InterPro domain: IPR026017

The lumazine-binding domain is about 100 residues. In its C-terminal section, this domain contains a conserved motif [KR]-V-N-[LI]-E which has been proposed to be the binding site for lumazine (Lum) and some of its derivatives. Riboflavin synthase alpha chain (RS-alpha), which binds two molecules of Lum, has two perfect copies of this motif, while lumazine protein (LumP), which binds one molecule of Lum, has a Glu instead of Lys/Arg in the first position of the second copy of the motif. Similarly, yellow fluorescent protein (YFP), which binds to one molecule of FMN, also seems to have a potentially dysfunctional binding site by substitution of Gly for Glu in the last position of the first copy of the motif.

The lumazine-binding domain of RS-alpha forms two Greek-key folds with the topology BBHBBBHB, where most of the substrate binding sites are located in beta-strands (B) 4 and 5 and in helix (H) 2 [ 1 , 2 , 3 ].

1. The structure of the N-terminal domain of riboflavin synthase in complex with riboflavin at 2.6A resolution. J. Mol. Biol. 331, 1053-63
2. The solution structure of the N-terminal domain of riboflavin synthase. J. Mol. Biol. 309, 949-60
3. Studies on the reaction mechanism of riboflavin synthase: X-ray crystal structure of a complex with 6-carboxyethyl-7-oxo-8-ribityllumazine. Structure 10, 1371-81