Structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Rickettsia prowazekii at 2.25 Å resolution

Abstract

Rickettsia prowazekii, a parasitic Gram-negative bacterium, is in the second-highest biodefense category of pathogens of the National Institute of Allergy and Infectious Diseases, but only a handful of structures have been deposited in the PDB for this bacterium; to date, all of these have been solved by the SSGCID. Owing to its small genome (about 800 protein-coding genes), it relies on the host for many basic biosynthetic processes, hindering the identification of potential antipathogenic drug targets. However, like many bacteria and plants, its metabolism does depend upon the type II fatty-acid synthesis (FAS) pathway for lipogenesis, whereas the predominant form of fatty-acid biosynthesis in humans is via the type I pathway. Here, the structure of the third enzyme in the FAS pathway, 3-ketoacyl-(acyl-carrier-protein) reductase, is reported at a resolution of 2.25 Å. Its fold is highly similar to those of the existing structures from some well characterized pathogens, such as Mycobacterium tuberculosis and Burkholderia pseudomallei, but differs significantly from the analogous mammalian structure. Hence, drugs known to target the enzymes of pathogenic bacteria may serve as potential leads against Rickettsia, which is responsible for spotted fever and typhus and is found throughout the world.

Figure 1

Fatty-acid biosynthetic pathway for R. prowazekii. The R. prowazekii fatty-acid biosynthesis map from the KEGG PATHWAY database (Kanehisa & Goto, 2000 ▶) is shown with FabG highlighted in red.

Figure 2

Crystal structure of R. prowazekii 3-ketoacyl-(ACP) reductase (FabG). FabG from R. prowazekii crystallizes with two molecules per asymmetric unit, which are shown as ribbon diagrams with purple helices and yellow strands. The active-site residues (Ser143, Tyr156 and Arg160) are grouped near the loop connecting α5 and β5. Secondary-structure elements are labeled from both chains. A tetramer is generated by crystallographic symmetry. Molecules A′ and B′ are shown as ribbon diagrams with blue helices and yellow strands. The figure was generated with CCP4mg (McNicholas et al., 2011 ▶).

Figure 3

Structural superimpositions of monomeric units for FabG. In this figure, the monomers of FabG from R. prowazekii (PDB entry 3f9i; purple helices, yellow strands), from E. coli (PDB entry 1i01; magenta), from M. tuberculosis (PDB entry 1uzm; light blue) and the NADP⁺-bound structure from V. cholerae (PDB entry 3rsk, pink) are superimposed. There is a significant structural variability between these structures in the proximity of the NADP⁺-binding site.

Figure 4

Alignment of solved structures of bacterial 3-ketoacyl-(ACP) reductases. Multiple sequence and secondary-structure alignment of bacterial orthologs. Numbering along the top is based on the alignment consensus. Predicted α-helices, β-strands, coils and turns are shown as pink cylinders, yellow arrows, grey corkscrews and blue curved arrows, respectively. Sequences are taken from the PDB. From top to bottom: E. coli, 1i01 (Price et al., 2001 ▶); M. tuberculosis, 1uzm (Cohen-Gonsaud et al., 2002 ▶); Pseudomonas aeruginosa, 2b4q (Miller et al., 2006 ▶); Aquifex aeolicus, 2pnf (Q. Mao, R. Huether, W. L. Duax & T. C. Umland, unpublished work); R. prowazekii, 3f9i (this work); Burkholderia pseudomallei, 3ftp (Seattle Structural Genomics Center for Infectious Disease, unpublished work); Bartonella henselae, 3grp (B. L. Staker, unpublished work); Brucella melitensis, 3n74 (Seattle Structural Genomics Center for Infectious Disease, unpublished work). This figure was prepared with Geneious (Drummond et al., 2010 ▶).