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

* Residue conservation analysis

PDB id:

3ejb

Name:

Oxidoreductase/lipid transport

Title:

Crystal structure of p450bioi in complex with tetradecanoic acid ligated acyl carrier protein

Structure:

Acyl carrier protein. Chain: a, c, e, g. Synonym: acp, cytosolic-activating factor, caf, fatty acid synthase acyl carrier protein. Engineered: yes. Biotin biosynthesis cytochrome p450-like enzyme. Chain: b, d, f, h. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: acpp, b1094, jw1080. Expressed in: escherichia coli. Expression_system_taxid: 562. Bacillus subtilis. Organism_taxid: 1423. Strain: gp208.

Resolution:

2.00Å R-factor: 0.224 R-free: 0.266

Authors:

M.J.Cryle,I.Schlichting

Key ref:

M.J.Cryle and I.Schlichting (2008). Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450(BioI) ACP complex. Proc Natl Acad Sci U S A, 105, 15696-15701. PubMed id: 18838690 DOI: 10.1073/pnas.0805983105

Date:

18-Sep-08 Release date: 07-Oct-08

Protein chains

P0A6A8  (ACP_ECOLI) -  Acyl carrier protein from Escherichia coli (strain K12)

Seq: 78 a.a.

Struc: 78 a.a.

Protein chains

P53554  (BIOI_BACSU) -  Biotin biosynthesis cytochrome P450 from Bacillus subtilis (strain 168)

Seq: 395 a.a.

Struc: 380 a.a.

Enzyme reactions

• Enzyme class: Chains B, D, F, H: E.C.1.14.14.46 - pimeloyl-[acyl-carrier protein] synthase.
• Reaction: a C2-C8-saturated long-chain fatty acyl-[ACP] + 2 reduced [flavodoxin] + 3 O2 = 6-carboxyhexanoyl-[ACP] + a fatty aldehyde + 2 oxidized [flavodoxin] + 3 H2O + 3 H⁺
• Cofactor: Heme-thiolate

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

Key reference

DOI no: 10.1073/pnas.0805983105

Proc Natl Acad Sci U S A 105:15696-15701 (2008)

PubMed id: 18838690

Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450(BioI) ACP complex.

M.J.Cryle, I.Schlichting.

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.

Selected figure(s)

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).

Figures were selected by an automated process.