PDBsum entry 3ejb

Oxidoreductase/lipid transport

PDB id: 3ejb

Contents

Protein chains

78 a.a.

380 a.a.

Ligands

ZMP ×4

HTG ×8

HEM ×4

Metals

_CL ×2

Waters ×1338

References listed in PDB file

Key reference

Title

Structural insights from a p450 carrier protein complex reveal how specificity is achieved in the p450(bioi) acp complex.

Authors

M.J.Cryle, I.Schlichting.

Ref.

Proc Natl Acad Sci U S A, 2008, 105, 15696-15701. [DOI no: 10.1073/pnas.0805983105]

PubMed id

18838690

Abstract

Cytochrome P450(BioI) (CYP107H1) from the biotin operon of Bacillus subtilis forms a seven-carbon diacid through a multistep oxidative cleavage of a fatty acid linked to acyl carrier protein (ACP). Crystal structures of P450(BioI) in complex with three different length fatty acyl-ACP (Escherichia coli) ligands show that P450(BioI) binds the fatty acid such as to force the carbon chain into a U-shape above the active site heme. This positions the C7 and C8 carbons for oxidation, with a large additional cavity extending beyond the heme to accommodate the methyl termini of fatty acids beyond the site of cleavage. The structures explain the experimentally observed lack of stereo- and regiospecificity in the hydroxylation and cleavage of free fatty acids. The P450(BioI)-ACP complexes represent the only structurally characterized P450-carrier protein complexes to date, which has allowed the generation of a model of the interaction of the vancomycin biosynthetic P450 OxyB with its proposed carrier protein bound substrate.

Figure 1.
Mechanism of oxidative cleavage of fatty acids by P450[BioI] (observed for R: OH, n ≥ 1; hypothesized for R: S-acyl ACP).

Figure 4.
Phosphopantetheine linker region of the P450[BioI]-ACP complex (phosphopantetheine linker and C[14] fatty acid shown in cyan, waters shown in green, detergent—n-heptyl β-D-thioglucopyranoside—shown in yellow, distances averaged across the four molecules in the crystallographic asymmetric unit, hydrogen bonds shown as dashed black lines). (A) Residues interacting with the phosphate group via water-mediated hydrogen bonds. (B) Residues interacting with the hydroxyl group of the phosphopantetheine linker via water-mediated hydrogen bonds (≈90° rotation of A).