Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106382.93 
• Atom Count: 7412 
• Residue Count: 910 
• Unique protein chains: 1

4KEW

structure of the A82F BM3 heme domain in complex with omeprazole

• DOI: 10.2210/pdb4KEW/pdb

• Classification: Oxidoreductase/Oxidoreductase inhibitor
• Organism(s): Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512)
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2013-04-26 Released: 2013-07-10 
• Deposition Author(s): Leys, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.237 
• R-Value Work: 0.188 

Literature

Key Mutations Alter the Cytochrome P450 BM3 Conformational Landscape and Remove Inherent Substrate Bias.

Butler, C.F., Peet, C., Mason, A.E., Voice, M.W., Leys, D., Munro, A.W.

(2013) J.Biol.Chem. 288: 25387-25399

• PubMed: 23828198 
• DOI: 10.1074/jbc.M113.479717
• Primary Citation of Related Structures:  
  4KF2, 4KF0, 4KEY


• PubMed Abstract: 
  

Cytochrome P450 monooxygenases (P450s) have enormous potential in the production of oxychemicals, due to their unparalleled regio- and stereoselectivity. The Bacillus megaterium P450 BM3 enzyme is a key model system, with several mutants (many distant from the active site) reported to alter substrate selectivity. It has the highest reported monooxygenase activity of the P450 enzymes, and this catalytic efficiency has inspired protein engineering to enable its exploitation for biotechnologically relevant oxidations with structurally diverse substrates. However, a structural rationale is lacking to explain how these mutations have such effects in the absence of direct change to the active site architecture. Here, we provide the first crystal structures of BM3 mutants in complex with a human drug substrate, the proton pump inhibitor omeprazole. Supported by solution data, these structures reveal how mutation alters the conformational landscape and decreases the free energy barrier for transition to the substrate-bound state. Our data point to the importance of such "gatekeeper" mutations in enabling major changes in substrate recognition. We further demonstrate that these mutants catalyze the same 5-hydroxylation reaction as performed by human CYP2C19, the major human omeprazole-metabolizing P450 enzyme.

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Organizational Affiliation: 

Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Bifunctional P-450/NADPH-P450 reductase	A, B	455	Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512)	Mutation(s): 1  Gene Names: cyp102A1 (cyp102)
Find proteins for P14779 (Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512)) Go to UniProtKB:  P14779

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
1C6	A, B	6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole omeprazole, prilosec C17 H19 N3 O2 S XURCIPRUUASYLR-UHFFFAOYSA-N
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1C6	Kd: 1670 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.237 
• R-Value Work: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 59.430	α = 90.00
b = 129.510	β = 90.00
c = 145.090	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
XDS	data reduction
ADSC	data collection
REFMAC	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-26 
• Released Date: 2013-07-10 
• Deposition Author(s): Leys, D.

Revision History 

• Version 1.0: 2013-07-10
  Type: Initial release
• Version 1.1: 2013-10-02
  Type: Database references