KDOP synthase from <i>B. pseudomallei</i>.

<p>KDOP synthase (2-dehydro-3-deoxyphosphooctonate aldolase, BURPS1710b_3264, PDB: 3UND with bound D-arabinose-5-phosphate), a KDO2-lipid A biosynthesis enzyme with a TIM barrel structure, was one of five structures solved for orthologs of the putative essential <i>B. thailandensis</i> gene, Bth_I1893.</p

Isochorismatase from <i>B. thailandensis</i>.

<p>The isochorismatase family protein (BTH_II2229, PDB: 3TXY) from <i>B. thailandensis</i>, is shown in electrostatics surface representation with bound isochorismate taken from the <i>P. aeruginosa</i> ischorismatase, PhzD (PDB: 1NF8). 3TXY and 1NF8 have 30% sequence identity and an overall Cα RMSD of 1.7 Å. By aligning 1NF8 and 3TXY, the active site of 3TXY can be identified as a large pocket with a combination of hydrophobic (white) and positively charged (blue) amino acid residues.</p

Peptidyl-tRNA hydrolase from <i>B. thailandensis</i>.

<p>(A) The electrostatic surface of unliganded peptidyl-tRNA hydrolase (PTH, Bth_I0472, PDB: 3V2I) from <i>B. thailandensis</i> is superimposed with a cartoon representation of a structure from <i>P. aeruginosa</i> with bound adipic acid (PDB: 4DHW). The channel in unliganded 3V2I is closed due to adjacent flexible loops. (B) The electrostatics surface of 4DHW reveals an open, charged channel. 3V2I and 4DHW have 44% sequence identity and a similar overall fold (2.0 Å RMSD over all common Cα atoms). Discovery of a ligand that binds the alternately charged channel (positive/negative/positive) could block the reaction and prevent protein synthesis.</p

<i>Burkholderia</i> protein structures.

<p>An expanded version of this table is available in the Supporting Information (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053851#pone.0053851.s002" target="_blank">Table S2</a>).</p><p>Structures described in detail in the manuscript are indicated in bold.</p>*<p>Best hit (if any) in a BlastP search against the human proteome, using an <i>E</i>-value cutoff of 1×10⁻¹⁰ (UniProtKB AC).</p>#<p>BURPS1710b_2511 was screened using a fragment-based approach, yielding 17 PDB structures and 16 unique ligand-bound complexes: 3F0D, 3F0E, 3F0F, 3F0G, 3IEQ, 3IEW, 3MBM, 3P0Z, 3P10, 3Q8H, 3QHD, 3IKE, 3IKF, 3JVH, 3K14, 3K2X, 3KE1.</p

FabH structures from <i>B. pseudomallei</i> and B. xenovorans.

<p>(A) FabH (3-oxoacyl-(acyl-carrier-protein) synthase III) from <i>B. pseudomallei 1710b</i> (BURPS1710b_0096, PDB: 3GWA, cyan) and <i>B. xenovorans LB400 B</i> (Bxe_A1072, PDB: 4DFE, magenta) have similar overall structures, with a Cα RMSD of 1.8 Å between individual chains of 3GWA and 4DFE. There is no close human homolog based on a BlastP search of the human proteome. (B) In 4DFE, a hydrophobic tunnel to the active site is adjacent to a positively-charged surface patch (marked in blue).</p

Thymidylate synthase (TS) from <i>B. thailandensis</i>, <i>E. coli</i> and <i>Homo sapiens</i>.

<p>TS from human (cyan, PDB: 1SYN) and <i>E. coli</i> (magenta, PDB: 1JU6) show similar active site structure as TS from <i>B. thailandensis</i> (green, PDB: 3V8H, C-terminal residues removed for clarity). A canonical active site tryptophan (W83 in <i>E. coli</i>) for bacterial sequences is replaced in <i>B. thailandensis</i> by asparagine, the residue observed in this position in human TS (side chains shown in stick representation, below and to the right of the bound ligand, citric acid).</p

Identification of essential genes using saturation transposon mutagenesis and Tn-seq.

<p>Identification of essential genes using saturation transposon mutagenesis and Tn-seq.</p