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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1002/cbic.201500524
  • Primary Citation of Related Structures:  
    4YT3, 5IKI

  • 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 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.


  • Organizational Affiliation

    Department of Biochemistry, Saarland University, Campus B2.2, 66123, Saarbrücken, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450(MEG)
A, B
410Priestia megateriumMutation(s): 0 
Gene Names: cyp106A2
EC: 1.14.99 (PDB Primary Data), 1.14.15.8 (PDB Primary Data)
UniProt
Find proteins for Q06069 (Priestia megaterium)
Explore Q06069 
Go to UniProtKB:  Q06069
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06069
Sequence Annotations
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  • Reference Sequence
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description