8QRD | pdb_00008qrd

OleP in complex with testosterone in high salt crystallization conditions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.212 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Binding of steroid substrates reveals the key to the productive transition of the cytochrome P450 OleP.

Costanzo, A.Fata, F.Freda, I.De Sciscio, M.L.Gugole, E.Bulfaro, G.Di Renzo, M.Barbizzi, L.Exertier, C.Parisi, G.D'Abramo, M.Vallone, B.Savino, C.Montemiglio, L.C.

(2024) Structure 32: 1465-1476.e3

  • DOI: https://doi.org/10.1016/j.str.2024.06.005
  • Primary Citation Related Structures: 
    8QRD, 8QYI

  • PubMed Abstract: 

    OleP is a bacterial cytochrome P450 involved in oleandomycin biosynthesis as it catalyzes regioselective epoxidation on macrolide intermediates. OleP has recently been reported to convert lithocholic acid (LCA) into murideoxycholic acid through a highly regioselective reaction and to unspecifically hydroxylate testosterone (TES). Since LCA and TES mainly differ by the substituent group at the C17, here we used X-ray crystallography, equilibrium binding assays, and molecular dynamics simulations to investigate the molecular basis of the diverse reactivity observed with the two steroids. We found that the differences in the structure of TES and LCA affect the capability of these molecules to directly form hydrogen bonds with N-terminal residues of OleP internal helix I. The establishment of these contacts, by promoting the bending of helix I, fosters an efficient trigger of the open-to-closed structural transition that occurs upon substrate binding to OleP and contributes to the selectivity of the subsequent monooxygenation reaction.


  • Organizational Affiliation
    • Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy.

Macromolecule Content 

  • Total Structure Weight: 279.45 kDa 
  • Atom Count: 20,262 
  • Modeled Residue Count: 2,380 
  • Deposited Residue Count: 2,460 
  • 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
410Streptomyces 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
EB [auth E]
FA [auth C]
G [auth A]
KB [auth F]
P [auth B]
EB [auth E],
FA [auth C],
G [auth A],
KB [auth F],
P [auth B],
UA [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
TES
(Subject of Investigation/LOI)

Query on TES



Download:Ideal Coordinates CCD File
FB [auth E]
GA [auth C]
H [auth A]
LB [auth F]
Q [auth B]
FB [auth E],
GA [auth C],
H [auth A],
LB [auth F],
Q [auth B],
VA [auth D]
TESTOSTERONE
C19 H28 O2
MUMGGOZAMZWBJJ-DYKIIFRCSA-N
FMT

Query on FMT



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth D]
BA [auth B]
BB [auth D]
CA [auth B]
AA [auth B],
AB [auth D],
BA [auth B],
BB [auth D],
CA [auth B],
CB [auth D],
DA [auth B],
GB [auth E],
HA [auth C],
HB [auth E],
I [auth A],
IA [auth C],
IB [auth E],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
MB [auth F],
N [auth A],
NA [auth C],
NB [auth F],
OA [auth C],
OB [auth F],
PA [auth C],
PB [auth F],
QA [auth C],
QB [auth F],
R [auth B],
RA [auth C],
S [auth B],
SA [auth C],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
WA [auth D],
X [auth B],
XA [auth D],
Y [auth B],
YA [auth D],
Z [auth B],
ZA [auth D]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
DB [auth D]
EA [auth B]
JB [auth E]
O [auth A]
RB [auth F]
DB [auth D],
EA [auth B],
JB [auth E],
O [auth A],
RB [auth F],
TA [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.212 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 248.195α = 90
b = 109.738β = 129.41
c = 160.13γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Database references, Structure summary