐binding domains, forming the fourth β‐strand of the Rossman fold and the connecting loop. On the basis of these and previously described motifs, we present a classification of dinucleotide‐binding proteins that could also serve as an evolutionary scheme. Like the DBM, the ATG motif appears to predate the divergence of NAD(P)H‐ and FAD‐binding proteins. We propose that flavoproteins have evolved from a well‐differentiated NAD(P)H‐binding protein. The bulk of the substrate‐binding domain was formed by an insertion after the fourth β‐strand, either of a closely related NAD(P)H‐binding domain or of a domain of completely different origin. Proteins 2000;38:95–114. © 2000 Wiley‐Liss, Inc.