5O98

Binary complex of Catharanthus roseus Vitrosamine Synthase with NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of a Short-Chain Dehydrogenase from Catharanthus roseus that Produces a New Monoterpene Indole Alkaloid.

Stavrinides, A.K.Tatsis, E.C.Dang, T.T.Caputi, L.Stevenson, C.E.M.Lawson, D.M.Schneider, B.O'Connor, S.E.

(2018) Chembiochem 19: 940-948

  • DOI: 10.1002/cbic.201700621

  • PubMed Abstract: 
  • Monoterpene indole alkaloids, a large class of plant natural products, derive from the biosynthetic intermediate strictosidine aglycone. Strictosidine aglycone, which can exist as a variety of isomers, can be reduced to form numerous different struct ...

    Monoterpene indole alkaloids, a large class of plant natural products, derive from the biosynthetic intermediate strictosidine aglycone. Strictosidine aglycone, which can exist as a variety of isomers, can be reduced to form numerous different structures. We have discovered a short chain alcohol dehydrogenase (SDR) from monoterpene indole alkaloid producing plants (Catharanthus roseus and Rauvolfia serpentina) that reduce strictosidine aglycone and produce an alkaloid that does not correspond to any previously reported compound. Here we report the structural characterization of this product, which we have named vitrosamine, as well as the crystal structure of the SDR. This discovery highlights the structural versatility of the strictosidine aglycone biosynthetic intermediate and expands the range of enzymatic reactions that SDRs can catalyze. This discovery further highlights how a sequence-based gene mining discovery approach in plants can reveal cryptic chemistry that would not be uncovered by classical natural product chemistry approaches.


    Organizational Affiliation

    UNITED KINGDOM.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alcohol dehydrogenase 1
A, B
317Catharanthus roseusMutation(s): 0 
Find proteins for A0A0C5DR25 (Catharanthus roseus)
Go to UniProtKB:  A0A0C5DR25
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.830α = 90.00
b = 61.020β = 90.00
c = 162.030γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom311363
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004561/1 (MET)
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N007905/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomDoctoral Training Partnership

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-04-04
    Type: Data collection, Database references
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references