PDBsum entry 1fj4

Transferase

PDB id: 1fj4

Contents

Protein chains

403 a.a. *

Ligands

TLM ×4

Waters ×306

* Residue conservation analysis

PDB id:

1fj4

Name:

Transferase

Title:

The structure of beta-ketoacyl-[acyl carrier protein] synthase i in complex with thiolactomycin, implications for drug design

Structure:

Beta-ketoacyl-[acyl carrier protein] synthase i. Chain: a, b, c, d. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.35Å R-factor: 0.197 R-free: 0.253

Authors:

A.C.Price,K.Choi,R.J.Heath,Z.Li,S.W.White,C.O.Rock

Key ref:

A.C.Price et al. (2001). Inhibition of beta-ketoacyl-acyl carrier protein synthases by thiolactomycin and cerulenin. Structure and mechanism. J Biol Chem, 276, 6551-6559. PubMed id: 11050088 DOI: 10.1074/jbc.M007101200

Date:

07-Aug-00 Release date: 23-Aug-00

Protein chains

P0A953  (FABB_ECOLI) -  3-oxoacyl-[acyl-carrier-protein] synthase 1 from Escherichia coli (strain K12)

Seq: 406 a.a.

Struc: 403 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.1.41 - beta-ketoacyl-[acyl-carrier-protein] synthase I.
• Reaction: a fatty acyl-[ACP] + malonyl-[ACP] + H⁺ = a 3-oxoacyl-[ACP] + holo- [ACP] + CO2

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1074/jbc.M007101200

J Biol Chem 276:6551-6559 (2001)

PubMed id: 11050088

Inhibition of beta-ketoacyl-acyl carrier protein synthases by thiolactomycin and cerulenin. Structure and mechanism.

A.C.Price, K.H.Choi, R.J.Heath, Z.Li, S.W.White, C.O.Rock.

ABSTRACT

The beta-ketoacyl-acyl carrier protein (ACP) synthases are key regulators of type II fatty acid synthesis and are the targets for two natural products, thiolactomycin (TLM) and cerulenin. The high resolution structures of the FabB-TLM and FabB-cerulenin binary complexes were determined. TLM mimics malonyl-ACP in the FabB active site. It forms strong hydrogen bond interactions with the two catalytic histidines, and the unsaturated alkyl side chain interaction with a small hydrophobic pocket is stabilized by pi stacking interactions. Cerulenin binding mimics the condensation transition state. The subtle differences between the FabB-cerulenin and FabF-cerulenin (Moche, M., Schneider, G., Edwards, P., Dehesh, K., and Lindqvist, Y. (1999) J. Biol. Chem. 244, 6031-6034) structures explain the differences in the sensitivity of the two enzymes to the antibiotic and may reflect the distinct substrate specificities protein was prepared to convert the FabB His-His-Cys active site triad into the FabH His-Asn-Cys configuration to test the importance of the two His residues in TLM and was significantly more resistant to both antibiotics than FabB and had an affinity for TLM an order of magnitude less than the wild-type enzyme, illustrating that the two-histidine active site architecture is critical to protein-antibiotic interaction. These data provide a structural framework for understanding antibiotic sensitivity within this group of enzymes.

Selected figure(s)

Figure 7.
Fig. 7. Overlay of TLM and cerulenin in the FabB active site. The FabB-TLM and FabB-cerulenin structures were superimposed to illustrate the differences in the binding of the antibiotics in the active site. The coloring scheme in this figure is the same as in Figs. 3 and 4. TLM binds on the malonyl-ACP side and cerulenin occupies the acyl-enzyme intermediate half. The O-1 of TLM and O-2 of cerulenin are the only portions of the antibiotics that overlap in the structure, and they form hydrogen bonds with the His-His dyad in the active site. Note that the protein structure shown is that of the FabB-TLM complex. Binding of the two antibiotics results in essentially identical changes in the conformations of the active site residues.

Figure 8.
Fig. 8. Schematic diagrams illustrating how cerulenin and TLM mimic substrates in the active site of FabB. Upper panel, the thiolactone ring of TLM mimics the bent conformation of the thiomalonate, and this is emphasized by the shaded atoms. The O-1s form hydrogen bonds with His-298 and His-333, and the C-1, C-2, and C-3s of malonate are mimicked by the C-1, C-2, and C-9s of TLM. The O-2 of TLM points out the active site tunnel that would be occupied by the pantetheine arm of the malonyl-ACP substrate. Lower panel, cerulenin mimics the condensation transition state and spans the two halves of the active site. The O-3 of cerulenin lies in the oxyanion hole formed by the amides of Cys-163 and Phe-392 enclosed by the phenyl side chain of Phe-392. This structure mimics the postulated location of the oxyanion of the tetrahedral transition state. The side chain of Cys-163 rotates in the cerulenin structure to form a covalent bond with C-2, but in the transition state, it is postulated to reside in the location observed in the native enzyme. The acyl chain of cerulenin feeds into the hydrophobic groove that accommodates the long chain acyl-enzyme intermediate.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 6551-6559) copyright 2001.

Figures were selected by an automated process.