5MNV

Structural and functional characterization of OleP in complex with 6DEB in PEG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Substrate-induced conformational change in cytochrome P450 OleP.

Parisi, G.Montemiglio, L.C.Giuffre, A.Macone, A.Scaglione, A.Cerutti, G.Exertier, C.Savino, C.Vallone, B.

(2019) FASEB J. 33: 1787-1800

  • DOI: 10.1096/fj.201800450RR
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The regulation of cytochrome P450 activity is often achieved by structural transitions induced by substrate binding. We describe the conformational transition experienced upon binding by the P450 OleP, an epoxygenase involved in oleandomycin biosynth ...

    The regulation of cytochrome P450 activity is often achieved by structural transitions induced by substrate binding. We describe the conformational transition experienced upon binding by the P450 OleP, an epoxygenase involved in oleandomycin biosynthesis. OleP bound to the substrate analog 6DEB crystallized in 2 forms: one with an ensemble of open and closed conformations in the asymmetric unit and another with only the closed conformation. Characterization of OleP-6DEB binding kinetics, also using the P450 inhibitor clotrimazole, unveiled a complex binding mechanism that involves slow conformational rearrangement with the accumulation of a spectroscopically detectable intermediate where 6DEB is bound to open OleP. Data reported herein provide structural snapshots of key precatalytic steps in the OleP reaction and explain how structural rearrangements induced by substrate binding regulate activity.-Parisi, G., Montemiglio, L. C., Giuffrè, A., Macone, A., Scaglione, A., Cerutti, G., Exertier, C., Savino, C., Vallone, B. Substrate-induced conformational change in cytochrome P450 OleP.


    Organizational Affiliation

    Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P-450
A, B, C, D, E, F, G, H, I
407Streptomyces antibioticusMutation(s): 0 
Gene Names: oleP
Find proteins for Q59819 (Streptomyces antibioticus)
Go to UniProtKB:  Q59819
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DEB
Query on DEB

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
6-DEOXYERYTHRONOLIDE B
C21 H38 O6
HQZOLNNEQAKEHT-IBBGRPSASA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.238 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 112.500α = 103.90
b = 116.700β = 104.30
c = 123.300γ = 114.70
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Istituto Pasteur Fondazione Cenci-BolognettiItaly--

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-11-14
    Type: Data collection, Database references
  • Version 1.2: 2019-02-27
    Type: Data collection, Database references