3EJD

Crystal Structure of P450BioI in complex with hexadec-9Z-enoic acid ligated Acyl Carrier Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450(BioI) ACP complex.

Cryle, M.J.Schlichting, I.

(2008) Proc.Natl.Acad.Sci.Usa 105: 15696-15701

  • DOI: 10.1073/pnas.0805983105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytochrome P450(BioI) (CYP107H1) from the biotin operon of Bacillus subtilis forms a seven-carbon diacid through a multistep oxidative cleavage of a fatty acid linked to acyl carrier protein (ACP). Crystal structures of P450(BioI) in complex with thr ...

    Cytochrome P450(BioI) (CYP107H1) from the biotin operon of Bacillus subtilis forms a seven-carbon diacid through a multistep oxidative cleavage of a fatty acid linked to acyl carrier protein (ACP). Crystal structures of P450(BioI) in complex with three different length fatty acyl-ACP (Escherichia coli) ligands show that P450(BioI) binds the fatty acid such as to force the carbon chain into a U-shape above the active site heme. This positions the C7 and C8 carbons for oxidation, with a large additional cavity extending beyond the heme to accommodate the methyl termini of fatty acids beyond the site of cleavage. The structures explain the experimentally observed lack of stereo- and regiospecificity in the hydroxylation and cleavage of free fatty acids. The P450(BioI)-ACP complexes represent the only structurally characterized P450-carrier protein complexes to date, which has allowed the generation of a model of the interaction of the vancomycin biosynthetic P450 OxyB with its proposed carrier protein bound substrate.


    Organizational Affiliation

    Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany. Max.Cryle@mpimf-heidelberg.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein
A, C, E, G
97Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: acpP
Find proteins for P0A6A8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6A8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Biotin biosynthesis cytochrome P450-like enzyme
B, D, F, H
404Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: bioI (CYP107H)
EC: 1.14.14.46
Find proteins for P53554 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P53554
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
HTG
Query on HTG

Download SDF File 
Download CCD File 
A, C, D, E, F, G, H
HEPTYL 1-THIOHEXOPYRANOSIDE
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
ZMQ
Query on ZMQ

Download SDF File 
Download CCD File 
A, C, E, G
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-hexadec-9-enethioate
C27 H51 N2 O8 P S
IKLUIZJWBLJHAQ-HAAQQRBASA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
B, D, F, H
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: 2.1 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.241 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.300α = 109.00
b = 92.100β = 89.20
c = 107.700γ = 90.10
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
XSCALEdata scaling
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-03-08
    Type: Non-polymer description