 |
PDBsum entry 1izo
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Oxidoreductase
|
PDB id
|
|
|
|
1izo
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Substrate recognition and molecular mechanism of fatty acid hydroxylation by cytochrome p450 from bacillus subtilis. Crystallographic, Spectroscopic, And mutational studies.
|
|
|
Authors
|
|
D.S.Lee,
A.Yamada,
H.Sugimoto,
I.Matsunaga,
H.Ogura,
K.Ichihara,
S.Adachi,
S.Y.Park,
Y.Shiro.
|
|
|
Ref.
|
|
J Biol Chem, 2003,
278,
9761-9767.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
|
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.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Crystallization and preliminary X-Ray diffraction analysis of fatty-Acid hydroxylase cytochrome p450bsbeta from bacillus subtilis.
|
|
|
Authors
|
|
D.S.Lee,
A.Yamada,
I.Matsunaga,
K.Ichihara,
S.Adachi,
S.Y.Park,
Y.Shiro.
|
|
|
Ref.
|
|
Acta Crystallogr D Biol Crystallogr, 2002,
58,
687-689.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
Figure 2.
Figure 2 Bijvoet difference Patterson maps using the data
collected at 1.738 Å. Diffraction data in the resolution range
10-3 Å were used for calculation. The labels correspond to haem
iron-iron self vectors. The positions of the haem irons refined
to (0.909, 0.485, 0.059), (0.508, 0.267, 0.058) and (0.904,
0.156, 0.053) by vector-space refinement.
|
|
|
|
|
|
The above figure is
reproduced from the cited reference
with permission from the IUCr
|
|
|
|
|
|
|
