5IKI

CYP106A2 WITH SUBSTRATE ABIETIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of CYP106A2 in Substrate-Free and Substrate-Bound Form.

Janocha, S.Carius, Y.Hutter, M.Lancaster, C.R.Bernhardt, R.

(2016) Chembiochem 17: 852-860

  • DOI: 10.1002/cbic.201500524
  • Primary Citation of Related Structures:  
    5IKI, 4YT3

  • PubMed Abstract: 
  • CYP106A2 from Bacillus megaterium ATCC 13368 is known as a bacterial steroid hydroxylase that is also capable of hydroxylating a variety of terpenoids. To analyze the substrate specificity of this enzyme further, different resin acids of the abietane and ...

    CYP106A2 from Bacillus megaterium ATCC 13368 is known as a bacterial steroid hydroxylase that is also capable of hydroxylating a variety of terpenoids. To analyze the substrate specificity of this enzyme further, different resin acids of the abietane and pimarane types were tested with regard to binding and conversion. Product formation could be shown for all tested substrates. Spectroscopic studies revealed type I binding spectra for isopimaric acid, but dehydroabietic acid did not induce a high-spin shift of the enzyme. Interestingly, binding of abietic acid resulted in a type II difference spectrum typical for nitrogenous inhibitors. Co-crystallization of CYP106A2 with abietic acid and structure determination revealed bending of the heme cofactor when abietic acid was bound in the active site. Quantum chemical calculations strongly suggest that this heme distortion is the cause of the unusual spectroscopic characteristics.


    Related Citations: 
    • Identification of CYP106A2 as a regioselective allylic bacterial diterpene hydroxylase.
      Bleif, S., Hannemann, F., Lisurek, M., Von Kries, J.P., Zapp, J., Dietzen, M., Antes, I., Bernhardt, R.
      (2011) Chembiochem 12: 576

    Organizational Affiliation

    Department of Biochemistry, Saarland University, Campus B2.2, 66123, Saarbrücken, Germany. ritabern@mx.uni-saarland.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450(MEG) AB410Priestia megateriumMutation(s): 0 
Gene Names: cyp106A2
EC: 1.14.99 (PDB Primary Data), 1.14.15.8 (PDB Primary Data)
Find proteins for Q06069 (Bacillus megaterium)
Explore Q06069 
Go to UniProtKB:  Q06069
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
A9H
Query on A9H

Download Ideal Coordinates CCD File 
B
Abietic acid
C20 H30 O2
RSWGJHLUYNHPMX-ONCXSQPRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A9HKd:  63840   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.91α = 72.37
b = 57.39β = 75.19
c = 84.24γ = 75.7
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Structure summary