Volume 11, Issue 3, Pages 265-273 (March 2003) Crystal Structure of Human Riboflavin Kinase Reveals a β Barrel Fold and a Novel Active Site Arch  Subramanian Karthikeyan, Qingxian Zhou, Faika Mseeh, Nick V. Grishin, Andrei L. Osterman, Hong Zhang  Structure  Volume 11, Issue 3, Pages 265-273 (March 2003) DOI: 10.1016/S0969-2126(03)00024-8

Figure 1 The Overall Structure of hsRFK (A) Stereo view of ribbon diagram of human riboflavin kinase (hsRFK). Strands are labeled a–f, and α helices are labeled A–D. The two MgATP binding loops are labeled L1 and L2, respectively. The bound ligands MgADP and riboflavin (RBF) are shown as stick models. The Fo − Fc omit map is contoured at 2.0σ and shown for the two ligands. (B) Stereo Cα trace of hsRFK with every tenth residue labeled. The ADP and riboflavin molecules are shown as bonds and Mg2+ ion as a ball. This figure and Figures 2 and 3 are made using Molscript [31]. Structure 2003 11, 265-273DOI: (10.1016/S0969-2126(03)00024-8)

Figure 2 Fold Comparison of Riboflavin Kinase with Two Other β Barrel Flavin Binding Folds The last two helices (helices C and D) in hsRFK are omitted for clarity. The bound ligand(s) in each structure is shown in the ball-and-stick representation. The N and C termini and each β strand are labeled. β strands in ferric reductase are labeled in a circular permutated fashion according to the topology of phthalate dioxygenase reductase N-terminal domain. Structure 2003 11, 265-273DOI: (10.1016/S0969-2126(03)00024-8)

Figure 3 Stereo View of the Substrate Binding and Active Site of hsRFK (A) Stereo view of the MgADP binding site. (B) Stereo view of the riboflavin/FMN binding site. The bound ligands and relevent protein residues are shown in the ball-and-stick representation. The hydrogen bonds and Mg2+ ion coordination are indicated by dashed lines. The two MgATP binding loops are labeled L1 and L2, respectively. Structure 2003 11, 265-273DOI: (10.1016/S0969-2126(03)00024-8)

Figure 4 Multiple Sequence Alignment of Representative Sequences of Riboflavin Kinases Diagram of the secondary structure elements for hsRFK (gi|19923525) are shown at the top. Each sequence is identified by the SWISS-PROT entry name or, in the absence of a SWISS-PROT annotation, by the NCBI gene identification number (gi) followed by abbreviation of the species name. The first and the last residue numbers of the sequences in the alignment are indicated, and the total length of the protein is shown at the end. The number of omitted residues in the alignment is shown in parentheses. The locations of the MgADP binding Loop 1 and Loop 2 are marked. The invariant residues are highlighted in black and are shown in white letters. Uncharged residues in mainly hydrophobic sites are highlighted in yellow. Conserved small residues are highlighted in gray. Residues that are involved in substrate binding are colored red for flavin binding and blue for ADP/ATP binding. Additionally, the letters at the bottom of the alignment also indicate the roles of the residues, with A for ATP/ADP binding, F for flavin binding, and M for Mg2+ binding. The species name abbreviations are as follows: Hs, Homo sapiens; Dm, Drosophila melanogaster; At, Arabidopsis thaliana; Dd, Dictyostelium discoideum; Sc, Saccharomyces cerevisiae; Sp, Schizosaccharomyces pombe; Ce, Caenorhabditis elegans; Hp, Helicobacter pylori; Ssp, Synechocystis sp.; Dr, Deinococcus radiodurans; Ec, Escherichia coli; Aa, Aquifex aeolicus. Structure 2003 11, 265-273DOI: (10.1016/S0969-2126(03)00024-8)