5MNS | pdb_00005mns

Structural and functional characterization of OleP in complex with 6DEB in sodium formate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 
    0.258 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1096/fj.201800450RR
  • Primary Citation Related Structures: 
    5MNS, 5MNV

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 276.09 kDa 
  • Atom Count: 19,457 
  • Modeled Residue Count: 2,368 
  • Deposited Residue Count: 2,442 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome P-450
A, B, C, D, E
A, B, C, D, E, F
407Streptomyces antibioticusMutation(s): 0 
Gene Names: oleP
UniProt
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
DEB

Query on DEB



Download:Ideal Coordinates CCD File
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
6-DEOXYERYTHRONOLIDE B
C21 H38 O6
HQZOLNNEQAKEHT-IBBGRPSASA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free:  0.258 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 247.6α = 90
b = 110.8β = 129.6
c = 159.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Istituto Pasteur Fondazione Cenci-BolognettiItalyProt56/2013

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-23
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description