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PDBsum entry 2q9f
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Oxidoreductase
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PDB id
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2q9f
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References listed in PDB file
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Key reference
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Title
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Crystal structures of substrate-Bound and substrate-Free cytochrome p450 46a1, The principal cholesterol hydroxylase in the brain.
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Authors
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N.Mast,
M.A.White,
I.Bjorkhem,
E.F.Johnson,
C.D.Stout,
I.A.Pikuleva.
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Ref.
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Proc Natl Acad Sci U S A, 2008,
105,
9546-9551.
[DOI no: ]
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PubMed id
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Abstract
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By converting cholesterol to 24S-hydroxycholesterol, cytochrome P450 46A1
(CYP46A1) initiates the major pathway for cholesterol removal from the brain.
Two crystal structures of CYP46A1 were determined. First is the 1.9-A structure
of CYP46A1 complexed with a high-affinity substrate cholesterol 3-sulfate
(CH-3S). The second structure is that of the substrate-free CYP46A1 at 2.4-A
resolution. CH-3S is bound in the productive orientation and occupies the entire
length of the banana-shaped hydrophobic active-site cavity. A unique helix B'-C
loop insertion (residues 116-120) contributes to positioning cholesterol for
oxygenation catalyzed by CYP46A1. A comparison with the substrate-free structure
reveals substantial substrate-induced conformational changes in CYP46A1 and
suggests that structurally distinct compounds could bind in the enzyme active
site. In vitro assays were performed to characterize the effect of different
therapeutic agents on cholesterol hydroxylase activity of purified full-length
recombinant CYP46A1, and several strong inhibitors and modest coactivators of
CYP46A1 were identified. Structural and biochemical data provide evidence that
CYP46A1 activity could be altered by exposure to some therapeutic drugs and
potentially other xenobiotics.
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Figure 1.
CYP46A1 active site. (a) The composite-omit 2|F[o]|−|F[c]|
electron density map (green mesh) contoured at 1.5σ around the
heme (in pink) and CH-3S (in yellow). Amino acid residues (in
cyan) within 4 Å of CH-3S are shown. The heme iron and
water molecule 732 are represented as big brown and small red
spheres, respectively. The oxygen, nitrogen, and sulfur atoms
are in red, blue, and orange, respectively. Dashed cyan lines
indicate hydrogen bonds. Residues forming a circular scaffold
are labeled in red. (b) Enlarged view of the active site around
the sulfate anion of CH-3S and (c) in the vicinity of the heme
iron. Dashed gray lines connect the C24 and C25 of CH-3S and the
heme iron.
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Figure 2.
Superposition of CH-3S-bound CYP46A1 structure (colored from
blue at the N terminus to red at the C terminus) and vitamin
D[3]-bound CYP2R1 structure (in wheat) shown in stereoview.
CH-3S and vitamin D[3] are in yellow and cyan, respectively, and
heme is in pink in CYP46A1 and in light pink in CYP2R1.
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Secondary reference #1
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Title
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Use of complementary cation and anion heavy-Atom salt derivatives to solve the structure of cytochrome p450 46a1.
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Authors
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M.A.White,
N.Mast,
I.Bjorkhem,
E.F.Johnson,
C.D.Stout,
I.A.Pikuleva.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2008,
64,
487-495.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3 Patterson maps. These are xy Harker sections showing
the asymmetric unit. Bijvoet difference Patterson maps at (a) z
= 0.5 and (b) z = 0.25 are shown for the native data.
Isomorphous difference Patterson maps at z = 0.5 are shown for
(c) the NaI and (d) the CsCl quick-soak derivatives,
respectively. Maps are contoured starting at 3  in
0.5 steps.
Predicted Patterson peaks are labelled with a cross; observed
peaks are labelled with the atom name. The iron anomalous and
caesium isomorphous difference maps are at 2.6 Å
resolution, while the iodide isomorphous derivative map is
limited to 2.8 Å resolution. The origin peak at (1/2, 1/2,
1/2) has been removed.
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Figure 4.
Figure 4 Complementary cation and anion heavy-atom
salt-derivative sites. Cross-eyed stereoview of the incomplete
N-to-C-termini rainbow-colored CYP46A1 protein backbone and
heavy-atom sites (colored spheres: I, purple; Cs, green) showing
the nearby interacting residues as sticks. This figure was
created using PyMOL (DeLano, 2003[DeLano, W. L. (2003). The
PyMOL Molecular Graphics System. http://www.pymol.org . ]).
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the IUCr
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