6P29

N-demethylindolmycin synthase (PluN2) in complex with N-demethylindolmycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Convergent biosynthetic transformations to a bacterial specialized metabolite.

Du, Y.L.Higgins, M.A.Zhao, G.Ryan, K.S.

(2019) Nat.Chem.Biol. 15: 1043-1048

  • DOI: 10.1038/s41589-019-0331-5

  • PubMed Abstract: 
  • Microbes produce specialized metabolites to thrive in their natural habitats. However, it is rare that a given specialized metabolite is biosynthesized via pathways with distinct intermediates and enzymes. Here, we show that the core assembly mechani ...

    Microbes produce specialized metabolites to thrive in their natural habitats. However, it is rare that a given specialized metabolite is biosynthesized via pathways with distinct intermediates and enzymes. Here, we show that the core assembly mechanism of the antibiotic indolmycin in marine gram-negative Pseudoalteromonas luteoviolacea is distinct from its counterpart in terrestrial gram-positive Streptomyces species, with a molecule that is a shunt product in the Streptomyces pathway employed as a biosynthetic substrate for a novel metal-independent N-demethylindolmycin synthase in the P. luteoviolacea pathway. To provide insight into this reaction, we solved the 1.5 Å resolution structure in complex with product and identified the active site residues. Guided by our biosynthetic insights, we then engineered the Streptomyces indolmycin producer for titer improvement. This study provides a paradigm for understanding how two unique routes to a microbial specialized metabolite can emerge from convergent biosynthetic transformations.


    Organizational Affiliation

    Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. yldu@zju.edu.cn.,Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada. ksryan@chem.ubc.ca.,Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-demethylindolmycin synthase (PluN2)
A, B
140Pseudoalteromonas luteoviolacea CPMOR-1Mutation(s): 0 
Find proteins for A0A167HII1 (Pseudoalteromonas luteoviolacea CPMOR-1)
Go to UniProtKB:  A0A167HII1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NQ7
Query on NQ7

Download SDF File 
Download CCD File 
A, B
(5S)-2-amino-5-[(1R)-1-(1H-indol-3-yl)ethyl]-1,3-oxazol-4(5H)-one
C13 H13 N3 O2
JMQXZRUQJGJVSC-HQJQHLMTSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 54.070α = 90.00
b = 54.070β = 90.00
c = 176.930γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOSFLMdata reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)Canada--

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-28
    Type: Data collection, Database references
  • Version 1.2: 2019-10-30
    Type: Data collection, Database references