6ZI7

Crystal structure of OleP-oleandolide(DEO) bound to L-rhamnose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
CC [auth B]
CH [auth E]
G [auth A]
QD [auth C]
QF [auth D]
CC [auth B],
CH [auth E],
G [auth A],
QD [auth C],
QF [auth D],
TH [auth F]
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 
DC [auth B]
DH [auth E]
H [auth A]
RD [auth C]
RF [auth D]
DC [auth B],
DH [auth E],
H [auth A],
RD [auth C],
RF [auth D],
UH [auth F]
(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
RAM
Query on RAM

Download Ideal Coordinates CCD File 
I [auth A],
OC [auth B],
SF [auth D]
alpha-L-rhamnopyranose
C6 H12 O5
SHZGCJCMOBCMKK-HGVZOGFYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
AD [auth B]
AE [auth C]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth B],
AE [auth C],
AF [auth C],
AG [auth D],
AH [auth D],
AI [auth F],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth B],
BE [auth C],
BF [auth C],
BG [auth D],
BH [auth E],
BI [auth F],
CA [auth A],
CB [auth A],
CD [auth B],
CE [auth C],
CF [auth C],
CI [auth F],
DA [auth A],
DB [auth A],
DD [auth B],
DE [auth C],
DF [auth C],
DG [auth D],
DI [auth F],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth C],
EF [auth C],
EG [auth D],
EH [auth E],
EI [auth F],
FB [auth A],
FC [auth B],
FD [auth B],
FE [auth C],
FF [auth C],
FG [auth D],
FH [auth E],
FI [auth F],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GE [auth C],
GF [auth C],
GG [auth D],
GH [auth E],
GI [auth F],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth C],
HF [auth C],
HG [auth D],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IE [auth C],
IF [auth C],
IG [auth D],
IH [auth E],
J [auth A],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JE [auth C],
JF [auth C],
JG [auth D],
JH [auth E],
K [auth A],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KE [auth C],
KF [auth C],
KG [auth D],
KH [auth E],
L [auth A],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LE [auth C],
LF [auth C],
LG [auth D],
LH [auth E],
M [auth A],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth C],
MF [auth C],
MG [auth D],
MH [auth E],
N [auth A],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth C],
NF [auth C],
NG [auth D],
NH [auth E],
O [auth A],
OA [auth A],
OB [auth A],
OD [auth B],
OE [auth C],
OF [auth C],
OG [auth D],
OH [auth E],
P [auth A],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth C],
PF [auth C],
PG [auth D],
PH [auth E],
Q [auth A],
QA [auth A],
QB [auth A],
QG [auth D],
QH [auth E],
R [auth A],
RA [auth A],
RB [auth A],
RC [auth B],
RE [auth C],
RG [auth D],
RH [auth E],
S [auth A],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth C],
SE [auth C],
SG [auth D],
SH [auth F],
T [auth A],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth C],
TE [auth C],
TF [auth D],
TG [auth D],
U [auth A],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth C],
UE [auth C],
UF [auth D],
UG [auth D],
V [auth A],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth C],
VE [auth C],
VF [auth D],
VG [auth D],
VH [auth F],
W [auth A],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth C],
WE [auth C],
WF [auth D],
WG [auth D],
WH [auth F],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth C],
XE [auth C],
XF [auth D],
XG [auth D],
XH [auth F],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth C],
YE [auth C],
YF [auth D],
YG [auth D],
YH [auth F],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZD [auth C],
ZE [auth C],
ZF [auth D],
ZG [auth D]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
CG [auth D]
FA [auth A]
HH [auth E]
QC [auth B]
QE [auth C]
CG [auth D],
FA [auth A],
HH [auth E],
QC [auth B],
QE [auth C],
ZH [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 247.531α = 90
b = 110.683β = 129.46
c = 159.285γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



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