6ZI2

OleP-oleandolide(DEO) in low salt crystallization conditions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate.

Parisi, G.Freda, I.Exertier, C.Cecchetti, C.Gugole, E.Cerutti, G.D'Auria, L.Macone, A.Vallone, B.Savino, C.Montemiglio, L.C.

(2020) Biomolecules 10

  • DOI: https://doi.org/10.3390/biom10101411
  • Primary Citation of Related Structures:  
    6ZHZ, 6ZI2, 6ZI3, 6ZI7

  • PubMed Abstract: 

    The cytochrome P450 OleP catalyzes the epoxidation of aliphatic carbons on both the aglycone 8.8a-deoxyoleandolide (DEO) and the monoglycosylated L-olivosyl-8.8a-deoxyoleandolide (L-O-DEO) intermediates of oleandomycin biosynthesis. We investigated the substrate versatility of the enzyme. X-ray and equilibrium binding data show that the aglycone DEO loosely fits the OleP active site, triggering the closure that prepares it for catalysis only on a minor population of enzyme. The open-to-closed state transition allows solvent molecules to accumulate in a cavity that forms upon closure, mediating protein-substrate interactions. In silico docking of the monoglycosylated L-O-DEO in the closed OleP-DEO structure shows that the L-olivosyl moiety can be hosted in the same cavity, replacing solvent molecules and directly contacting structural elements involved in the transition. X-ray structures of aglycone-bound OleP in the presence of L-rhamnose confirm the cavity as a potential site for sugar binding. All considered, we propose L-O-DEO as the optimal substrate of OleP, the L-olivosyl moiety possibly representing the molecular wedge that triggers a more efficient structural response upon substrate binding, favoring and stabilizing the enzyme closure before catalysis. OleP substrate versatility is supported by structural solvent molecules that compensate for the absence of a glycosyl unit when the aglycone is bound.


  • Organizational Affiliation

    Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P-450
A, B, C, D, E
A, B, C, D, E, F, G, H, I
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 
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
X [auth H],
Z [auth I]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
QR8 (Subject of Investigation/LOI)
Query on QR8

Download Ideal Coordinates CCD File 
AA [auth I]
K [auth A]
M [auth B]
O [auth C]
Q [auth D]
AA [auth I],
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
S [auth E],
U [auth F],
W [auth G],
Y [auth H]
(3~{R},4~{S},5~{R},6~{S},7~{S},9~{S},11~{R},12~{S},13~{R},14~{R})-3,5,7,9,11,13,14-heptamethyl-4,6,12-tris(oxidanyl)-1-oxacyclotetradecane-2,10-dione
C20 H36 O6
OLPAVFVRSHWADO-ODNSKKOKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.066α = 104.43
b = 116.642β = 104.25
c = 125.17γ = 113.91
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
Pasteur InstituteItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description