The 1.3-Angstrom-Resolution Crystal Structure of β-Ketoacyl-Acyl Carrier Protein Synthase II fromStreptococcus pneumoniae

Abstract

The ␤-ketoacyl-acyl carrier protein synthases are members of the thiolase superfamily and are key regulators of bacterial fatty acid synthesis. As essential components of the bacterial lipid metabolic pathway, they are an attractive target for antibacterial drug discovery. We have determined the 1.3 Å resolution crystal structure of the ␤-ketoacyl-acyl carrier protein synthase II (FabF) from the pathogenic organism Streptococcus pneumoniae. The protein adopts a duplicated ␤␣␤␣␤␣␤␤ fold, which is characteristic of the thiolase superfamily. The two-fold pseudosymmetry is broken by the presence of distinct insertions in the two halves of the protein. These insertions have evolved to bind the specific substrates of this particular member of the thiolase superfamily. Docking of the pantetheine moiety of the substrate identifies the loop regions involved in substrate binding and indicates roles for specific, conserved residues in the substrate binding tunnel. The active site triad of this superfamily is present in spFabF as His 303, His 337, and Cys 164. Near the active site is an ion pair, Glu 346 and Lys 332, that is conserved in the condensing enzymes but is unusual in our structure in being stabilized by an Mg 2؉ ion which interacts with Glu 346. The active site histidines interact asymmetrically with Lys 332, whose positive charge is closer to His 303, and we propose a specific role for the lysine in polarizing the imidazole ring of this histidine. This asymmetry suggests that the two histidines have unequal roles in catalysis and provides new insights into the catalytic mechanisms of these enzymes.The ␤-ketoacyl-acyl carrier protein synthases catalyze the addition of two-carbon units onto the growing acyl chain during the elongation phase of fatty acid synthesis. This enzymatic activity involves what is an irreversible chemical event in biosynthetic pathways, the formation of a carbon-carbon bond via a Claisen-like condensation reaction (15). These condensing enzymes are members of a superfamily of enzymes whose members all catalyze essentially the same reaction. Included in the superfamily are the thiolases involved in fatty acid degradation (␤-oxidation) (46), or sterol biosynthesis (25), and the related enzymes that synthesize polyketides in plants and bacteria (18). Structural studies on this superfamily of enzymes have revealed that they share a common ␤␣␤␣␤␣␤␤ topology which is duplicated by an internal pseudodyad that may have arisen by gene duplication (26). Members of the superfamily that have been structurally characterized include the peroxisomal 3-ketoacyl-coenzyme A (3-ketoacyl-CoA) thiolases from a variety of organisms (26), an array of bacterial fatty acidcondensing enzymes (8,19,31,36,38,40,41,45), and the polyketide chalcone synthase (13). Based on the structural and functional differences between the enzymes, the superfamily is subdivided into three classes (31). The thiolases form one group, the fatty acid elongation-condensing enzymes form a second group, and those involved in polyketide synt...

Structural Basis for the Recognition of Mycolic Acid Precursors by KasA, a Condensing Enzyme and Drug Target from Mycobacterium Tuberculosis

“…5B and supplemental Fig. S2) (43). The vastly different but also flexible FabH capping domain, which is formed from insertions located at distinct sites in the primary sequence (supplemental Fig.…”

“…It was proposed that the dipole moment of helix ␣8 acidifies Cys-171 (supplemental Fig. S2) (43), leading to a zwitterionic His-311H ϩ -Cys-171 Ϫ ion pair in the free enzyme (box 1), which activates Cys-171 for the nucleophilic attack of the acyl-AcpM (box 2) (54). The His-311 ⑀-nitrogen (depicted in magenta as in Fig.…”

“…They are inhibited by the natural products cerulenin, thiolactomycin, and platensimycin (shown in the bottom blue box) and catalyze a Claisen condensation reaction between acylAcpM (acyl-CoA for FabH) and malonyl-AcpM via the three-step mechanism depicted in the top box (7,10). The reduction of the generated ␤-keto group to a methylene group is achieved via the subsequent actions of MabA, HadAB/BC, and InhA (43,62).…”

Structural insights into bacterial resistance to cerulenin

“…Overall, FabF from B. subtilis (Fig. 1B) is structurally very similar to several condensing enzymes [13,[18][19][20], displaying highest similarity to the orthologues from S. aureus and Listeria monocytogenes (3O04, unpublished), with which the sequence identities are close to 70% and the rmsd values are below 1 A. The general architecture of these proteins groups them within the thiolase-like fold [21,22].…”

The Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Pseudomonas aeruginosa

“…The resulting acyl-ACP is two carbons longer and either re-enters the cycle for another round of elongation or is transferred to glycerol phosphate to produce phospholipids when the chain lengths reach 16 -18 carbons (4, 5). The crystal structures of FabB (9), FabF (10,11),, FabA (15), and FabI (16) are known.Dehydratases, which catalyze the third step in the type II elongation cycle, are the focus of this study. FabA was the first dehydratase discovered.…”