PDBsum entry 1izo

Oxidoreductase

PDB id: 1izo

Contents

Protein chains

411 a.a. *

Ligands

HEM ×3

PAM ×3

Waters ×295

* Residue conservation analysis

PDB id:

1izo

Name:

Oxidoreductase

Title:

Cytochrome p450 bs beta complexed with fatty acid

Structure:

Cytochrome p450 152a1. Chain: a, b, c. Synonym: p450bsbeta. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.246 R-free: 0.280

Authors:

D.S.Lee,A.Yamada,H.Sugimoto,I.Matsunaga,H.Ogura,K.Ichihara,S.Adachi, S.Y.Park,Y.Shiro,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

D.S.Lee et al. (2003). Substrate recognition and molecular mechanism of fatty acid hydroxylation by cytochrome P450 from Bacillus subtilis. Crystallographic, spectroscopic, and mutational studies. J Biol Chem, 278, 9761-9767. PubMed id: 12519760 DOI: 10.1074/jbc.M211575200

Date:

10-Oct-02 Release date: 18-Mar-03

Protein chains

O31440  (CYPC_BACSU) -  Fatty-acid peroxygenase from Bacillus subtilis (strain 168)

Seq: 417 a.a.

Struc: 411 a.a.

Enzyme reactions

• Enzyme class: E.C.1.11.2.4 - fatty-acid peroxygenase.
• Reaction:
  1. a 1,2-saturated fatty acid + H2O2 = a 2-hydroxy fatty acid + H2O
  2. a 2,3-saturated fatty acid + H2O2 = a 3-hydroxy fatty acid + H2O
• Cofactor: Heme-thiolate

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

Added reference

DOI no: 10.1074/jbc.M211575200

J Biol Chem 278:9761-9767 (2003)

PubMed id: 12519760

Substrate recognition and molecular mechanism of fatty acid hydroxylation by cytochrome P450 from Bacillus subtilis. Crystallographic, spectroscopic, and mutational studies.

D.S.Lee, A.Yamada, H.Sugimoto, I.Matsunaga, H.Ogura, K.Ichihara, S.Adachi, S.Y.Park, Y.Shiro.

ABSTRACT

Cytochrome P450 isolated from Bacillus subtilis (P450(BSbeta); molecular mass, 48 kDa) catalyzes the hydroxylation of a long-chain fatty acid (e.g. myristic acid) at the alpha- and beta-positions using hydrogen peroxide as an oxidant. We report here on the crystal structure of ferric P450(BSbeta) in the substrate-bound form, determined at a resolution of 2.1 A. P450(BSbeta) exhibits a typical P450 fold. The substrate binds to a specific channel in the enzyme and is stabilized through hydrophobic interactions of its alkyl side chain with some hydrophobic residues on the enzyme as well as by electrostatic interaction of its terminal carboxylate with the Arg(242) guanidium group. These interactions are responsible for the site specificity of the hydroxylation site in which the alpha- and beta-positions of the fatty acid come into close proximity to the heme iron sixth site. The fatty acid carboxylate group interacts with Arg(242) in the same fashion as has been reported for the active site of chloroperoxidase, His(105)-Glu(183), which is an acid-base catalyst in the peroxidation reactions. On the basis of these observations, a possible mechanism for the hydroxylation reaction catalyzed by P450(BSbeta) is proposed in which the carboxylate of the bound-substrate fatty acid assists in the cleavage of the peroxide O-O bond.

Selected figure(s)

Figure 5.
Fig. 5. The "Cys ligand loop" structure in the heme proximal side of P450[BS ](stereo view).

Figure 6.
Fig. 6. Heme pocket structure of P450[BS ](stereo view). Side (A) and top (B) views of the heme plane are illustrated. The heme (purple), palmitic acid (gray), and the hydrogen bonding network of the water molecules (dashed line) are shown. The carboxyl group of the substrate interacts with the guanidium group of Arg242 (light blue) in the I helix (green ribbon). Oxygen and nitrogen atoms are colored red and blue, respectively. The fifth ligand Cys is represented in yellow.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 9761-9767) copyright 2003.

Figures were selected by an automated process.