OleP, the cytochrome P450 epoxidase from Streptomyces antibioticus involved in Oleandomycin biosynthesis: functional analysis and crystallographic structure in complex with clotrimazole.

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Functional analysis and crystallographic structure of clotrimazole bound OleP, a cytochrome P450 epoxidase from Streptomyces antibioticus involved in oleandomycin biosynthesis.

Montemiglio, L.C.Parisi, G.Scaglione, A.Sciara, G.Savino, C.Vallone, B.

(2015) Biochim Biophys Acta 1860: 465-475

  • DOI: https://doi.org/10.1016/j.bbagen.2015.10.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    OleP is a cyt P450 from Streptomyces antibioticus carrying out epoxigenation of the antibiotic oleandomycin during its biosynthesis. The timing of its reaction has not been fully clarified, doubts remain regarding its substrate and catalytic mechanism. The crystal structure of OleP in complex with clotrimazole, an inhibitor of P450s used in therapy, was solved and the complex formation dynamics was characterized by equilibrium and kinetic binding studies and compared to ketoconazole, another azole differing for the N1-substituent. Clotrimazole coordinates the heme and occupies the active site. Most of the residues interacting with clotrimazole are conserved and involved in substrate binding in MycG, the P450 epoxigenase with the highest homology with OleP. Kinetic characterization of inhibitor binding revealed OleP to follow a simple bimolecular reaction, without detectable intermediates. Clotrimazole-bound OleP adopts an open form, held by a π-π stacking chain that fastens helices F and G and the FG loop. Affinity is affected by the interactions of the N1 substituent within the active site, given the one order of magnitude difference of the off-rate constants between clotrimazole and ketoconazole. Based on structural similarities with MycG, we propose a binding mode for both oleandomycin intermediates, that are the candidate substrates of OleP. Among P450 epoxigenases OleP is the only one that introduces an epoxide on a non-activated C–C bond. The data here presented are necessary to understand the rare chemistry carried out by OleP, to engineer it and to design more selective and potent P450-targeted drugs.

  • Organizational Affiliation

    Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome, Italy; Department of Biochemical Sciences, "Sapienza" University of Rome, P.le A. Moro 5, 00185 Rome, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P-450
A, B
407Streptomyces antibioticusMutation(s): 0 
Gene Names: oleP
Find proteins for Q59819 (Streptomyces antibioticus)
Explore Q59819 
Go to UniProtKB:  Q59819
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59819
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
C34 H32 Fe N4 O4
Query on CL6

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
C22 H17 Cl N2
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.937α = 90
b = 117.379β = 90
c = 174.664γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Istituto Pasteur-Fondazione Cenci BolognettiItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description