PDBsum entry: 2fad

Biosynthetic protein

PDB id: 2fad

Contents

Protein chains

77 a.a. *

Ligands

PM5 ×2

Metals

_NA

_ZN ×8

Waters ×191

* Residue conservation analysis

PDB id:

2fad

Name:

Biosynthetic protein

Title:

Crystal structure of e. Coli heptanoyl-acp

Structure:

Acyl carrier protein. Chain: a, b. Synonym: acp, cytosolic-activating factor, caf, fatty acid acyl carrier protein. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: acpp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.60Å R-factor: 0.209 R-free: 0.256

Authors:

A.Roujeinikova

Key ref:

A.Roujeinikova et al. (2007). Structural studies of fatty acyl-(acyl carrier protein) thioesters reveal a hydrophobic binding cavity that can expand to fit longer substrates. J Mol Biol, 365, 135-145. PubMed id: 17059829 DOI: 10.1016/j.jmb.2006.09.049

Date:

07-Dec-05 Release date: 26-Sep-06

Protein chains

P0A6A8  (ACP_ECOLI) -  Acyl carrier protein

Seq: 78 a.a.

Struc: 77 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: lipid biosynthetic process (2 terms)
• Biochemical function: cofactor binding (3 terms)

DOI no: 10.1016/j.jmb.2006.09.049

J Mol Biol 365:135-145 (2007)

PubMed id: 17059829

Structural studies of fatty acyl-(acyl carrier protein) thioesters reveal a hydrophobic binding cavity that can expand to fit longer substrates.

A.Roujeinikova, W.J.Simon, J.Gilroy, D.W.Rice, J.B.Rafferty, A.R.Slabas.

ABSTRACT

A knowledge of the structures of acyl chain loaded species of the acyl carrier protein (ACP) as used in fatty acid biosynthesis and a range of other metabolic events, is essential for a full understanding of the molecular recognition at the heart of these processes. To date the only crystal structure of an acylated species of ACP is that of a butyryl derivative of Escherichia coli ACP. We have now determined the structures of a family of acylated E. coli ACPs of varying acyl chain length. The acyl moiety is attached via a thioester bond to a phosphopantetheine linker that is in turn bound to a serine residue in ACP. The growing acyl chain can be accommodated within a central cavity in the ACP for transport during the elongation stages of lipid synthesis through changes in the conformation of a four alpha-helix bundle. The results not only clarify the means by which a substrate of varying size and complexity is transported in the cell but also suggest a mechanism by which interacting enzymes can recognize the loaded ACP through recognition of surface features including the conformation of the phosphopantetheine linker.

Selected figure(s)

Figure 2.
Figure 2. (a)–(e) Cross-sections across the molecules of (a) unliganded, (b) butyryl-, (c) hexanoyl-, (d) heptanoyl- and (e) decanoyl-ACP showing the hydrophobic cavities of ACP in the unliganded state and with the acyl chains bound. The orientation is the same for all structures. The acyl chain, the phosphopantetheine group and the side-chain of Ser36 are shown in CPK representation and coloured according to atom type, with carbon atoms in green, nitrogen in blue, oxygen in red and sulphur in orange. The protein moiety is shown as ribbon structure. (f) Two observed binding modes for the acylated phosphopantetheine group in the crystal structures of acyl-ACPs. Only the side-chains or the main-chain peptides of the protein residues that form hydrogen bonds with the prosthetic group are shown for clarity. The superimposed structures of hexanoyl-ACP and subunit A of heptanoyl-ACP are shown in cyan and green, respectively, and those of butyryl-ACP, subunit B of heptanoyl-ACP and decanoyl-ACP coloured magenta, red and pink. In the latter three structures, a thin line is used to show a modelled position of the solvent-exposed β-alanine and pantoic acid moieties of the 4′-phosphopantetheine group for which no interpretable electron density was observed. The sulphur atoms in the thioester bonds are depicted as yellow spheres. (g) Changes in the probe-accessible volume of the hydrophobic cavity in ACP induced by the binding of fatty acyl chains (for calculations, atoms of the acyl chain and phosphopantetheine group have been excluded from the model). For hexanoyl- and heptanoyl-ACP, the average value for the two monomers in the asymmetric unit is shown. For decanoyl-ACP, the volume has been calculated for the monomer that has an acyl chain bound in its hydrophobic pocket.

Figure 3.
Figure 3. (a) rmsd of C^α atoms for pairwise superpositions of the protein moiety of hexanoyl-ACP (subunit A) with those of unliganded protein (red), butyryl- (dark-purple), hexanoyl- (subunit A, dark-blue) and heptanoyl-ACP (subunit A, blue) as a function of residues number (colour coding is consistent with (c)). (b) Stereo ribbon diagram of the superimposed structures of unliganded ACP (red) and decanoyl-ACP (green) showing angular displacements of the four helices induced by the binding of the acylated prosthetic group. The latter is drawn in ball-and stick representation and the axes of the helices are shown as thin rods. (c) Stereodiagram highlighting differences between the superimposed crystal structures of unliganded (red), butyryl- (dark-purple), hexanoyl- (dark-blue), heptanoyl- (blue) and decanoyl-ACP (green) in the region that forms the hydrophobic pocket. To mark the position of the acyl chain-binding site, the decanoyl moiety and the phosphopantetheine group are shown for decanoyl-ACP in a ball-and-stick representation. The protein moieties in butyryl-, hexanoyl- and heptanoyl-ACP adopt conformations that are intermediate between the structure of the unliganded protein and that of decanoyl-ACP. Binding of the acyl chains of an increasing length results in gradual overall swelling of the global protein fold.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 365, 135-145) copyright 2007.

Figures were selected by an automated process.