3AWM

Cytochrome P450SP alpha (CYP152B1) wild-type with palmitic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of H2O2-dependent cytochrome P450SPalpha with its bound fatty acid substrate: insight into the regioselective hydroxylation of fatty acids at the alpha position

Fujishiro, T.Shoji, O.Nagano, S.Sugimoto, H.Shiro, Y.Watanabe, Y.

(2011) J.Biol.Chem. 286: 29941-29950

  • DOI: 10.1074/jbc.M111.245225
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytochrome P450(SPα) (CYP152B1) isolated from Sphingomonas paucimobilis is the first P450 to be classified as a H(2)O(2)-dependent P450. P450(SPα) hydroxylates fatty acids with high α-regioselectivity. Herein we report the crystal structure of P450(S ...

    Cytochrome P450(SPα) (CYP152B1) isolated from Sphingomonas paucimobilis is the first P450 to be classified as a H(2)O(2)-dependent P450. P450(SPα) hydroxylates fatty acids with high α-regioselectivity. Herein we report the crystal structure of P450(SPα) with palmitic acid as a substrate at a resolution of 1.65 Å. The structure revealed that the C(α) of the bound palmitic acid in one of the alternative conformations is 4.5 Å from the heme iron. This conformation explains the highly selective α-hydroxylation of fatty acid observed in P450(SPα). Mutations at the active site and the F-G loop of P450(SPα) did not impair its regioselectivity. The crystal structures of mutants (L78F and F288G) revealed that the location of the bound palmitic acid was essentially the same as that in the WT, although amino acids at the active site were replaced with the corresponding amino acids of cytochrome P450(BSβ) (CYP152A1), which shows β-regioselectivity. This implies that the high regioselectivity of P450(SPα) is caused by the orientation of the hydrophobic channel, which is more perpendicular to the heme plane than that of P450(BSβ).


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fatty acid alpha-hydroxylase
A
415Sphingomonas paucimobilisMutation(s): 0 
Find proteins for O24782 (Sphingomonas paucimobilis)
Go to UniProtKB:  O24782
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download SDF File 
Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-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
PLM
Query on PLM

Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.151 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 94.440α = 90.00
b = 94.440β = 90.00
c = 113.553γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
DENZOdata reduction
HKL-2000data collection
SHELXDphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
SHELXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-06-05
    Type: Database references