Crystal Structure of Riboflavin Synthase Der-Ing Liao, Zdzislaw Wawrzak, Joseph C. Calabrese, Paul V. Viitanen, Douglas B. Jordan  Structure  Volume 9, Issue 5, Pages 399-408 (May 2001) DOI: 10.1016/S0969-2126(01)00600-1

Figure 1 Reaction Catalyzed by Riboflavin Synthase, RS R, ribityl; Nu, nucleophile. Detailed reaction schemes are proposed [2–6, 8–11] Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 2 Stereo View of the Final 2Fo-Fc Electron Density Map of Riboflavin Synthase The region of the interface between monomers A and C is contoured at 1 σ. Molecule A is depicted as a stick model colored in red, and molecule C is depicted as a stick model colored in gray Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 3 The Riboflavin Synthase Monomer (a) Stereo view of the Cα trace of RS. Every tenth residue is labeled. (b) Connectivity of the β strands of the two β barrels. The N and C barrels have the same topologies. The rmsd of Cα atoms between the two barrels is 1.1 Å for the 78 residues used for the structural alignment. (c) The two β barrels of the RS monomer. The N barrel is colored in yellow, and the C barrel is colored in red. (d) Alignment of the N-terminal and C-terminal halves of RS. Identical residues are connected by lines. Residues conserved among 15 species are in bold (see Supplementary Material for the alignment of RS from the 15 species). The locations of secondary structure elements are indicated Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 3 The Riboflavin Synthase Monomer (a) Stereo view of the Cα trace of RS. Every tenth residue is labeled. (b) Connectivity of the β strands of the two β barrels. The N and C barrels have the same topologies. The rmsd of Cα atoms between the two barrels is 1.1 Å for the 78 residues used for the structural alignment. (c) The two β barrels of the RS monomer. The N barrel is colored in yellow, and the C barrel is colored in red. (d) Alignment of the N-terminal and C-terminal halves of RS. Identical residues are connected by lines. Residues conserved among 15 species are in bold (see Supplementary Material for the alignment of RS from the 15 species). The locations of secondary structure elements are indicated Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 3 The Riboflavin Synthase Monomer (a) Stereo view of the Cα trace of RS. Every tenth residue is labeled. (b) Connectivity of the β strands of the two β barrels. The N and C barrels have the same topologies. The rmsd of Cα atoms between the two barrels is 1.1 Å for the 78 residues used for the structural alignment. (c) The two β barrels of the RS monomer. The N barrel is colored in yellow, and the C barrel is colored in red. (d) Alignment of the N-terminal and C-terminal halves of RS. Identical residues are connected by lines. Residues conserved among 15 species are in bold (see Supplementary Material for the alignment of RS from the 15 species). The locations of secondary structure elements are indicated Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 3 The Riboflavin Synthase Monomer (a) Stereo view of the Cα trace of RS. Every tenth residue is labeled. (b) Connectivity of the β strands of the two β barrels. The N and C barrels have the same topologies. The rmsd of Cα atoms between the two barrels is 1.1 Å for the 78 residues used for the structural alignment. (c) The two β barrels of the RS monomer. The N barrel is colored in yellow, and the C barrel is colored in red. (d) Alignment of the N-terminal and C-terminal halves of RS. Identical residues are connected by lines. Residues conserved among 15 species are in bold (see Supplementary Material for the alignment of RS from the 15 species). The locations of secondary structure elements are indicated Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 4 The Riboflavin Synthase Trimer (a) A ribbon drawing of the trimer. The N barrel is colored in yellow, and the C barrel is colored in red. The C-terminal helix is colored in cyan for molecule A, gray for molecule B, and brown for molecule C. The residues next to the undefined regions are labeled. (b) Contacts among the three C-terminal α helices of the RS trimer. The color codes are the same as in Figure 4a. Several hydrophobic interactions and one salt bridge are shown including residues: molecule A (Val191, Val195, Glu196, and Leu199), molecule B (Val195, Val198, and Leu199), and molecule C (Val191, Val192, Val195, Arg197, and Leu199). (c) An overlay of the three monomers of the RS trimer. Only the N barrels from the monomers are used for the structure alignment. Molecule A is colored in yellow, molecule B is colored in cyan, and molecule C is colored in magenta. Small degrees of domain variation among the monomers are evident. The two monomers that share a tight intermolecular interface (molecules A and C) have a smaller rmsd for Cα atoms (0.88 Å) between them than do molecules A and B (1.43 Å) or molecules B and C (1.08 Å). The degrees of similarity also vary for the individual folding domains between the monomers. Separate alignments of the N barrel, C barrel, and the C-terminal helix give rmsd for the Cα atoms of 0.69 Å, 0.61 Å, and 0.63 Å, respectively, for the residues used in the alignments of molecules A and C. For molecules A and B, the respective values are 0.86 Å, 0.78 Å, and 0.67 Å; and for molecules B and C, the respective values are 0.95 Å, 0.51 Å, and 0.65 Å Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 4 The Riboflavin Synthase Trimer (a) A ribbon drawing of the trimer. The N barrel is colored in yellow, and the C barrel is colored in red. The C-terminal helix is colored in cyan for molecule A, gray for molecule B, and brown for molecule C. The residues next to the undefined regions are labeled. (b) Contacts among the three C-terminal α helices of the RS trimer. The color codes are the same as in Figure 4a. Several hydrophobic interactions and one salt bridge are shown including residues: molecule A (Val191, Val195, Glu196, and Leu199), molecule B (Val195, Val198, and Leu199), and molecule C (Val191, Val192, Val195, Arg197, and Leu199). (c) An overlay of the three monomers of the RS trimer. Only the N barrels from the monomers are used for the structure alignment. Molecule A is colored in yellow, molecule B is colored in cyan, and molecule C is colored in magenta. Small degrees of domain variation among the monomers are evident. The two monomers that share a tight intermolecular interface (molecules A and C) have a smaller rmsd for Cα atoms (0.88 Å) between them than do molecules A and B (1.43 Å) or molecules B and C (1.08 Å). The degrees of similarity also vary for the individual folding domains between the monomers. Separate alignments of the N barrel, C barrel, and the C-terminal helix give rmsd for the Cα atoms of 0.69 Å, 0.61 Å, and 0.63 Å, respectively, for the residues used in the alignments of molecules A and C. For molecules A and B, the respective values are 0.86 Å, 0.78 Å, and 0.67 Å; and for molecules B and C, the respective values are 0.95 Å, 0.51 Å, and 0.65 Å Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 4 The Riboflavin Synthase Trimer (a) A ribbon drawing of the trimer. The N barrel is colored in yellow, and the C barrel is colored in red. The C-terminal helix is colored in cyan for molecule A, gray for molecule B, and brown for molecule C. The residues next to the undefined regions are labeled. (b) Contacts among the three C-terminal α helices of the RS trimer. The color codes are the same as in Figure 4a. Several hydrophobic interactions and one salt bridge are shown including residues: molecule A (Val191, Val195, Glu196, and Leu199), molecule B (Val195, Val198, and Leu199), and molecule C (Val191, Val192, Val195, Arg197, and Leu199). (c) An overlay of the three monomers of the RS trimer. Only the N barrels from the monomers are used for the structure alignment. Molecule A is colored in yellow, molecule B is colored in cyan, and molecule C is colored in magenta. Small degrees of domain variation among the monomers are evident. The two monomers that share a tight intermolecular interface (molecules A and C) have a smaller rmsd for Cα atoms (0.88 Å) between them than do molecules A and B (1.43 Å) or molecules B and C (1.08 Å). The degrees of similarity also vary for the individual folding domains between the monomers. Separate alignments of the N barrel, C barrel, and the C-terminal helix give rmsd for the Cα atoms of 0.69 Å, 0.61 Å, and 0.63 Å, respectively, for the residues used in the alignments of molecules A and C. For molecules A and B, the respective values are 0.86 Å, 0.78 Å, and 0.67 Å; and for molecules B and C, the respective values are 0.95 Å, 0.51 Å, and 0.65 Å Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 5 The Positions of the Residues of Riboflavin Synthase Conserved among Species (a) A ribbon drawing of molecules A and C. The N barrels are colored in yellow, and the C barrels are colored in red. The C-terminal helix is colored in cyan for molecule A and brown for molecule C. The conserved glycines are highlighted in gray. The conserved, nonglycine residues in molecule A are highlighted in blue, and those in molecule C are highlighted in magenta. (b) A close-up view of the conserved residues in the interface between molecules A and C. The Cα trace of molecule A is colored in cyan and is colored in brown for molecule C Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 5 The Positions of the Residues of Riboflavin Synthase Conserved among Species (a) A ribbon drawing of molecules A and C. The N barrels are colored in yellow, and the C barrels are colored in red. The C-terminal helix is colored in cyan for molecule A and brown for molecule C. The conserved glycines are highlighted in gray. The conserved, nonglycine residues in molecule A are highlighted in blue, and those in molecule C are highlighted in magenta. (b) A close-up view of the conserved residues in the interface between molecules A and C. The Cα trace of molecule A is colored in cyan and is colored in brown for molecule C Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 6 Modeling the Active Sites of Riboflavin Synthase from the Structure of the β Barrel of Phthalate Dioxygenase Reductase, 2PIA (a) An overlay of the β barrel of phthalate dioxygenase reductase (in blue) with the N barrel of RS (molecule A, colored in red). (b) The positions of FMN molecules extracted from the β barrel of phthalate dioxygenase reductase and overlaid onto the structure of RS (molecules A and C). Colors of RS are the same as in Figure 5a. (c) Close-up of the closed active site of RS occupied by DMRL molecules (modeled from the FMN placements) at the interface of molecules A and C. Protein residues with 3.5 Å of the DMRL molecules are shown. The bonds of molecule A are colored in cyan, those of molecule C are colored in brown, and those of DMRL are colored in yellow. Atoms are colored by atom type Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 6 Modeling the Active Sites of Riboflavin Synthase from the Structure of the β Barrel of Phthalate Dioxygenase Reductase, 2PIA (a) An overlay of the β barrel of phthalate dioxygenase reductase (in blue) with the N barrel of RS (molecule A, colored in red). (b) The positions of FMN molecules extracted from the β barrel of phthalate dioxygenase reductase and overlaid onto the structure of RS (molecules A and C). Colors of RS are the same as in Figure 5a. (c) Close-up of the closed active site of RS occupied by DMRL molecules (modeled from the FMN placements) at the interface of molecules A and C. Protein residues with 3.5 Å of the DMRL molecules are shown. The bonds of molecule A are colored in cyan, those of molecule C are colored in brown, and those of DMRL are colored in yellow. Atoms are colored by atom type Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)

Figure 6 Modeling the Active Sites of Riboflavin Synthase from the Structure of the β Barrel of Phthalate Dioxygenase Reductase, 2PIA (a) An overlay of the β barrel of phthalate dioxygenase reductase (in blue) with the N barrel of RS (molecule A, colored in red). (b) The positions of FMN molecules extracted from the β barrel of phthalate dioxygenase reductase and overlaid onto the structure of RS (molecules A and C). Colors of RS are the same as in Figure 5a. (c) Close-up of the closed active site of RS occupied by DMRL molecules (modeled from the FMN placements) at the interface of molecules A and C. Protein residues with 3.5 Å of the DMRL molecules are shown. The bonds of molecule A are colored in cyan, those of molecule C are colored in brown, and those of DMRL are colored in yellow. Atoms are colored by atom type Structure 2001 9, 399-408DOI: (10.1016/S0969-2126(01)00600-1)