Crystal Structure of 4-Amino-5-Hydroxymethyl-2- Methylpyrimidine Phosphate Kinase from Salmonella typhimurium at 2.3 Å Resolution  Gong Cheng, Eric M Bennett, Tadhg P Begley, Steven E Ealick  Structure  Volume 10, Issue 2, Pages 225-235 (February 2002) DOI: 10.1016/S0969-2126(02)00708-6

Figure 1 The Two Phosphorylation Reactions that are Catalyzed by HMPP Kinase Structure 2002 10, 225-235DOI: (10.1016/S0969-2126(02)00708-6)

Figure 2 The Structure of the HMPP Kinase Monomer (A) Stereoview of a Cα trace colored by residue number and with every tenth residue labeled with a sequence number. Breaks in the backbone are connected with dashed lines. (B) Topology diagram. The α helices are shown as rectangles, and the β strands are shown as arrows. Helices 5 and 10 are 310 helices. The dotted line depicts the disordered loops. Each secondary structural element is labeled in its center with its designator and with its beginning and ending sequence number. The elements common to all members of the ribokinase family are in light blue for α helices and in light green for β strands. (C) A ribbon diagram showing the overall fold (α helices, blue; β strands, green). The figure was prepared with MolScript [35], BobScript [35–37], and Raster3D [38, 39]. Structure 2002 10, 225-235DOI: (10.1016/S0969-2126(02)00708-6)

Figure 3 Ribbon Diagram of HMPP Kinase Dimer Viewed along the 2-Fold Axis The α helices are blue, and the β strands are green. The HMP molecules and sulfate ions are shown as ball and stick models. The HMP and sulfate binding sites and the binding site flap are labeled for each monomer. The closest contact between the two HMP molecules is about 20 Å. Structure 2002 10, 225-235DOI: (10.1016/S0969-2126(02)00708-6)

Figure 4 The Active Site of HMPP Kinase (A) Stereoview of the HMP and sulfate ions with key residues. Atoms are colored coded by atom type (carbon, black; nitrogen, blue; oxygen, red; sulfur, orange). Key hydrogen bonds are indicated by dashed lines. (B) A schematic drawing of the active site. Key hydrogen bonds are indicated by dashed lines. Structure 2002 10, 225-235DOI: (10.1016/S0969-2126(02)00708-6)

Figure 5 Superposition of Ribokinase Family Members Based on 107 Structurally Conserved Cα Positions Conserved elements from all family members are shown using thick lines. Nonconserved secondary structure elements for HMPP kinase are shown by a thin red line, with main chain breaks connected by dashed lines. Conserved secondary structural elements are labeled using HMPP kinase notation; nonconserved elements are not labeled. Colors: HMPP kinase, red; T. gondii AK, green; glucokinase, blue; human AK, aqua; ribokinase, purple; thiazole kinase, yellow. Structure 2002 10, 225-235DOI: (10.1016/S0969-2126(02)00708-6)

Figure 6 Comparison of Active Sites of the Various Ribokinase Family Members HMPP kinase backbone, grayscale; ligands from HMPP kinase, red; T. gondii AK, green; glucokinase, blue; human AK, aqua; ribokinase, purple; thiazole kinase, yellow. (A) Superposition of ligands in the ATP or ADP binding sites. Ligands are ATP from thiazole kinase, ADP from ribokinase and glucokinase, AMP-PCP from T. gondii AK, and adenosine from human AK. For HMPP kinase, the modeled position of ATP is shown. For ATP-dependent enzymes, the adenine base, α-phosphate, and β-phosphate superimpose most closely. Greater variation is seen in the position of the γ-phosphate, especially in the case of thiazole kinase, for which ATP was bound in the presence of product monophosphate (see text for discussion). In glucokinase, the ADP shifts so that the α- and β-phosphates overlap with the β and γ phosphate sites of the ATP-dependent enzymes. (B) Superposition of substrates. The hydroxyl group accepting the phosphate is shown as a large sphere, with the rest of the substrate represented by bonds only. Substrates are shown for HMPP kinase (HMP), T. gondii AK (adenosine), human AK (adenosine), thiazole kinase (hydroxyethylthiazole), and ribokinase (ribose). Structure 2002 10, 225-235DOI: (10.1016/S0969-2126(02)00708-6)

Figure 7 Proposed Mechanism for the Two Activities of HMPP Kinase (A) Enzyme-substrate complex for the first phosphorylation reaction (HMP + ATP ↔ HMP-P +ADP). (B) Products for the first phosphorylation reaction. (C) Alternate conformation for the HMP-P in which the phosphate group is repositioned for the second phosphorylation reaction. (D) Enzyme-substrate complex for the second phosphorylation reaction (HMP-P + ATP ↔ HMP-PP +ADP). (E) Products for the second phosphorylation reaction. Structure 2002 10, 225-235DOI: (10.1016/S0969-2126(02)00708-6)

Figure 8 Superposition of the Anion Hole Regions of Ribokinase Family Members The figure illustrates residues that restrict the conformation of the phosphorylated product. Phe170, Gln38, and adenosine are shown in light blue for human adenosine kinase. Tyr169 and adenosine are shown in green for T. gondii adenosine kinase. Lys43 and ribose are shown in purple for ribokinase. Structure 2002 10, 225-235DOI: (10.1016/S0969-2126(02)00708-6)

Figure 9 Topology Diagrams of Ribokinase Family Secondary structure elements that are common to all family members are shown in the same color (central β sheet, blue; α helices on each side, red and green). The secondary structural elements in gray represent an insertion relative to THZ kinase. The secondary structural elements in yellow represent an insertion relative to HMPP kinase. The secondary structural elements in black represent an insertion relative to ribokinase. The secondary structural elements in light blue represent insertions relative to adenosine kinase. The structural elements chosen for assignment to insertions minimize the total number of insertions and conserve edge strands of sheets. The comparison suggests that the enzymes evolved in the following order: THZ kinase to HMPP kinase to ribokinase to adenosine kinase to glucokinase. The figure was prepared with TOPS [40]. Structure 2002 10, 225-235DOI: (10.1016/S0969-2126(02)00708-6)