Current Progress in the Structural and Biochemical Characterization of Proteins Involved in the Assembly of Lipopolysaccharide

Figure 5

LpxD. (a) Heterohexamer of LpxD and R3-hydroxymyristoyl-ACP (PDB: 4IHF) [44]. ACP chains are colored red, yellow, and chartreuse, and LpxD chains are colored blue, cyan, and sea green. (b) LigPlot+ diagram of acyl donor substrate from (a) [45]. Distances of hydrogen-bond and salt-bridge interactions shown in Ångstroms are as follows: 3.2 from acyl chain β-hydroxyl to Q236 Nε and 2.6 to D232 Oδ2, 3.0 from acyl chain carbonyl to G257 N 3.0 from phosphate to N310 Nδ and 2.7 and 2.9, respectively, to R314 Nη and Nε. (c) Acyl chain binding in LpxD/ACP heterohexamer (PDB: 4IHG) [44]. Subscripts are used below to distinguish protein chains in the complex. Hydrogen-bonds are shown, and corresponding distances in Ångstroms are as follows: 2.9 from putative 2′-R3-hydroxymyristate carboxylate to G257_C N 2.1 from putative 2′-R3-hydroxymyristate carboxylate to H239_C Nε, 3.0 from putative 2′-R3-hydroxymyristate β-hydroxyl to D232_B Oδ2 and 3.6 to F183_C N and 2.8 from putative 3′-R3-hydroxymyristate carboxylate to F183_C O and 3.2 to S of phosphopantetheine attached to ACP S36_H. (d) UDP-N-acetylglucosamine and palmitate binding to LpxD trimer (PDB: 2IU9) [42]. Hydrogen-bonds are shown with the following distances in Ångstroms: 2.8 from palmitate carboxylate to Q244_A Nε and 2.9 to D240_B Oδ2, 2.6 from 2′-acetyl carbonyl to H247_A Nε, 2.8 from uracil O2 to I33_B N 2.7 from uracil N3 to F43_B O 2.8 from uracil O4 to D45_B N 2.6 from ribose 3′-hydroxyl to E32_B Oε2 and 2.9 to Q248_A Oε, 3.0 from ribose 2′-hydroxyl to E34_B Oε1, 2.4 from β-phosphate to Y49_B Oη and 3.2 to N46_B Nδ, 2.7 from α-phosphate to H284_A Nε, and 3.1 from glucosamine 6′-hydroxyl to N46_B Nδ.

(a)

(b)

(c)

(d)