6P29 | pdb_00006p29

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

• PDB DOI: https://doi.org/10.2210/pdb6P29/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Pseudoalteromonas luteoviolacea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-21 Released: 2019-08-07 
• Deposition Author(s): Du, Y.L., Higgins, M.A., Zhao, G., Ryan, K.S.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

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

• PubMed: 31406372 
• DOI: https://doi.org/10.1038/s41589-019-0331-5
• Primary Citation Related Structures: 
  6P29


• 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 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.

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Organizational Affiliation: 
• Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. [e-mail].
Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.
Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.4 kDa 
• Atom Count: 2,424 
• Modeled Residue Count: 263 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-demethylindolmycin synthase (PluN2)	A, B	140	Pseudoalteromonas luteoviolacea	Mutation(s): 0  Gene Names: N473_05385
UniProt
Find proteins for A0A167HII1 (Pseudoalteromonas luteoviolacea CPMOR-1) Explore A0A167HII1  Go to UniProtKB:  A0A167HII1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NQ7 (Subject of Investigation/LOI)	C [auth A], E [auth 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
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.07	α = 90
b = 54.07	β = 90
c = 176.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Du, Y.L., Higgins, M.A., Zhao, G., Ryan, K.S.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2019-08-28
  Changes: Data collection, Database references
• Version 1.2: 2019-10-30
  Changes: Data collection, Database references
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references