Figure 5

A non-cyclic permutation. A novel non-cyclic permutation discovered between AML1/Core Binding Factor (AML1/CBF, PDB ID 1e50, Chain F, top) and riboflavin synthase (PDBID 1pkv, chain A, bottom) a) These two proteins superimpose well spatially, with an RMSD of 1.23 Å and an alignment length of 42 residues, with a significant p-value of 2.8 × 10^-4 after Bonferroni correction. Aligned residues are colored blue. b) These proteins are related by multiple permutations. The steps to transform the topology of AML1/CBF (top) to riboflavin (bottom) are as follows: c) Remove the the loops connecting strand 1 to helix 2, strand 4 to strand 5, and strand 5 to helix 6; d) Connect the C-terminal end of strand 4 to the original N-termini; e) Connect the C-terminal end of strand 5 to the N-terminal end of helix 2; f) Connect the original C-termini to the N-terminal end of strand 5. The N-terminal end of strand 6 becomes the new N-termini and the C-terminal end of strand 1 becomes the new C-termini. We now have the topology diagram of riboflavin synthase.