2Q9F

Crystal structure of human cytochrome P450 46A1 in complex with cholesterol-3-sulphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of substrate-bound and substrate-free cytochrome P450 46A1, the principal cholesterol hydroxylase in the brain.

Mast, N.White, M.A.Bjorkhem, I.Johnson, E.F.Stout, C.D.Pikuleva, I.A.

(2008) Proc.Natl.Acad.Sci.Usa 105: 9546-9551

  • DOI: 10.1073/pnas.0803717105
  • Primary Citation of Related Structures:  2Q9G
  • Also Cited By: 3MDM, 3MDR, 3MDT, 3MDV

  • PubMed Abstract: 
  • 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 complex ...

    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.


    Related Citations: 
    • Use of complementary cation and anion heavy-atom salt derivatives to solve the structure of cytochrome P450 46A1.
      White, M.A.,Mast, N.,Bjorkhem, I.,Johnson, E.F.,Stout, C.D.,Pikuleva, I.A.
      (2008) Acta Crystallogr.,Sect.D 64: 487


    Organizational Affiliation

    Department of Pharmacology and Toxicology, The Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 46A1
A
456Homo sapiensGene Names: CYP46A1 (CYP46)
EC: 1.14.14.25
Find proteins for Q9Y6A2 (Homo sapiens)
Go to Gene View: CYP46A1
Go to UniProtKB:  Q9Y6A2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
C3S
Query on C3S

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Download CCD File 
A
CHOLEST-5-EN-3-YL HYDROGEN SULFATE
CHOLESTEROL-SULFATE
C27 H46 O4 S
BHYOQNUELFTYRT-DPAQBDIFSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C3SKd: 7 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 121.850α = 90.00
b = 121.850β = 90.00
c = 144.030γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
SOLVEphasing
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance