2ZQX

Cytochrome P450BSbeta cocrystallized with heptanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Understanding substrate misrecognition of hydrogen peroxide dependent cytochrome P450 from Bacillus subtilis.

Shoji, O.Fujishiro, T.Nagano, S.Tanaka, S.Hirose, T.Shiro, Y.Watanabe, Y.

(2010) J.Biol.Inorg.Chem. --: --

  • DOI: 10.1007/s00775-010-0692-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytochrome P450(BSβ), a H(2)O(2)-dependent cytochrome P450 catalyzing the hydroxylation of long-alkyl-chain fatty acids, lacks the general acid-base residue around the heme, which is indispensable for the efficient generation of the active species us ...

    Cytochrome P450(BSβ), a H(2)O(2)-dependent cytochrome P450 catalyzing the hydroxylation of long-alkyl-chain fatty acids, lacks the general acid-base residue around the heme, which is indispensable for the efficient generation of the active species using H(2)O(2). On the basis of the crystal structure of the palmitic acid bound form of cytochrome P450(BSβ), it was suggested that the role of the general acid-base function was provided by the carboxylate group of fatty acids. The participation of the carboxylate group of the substrate was supported by the fact that cytochrome P450(BSβ) can catalyze oxidations of nonnatural substrates such as styrene and ethylbenzene in the presence of a series of short-alkyl-chain carboxylic acids as a dummy molecule of fatty acid. We refer to a series of short-alkyl-chain carboxylic acids as a "decoy molecule". As shown here, we have clarified the crystal structure of the decoy-molecule-bound form and elucidated that the location of its carboxylate group is virtually the same as that of palmitic acid in the heme cavity, indicating that the carboxylate group of the decoy molecule serves as the general acid-base catalyst. This result further confirms that the role of the acid-base function is satisfied by the carboxylate group of the substrates. In addition, the structure analysis of the substrate-free form has clarified that no remarkable structural change is induced by the binding of the decoy molecule as well as fatty acid. Consequently, whether the carboxylate group is positioned in the active site provides the switching mechanism of the catalytic cycle of cytochrome P450(BSβ).


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 152A1
A, B, C
417Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: cypC (CYP152A1)
EC: 1.11.2.4
Find proteins for O31440 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31440
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.229 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 172.230α = 90.00
b = 172.230β = 90.00
c = 277.919γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance