5O7Y

Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum in complex with succinate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of thebaine 6-O-demethylase from the morphine biosynthesis pathway.

Kluza, A.Niedzialkowska, E.Kurpiewska, K.Wojdyla, Z.Quesne, M.Kot, E.Porebski, P.J.Borowski, T.

(2018) J Struct Biol 202: 229-235

  • DOI: https://doi.org/10.1016/j.jsb.2018.01.007
  • Primary Citation of Related Structures:  
    5O7Y, 5O9W

  • PubMed Abstract: 

    Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum (opium poppy), which belongs to the non-heme 2-oxoglutarate/Fe(II)-dependent dioxygenases (ODD) family, is a key enzyme in the morphine biosynthesis pathway. Initially, T6ODM was characterized as an enzyme catalyzing O-demethylation of thebaine to neopinone and oripavine to morphinone. However, the substrate range of T6ODM was recently expanded to a number of various benzylisoquinoline alkaloids. Here, we present crystal structures of T6ODM in complexes with 2-oxoglutarate (T6ODM:2OG, PDB: 5O9W) and succinate (T6ODM:SIN, PDB: 5O7Y). Both metal and 2OG binding sites display similarity to other proteins from the ODD family, but T6ODM is characterized by an exceptionally large substrate binding cavity, whose volume can partially explain the promiscuity of this enzyme. Moreover, the size of the cavity allows for binding of multiple molecules at once, posing a question about the substrate-driven specificity of the enzyme.


  • Organizational Affiliation

    Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thebaine 6-O-demethylase367Papaver somniferumMutation(s): 0 
Gene Names: T6ODMDIOX1
EC: 1.14.11.31
UniProt
Find proteins for D4N500 (Papaver somniferum)
Explore D4N500 
Go to UniProtKB:  D4N500
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4N500
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIN (Subject of Investigation/LOI)
Query on SIN

Download Ideal Coordinates CCD File 
C [auth A]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
U [auth A],
V [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI (Subject of Investigation/LOI)
Query on NI

Download Ideal Coordinates CCD File 
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.231α = 90
b = 87.028β = 90
c = 94.171γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Centre, PolandPolandUMO-2014/14/E/NZ1/00053

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection
  • Version 1.2: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.3: 2020-04-22
    Changes: Database references
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description