Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 95.57 kDa 
• Atom Count: 6410 
• Residue Count: 782 
• Unique protein chains: 1

5IKI

CYP106A2 WITH SUBSTRATE ABIETIC ACID

• DOI: 10.2210/pdb5IKI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-03 Released: 2016-05-25 
• Deposition Author(s): Janocha, S., Carius, Y., Bernhardt, R., Lancaster, C.R.D.

---

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 

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

• PubMed: 26864272 
• 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 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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450(MEG)	A, B	410	Priestia megaterium	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
A9H	B	Abietic acid C20 H30 O2 RSWGJHLUYNHPMX-ONCXSQPRSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
A9H	Kd:  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 = 48.91	α = 72.37
b = 57.39	β = 75.19
c = 84.24	γ = 75.7

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-03 
• Released Date: 2016-05-25 
Deposition Author(s): Janocha, S., Carius, Y., Bernhardt, R., Lancaster, C.R.D.

Revision History 

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