8B25

Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga - stemmadenine acetate bound structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism.

Langley, C.Tatsis, E.Hong, B.Nakamura, Y.Paetz, C.Stevenson, C.E.M.Basquin, J.Lawson, D.M.Caputi, L.O'Connor, S.E.

(2022) Angew Chem Int Ed Engl 61: e202210934-e202210934

  • DOI: https://doi.org/10.1002/anie.202210934
  • Primary Citation of Related Structures:  
    8A3N, 8B1V, 8B25, 8B26, 8B27

  • PubMed Abstract: 

    Medium-chain alcohol dehydrogenases (ADHs) comprise a highly conserved enzyme family that catalyse the reversible reduction of aldehydes. However, recent discoveries in plant natural product biosynthesis suggest that the catalytic repertoire of ADHs has been expanded. Here we report the crystal structure of dihydroprecondylocarpine acetate synthase (DPAS), an ADH that catalyses the non-canonical 1,4-reduction of an α,β-unsaturated iminium moiety. Comparison with structures of plant-derived ADHs suggest the 1,4-iminium reduction does not require a proton relay or the presence of a catalytic zinc ion in contrast to canonical 1,2-aldehyde reducing ADHs that require the catalytic zinc and a proton relay. Furthermore, ADHs that catalysed 1,2-iminium reduction required the presence of the catalytic zinc and the loss of the proton relay. This suggests how the ADH active site can be modified to perform atypical carbonyl reductions, providing insight into how chemical reactions are diversified in plant metabolism.


  • Organizational Affiliation

    Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll Straße 8, Jena, 07745, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroprecondylocarpine acetate synthase 2
A, B
365Tabernanthe ibogaMutation(s): 0 
UniProt
Find proteins for A0A5B8X8Z0 (Tabernanthe iboga)
Explore A0A5B8X8Z0 
Go to UniProtKB:  A0A5B8X8Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5B8X8Z0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OSO (Subject of Investigation/LOI)
Query on OSO

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
stemmadenine acetate
C23 H29 N2 O4
ZNCUMLJVNWXVLT-ISNKGDJGSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
K [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.186α = 90
b = 79.845β = 90
c = 130.922γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
European Research Council (ERC)European Union788301

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2022-11-30
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description