3EJB

Crystal Structure of P450BioI in complex with tetradecanoic acid ligated Acyl Carrier Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

Starting Model: experimental
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This is version 1.5 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 U S A 105: 15696-15701

  • DOI: https://doi.org/10.1073/pnas.0805983105
  • Primary Citation of Related Structures:  
    3EJB, 3EJD, 3EJE

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein
A, C, E, G
97Escherichia coli K-12Mutation(s): 0 
Gene Names: acpPb1094JW1080
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12))
Explore P0A6A8 
Go to UniProtKB:  P0A6A8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6A8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Biotin biosynthesis cytochrome P450-like enzyme
B, D, F, H
404Bacillus subtilisMutation(s): 0 
Gene Names: bioICYP107HBSU30190
EC: 1.14 (PDB Primary Data), 1.14.14.46 (UniProt)
UniProt
Find proteins for P53554 (Bacillus subtilis (strain 168))
Explore P53554 
Go to UniProtKB:  P53554
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53554
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
L [auth B],
P [auth D],
T [auth F],
Y [auth H]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ZMP
Query on ZMP

Download Ideal Coordinates CCD File 
I [auth A],
N [auth C],
R [auth E],
W [auth G]
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
HTG
Query on HTG

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
O [auth C]
Q [auth D]
S [auth E]
J [auth A],
K [auth A],
O [auth C],
Q [auth D],
S [auth E],
U [auth F],
X [auth G],
Z [auth H]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth B],
V [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.3α = 109
b = 92.1β = 89.2
c = 107.7γ = 90.1
Software Package:
Software NamePurpose
XDSdata scaling
Cootmodel building
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2016-08-24
    Changes: Non-polymer description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-09
    Changes: Structure summary