Volume 10, Issue 3, Pages 329-342 (March 2002) Structure of Acetylglutamate Kinase, a Key Enzyme for Arginine Biosynthesis and a Prototype for the Amino Acid Kinase Enzyme Family, during Catalysis  Santiago Ramón-Maiques, Alberto Marina, Fernando Gil-Ortiz, Ignacio Fita, Vicente Rubio  Structure  Volume 10, Issue 3, Pages 329-342 (March 2002) DOI: 10.1016/S0969-2126(02)00721-9

Figure 1 Acetylated (A) and Nonacetylated (B) Routes of Ornithine Biosynthesis Structure 2002 10, 329-342DOI: (10.1016/S0969-2126(02)00721-9)

Figure 2 The NAGK Subunit (A) Stereoview of the Cα trace. AMPPNP and NAG are shown in ball and stick representation, in gray. (B) Subunit topology. The main β sheet is shadowed. The arrow indicates the dyadic axis. (C) Correspondence between the amino acid sequence and the secondary structure. The main β sheet is shadowed. Triangles under the sequence denote residues having decreased accessibility upon the binding of NAG (open), AMPPNP (closed), or both (shadowed). Shadowed circles denote decreased accessibility upon dimer formation. The black and gray sequence backgrounds indicate conservation or conservative replacement, respectively (I-L-M-V, A-G, D-N, and T-S) in at least 22 of 24 genuine or putative NAGK sequences (SwissProt accession numbers P11445, O67848, O28988, Q07905, P36840, P57157, Q59281, O08320, Q60382, O26285, P94989, P31595, P73326, Q9X2A4, O50147, Q9YBY9, Q9V1I5, Q9SCL7, Q9PIR8, Q9PEM7, Q9LCS6, Q9L1A3, Q9HTN2, and Q9KNT7). Structure 2002 10, 329-342DOI: (10.1016/S0969-2126(02)00721-9)

Figure 3 The NAGK Dimer (A) Cartoon representation of the dimer with the dyadic axis (black ellipse) perpendicular to the paper and the main β sheet (colored green for one monomer and blue for the other) with its C edge pointing toward the viewer. Substrates are shown in black, in bond representation. The small β sheet is colored orange, the β hairpins are yellow, and the α helices are gray in both subunits. Helices B and C are semitransparent to allow viewing the structure behind them. β strands and helices are identified with numbers and letters in one subunit. (B) Hydrogen bonds mediated by strand β5, by Asp106, and by Lys86. Except for Asp106 and Lys86, side chains have been omitted for clarity. Different colors are used for the two subunits. Water molecules are light blue, and broken red lines denote hydrogen bonds. (C) Semitransparent representation of the dimerization surface (calculated with MSMS [57]) of one subunit, viewed from the other subunit, with its nonpolar atoms colored red. Secondary structure elements involved in intersubunit interactions and important residues of the interface are represented and identified. Prepared with DINO [58]. Structure 2002 10, 329-342DOI: (10.1016/S0969-2126(02)00721-9)

Figure 4 Binding of the Substrates to NAGK (A) Stereoview of the Cα trace of the binding sites. AMPPNP and NAG are shown in ball and stick representation, and are colored. Amino acid side chains are in color, in thinner trace. (B and C) Schematic plots (drawn with LIGPLOT [59]) of the interactions between the protein and NAG (B) or AMPPNP (C). The letter w denotes a water molecule. Distances are in Å. Structure 2002 10, 329-342DOI: (10.1016/S0969-2126(02)00721-9)

Figure 5 2Fobs−Fcalc Density Map and Model of MgAMPPNP and NAG Bound to the Enzyme, and Comparison with ADP Binding by CK-like CPS (A) 2Fobs−Fcalc density map contoured at 0.8 σ for bound MgAMPPNP (including, in light blue, two water molecules coordinated to Mg) and NAG. Helices B and E and the side chains of lysines 8, 61, and 217 are shown. Drawn with BOBSCRIPT [60]. (B) Stereoview of bond representation of bound MgAMPPNP, NAG, and nearby NAGK groups (in black) superimposed with bound ADP and nearby groups in CK-like CPS from Pyrococcus furiosus (in red; Protein Data Bank accession number 1e19). Structure 2002 10, 329-342DOI: (10.1016/S0969-2126(02)00721-9)

Figure 6 Comparison of Amino Acid Kinase Pfam Family Members (A) Ribbon diagrams of the monomers of NAGK with bound MgAMPPNP and NAG, of CK-like CPS from P. furiosus with bound MgADP (PDB 1e19), and of CK from Enterococcus faecalis with bound sulfate (PDB 1b7b). Ligands are represented as ball and stick models. An arrow signals the peripheral domain of CKs and the corresponding β3-β4 hairpin of NAGK. Helix B is also identified. (B) Alignment of representative amino acid kinase Pfam family members (PF00696; http://www.sanger.ac.uk/cgi-bin/Pfam): E. coli NAGK, glutamate-5-kinase (G5K), aspartokinase I (AK), and UMP kinase (UMPK), and P. furiosus CK-like CPS (CK-CPS). The Pfam alignment was modified to maximize coincidence of secondary structure elements of NAGK and CK-CPS (arrows and cylinders above and below the corresponding sequences; blue and pink arrows, main and small β sheets, respectively; orange arrows, β12-β13 hairpin or equivalent in CK-CPS; colored in green are the β3-β4 hairpin of NAGK and the peripheral domain of CK-CPS) and to maximize the stacking of regions of high conservation (highlighted with a yellow background) within each enzyme class. Some important residues that are conserved among the different enzyme classes are colored red. An internal region of E. coli AK (residues 59–114) is missing in many AKs and is not aligned. Residues involved in the binding of the nucleotide are indicated with orange triangles, and those involved in binding NAG or sulfate with blue triangles. Structure 2002 10, 329-342DOI: (10.1016/S0969-2126(02)00721-9)