Structure and Mechanism of Homoserine Kinase Tianjun Zhou, Matthew Daugherty, Nick V. Grishin, Andrei L. Osterman, Hong Zhang  Structure  Volume 8, Issue 12, Pages 1247-1257 (December 2000) DOI: 10.1016/S0969-2126(00)00533-5

Figure 1 Multiple Alignment of the GHMP Superfamily The three highly conserved motifs as defined in Bork et al. (1993) [4] are underlined and marked as motifs 1–3. The first column lists the protein (gene) names, and the second column lists abbreviated species names. Protein name abbreviations are as follows: HK, homoserine kinase; IPK, isopentenyl monophosphate kinase; SK, shikimate kinase (M. D., V. Vonstein, R. Overbeek, I. Anderson and A. O., submitted); UNK, unknown; MPD, mevalonate pyrophosphate decarboxylase; MK, mevalonate kinase; PMK, phosphomevalonate kinase; and GK, galactokinase. Species name abbreviations are as follows: Mj, Methanococcus jannaschii; Ec, Escherichia coli; Sc, Saccharomyces cerevisiae; At, Arabidopsis thaliana; Se, Samonella enterica; Ce, Caenorhabditis elegans; and Hs, Homo sapiens. To the right, the numbers indicate the positions of the first residue of the aligned region in the respective protein sequence. Numbers in parentheses indicate how many residues in an insertion are not shown. The numbers at the end of each sequence indicate the last residue number in the aligned region followed by the number of total residues in the protein. The NCBI gene identification number (gi) is at end of the alignment. The secondary structure elements in the HSK crystal structure are indicated above the sequences, with arrows representing β strands and cylinders denoting α helices. The letter coding for the secondary-structural elements is the same as in Figure 3b. The invariant residues are highlighted in black and are shown in white letters. The mostly conserved residues are highlighted in gray. Uncharged residues in mainly hydrophobic sites are highlighted in yellow. Residues that bind ADP or are in the active site of HSK are highlighted in light blue Structure 2000 8, 1247-1257DOI: (10.1016/S0969-2126(00)00533-5)

Figure 2 Quality of the Structures (a) Stereoview of the Cα traces of superimposed independent HSK molecules in the HSK and HSK-ADP complex crystals. The four HSK molecules in the asymmetric unit of the uncomplexed form are colored blue; the four HSK molecules in the HSK-ADP complex are colored red. Each 20th residue is numbered. Only one ADP molecule is shown in the figure. (b) The difference density for ADP in the HSK-ADP complex. The map was calculated with Fo-Fc amplitudes and phases from the partially refined model prior to the inclusion of ADP. The map is contoured at 3.2σ. This figure and all subsequent figures were prepared with Molscript [58], Bobscript [59], Gl_render (L. Esser, unpublished program), and POV-ray [60] Structure 2000 8, 1247-1257DOI: (10.1016/S0969-2126(00)00533-5)

Figure 3 Overall Fold of HSK (a) Stereoview Cα trace of HSK monomer. Each 20th residue is numbered; the N and C termini are labeled. The bound ADP in the HSK-ADP complex is shown in red. (b) Ribbon diagram of HSK in the same orientation as (a). The bound ADP molecule is shown in a ball-and-stick representation. The molecule is colored from dark blue to red according to the amino acid sequence. The β strands are labeled from a to m, and α helices are labeled from A to J Structure 2000 8, 1247-1257DOI: (10.1016/S0969-2126(00)00533-5)

Figure 4 Fold Comparison between HSK and EF-G Domains IV and V (a) The N- and C-terminal domains of HSK are separated for clarity and are shown in an “open-book” presentation. EF-G ([20]; PDB code 1dar) domains IV and V are shown in the superimposed orientations with the N- and C-terminal domains of HSK, respectively. The superimposed secondary-structural elements are colored cyan for helices and yellow for strands, while the additional structural elements are shown in gray. The numbers of the first and the last residue in each domain are labeled. Secondary-structural elements are labeled by color-coded italicized letters; lower case is for β strands, and upper case is for α helices. Letter colors correspond to the colors of the structural elements. The ADP molecule in HSK is shown in a ball-and-stick representation. (b) Structure-based sequence alignment of HSK and EF-G domains IV and V. Color and letter coding of structural elements in the sequence is the same as in (a). The residue number of the first amino acid in each line and the last amino acid in the alignment are indicated. Numbers in parentheses interrupting the sequence indicate the number of residues in insertions not shown in the alignment. Invariant residues are shown in white on black. Conserved substitutions are shown in bold letters Structure 2000 8, 1247-1257DOI: (10.1016/S0969-2126(00)00533-5)

Figure 5 Ribbon Presentation of HSK Dimer The N- and C-terminal domains in monomer 1 (left) are colored green and cyan, respectively; they are colored yellow and orange, respectively, in monomer 2 (right). The bound ADP molecules are shown in a ball-and-stick representation Structure 2000 8, 1247-1257DOI: (10.1016/S0969-2126(00)00533-5)

Figure 6 ADP Binding in HSK (a) Stereoview of the ADP binding site. The protein is colored cyan for residues in the N-terminal domain and green for residues in the C-terminal domain; the ADP is colored yellow. The ADP molecule, the phosphate binding loop, the cis-Pro loop, and the side chains of other protein residues involved in ADP binding are shown in ball-and-stick representations. The hydrogen bonds are indicated by dotted lines. (b) Stereoview overlay of the phosphate binding loops and bound substrate(s) in adenylate kinase (AK, in green; PDB code 1ake), phosphoenolpyruvate carboxykinase (PCK, in cyan; PDB code 1aq2), and HSK (in red). The side chains of the conserved lysine in the P loops of AK and PCK along with Ser-97 at an equivalent position in HSK are shown in a ball-and-stick representation. Other abbreviations are AP5, bis(adenosine)-5'-pentaphosphate; and PYR, pyruvate Structure 2000 8, 1247-1257DOI: (10.1016/S0969-2126(00)00533-5)

Figure 7 Molecular Surface of the Substrate Binding Site of HSK A homoserine (Hse) molecule was modeled in the putative binding site next to the bound ADP. The surface is rendered semitransparent, with the phosphate binding loop and relevant active site residues shown in ribbon and ball-and-stick representations, respectively. The surface is colored by electrostatic potential calculated with GRASP [61]. Residues 182–187 blocked the middle of the cavity at the front and were removed for clarity Structure 2000 8, 1247-1257DOI: (10.1016/S0969-2126(00)00533-5)