6E6T

Dieckmann cyclase, NcmC, bound to cerulenin

• PDB DOI: https://doi.org/10.2210/pdb6E6T/pdb

• Classification: LYASE/ANTIBIOTIC
• Organism(s): Saccharothrix syringae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-07-25 Released: 2019-07-31 
• Deposition Author(s): Cogan, D.P., Nair, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.218 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

Structural Basis for Enzymatic Off-Loading of Hybrid Polyketides by Dieckmann Condensation.

Cogan, D.P., Ly, J., Nair, S.K.

(2020) ACS Chem Biol 

• PubMed: 33017142 
• DOI: https://doi.org/10.1021/acschembio.0c00579
• Primary Citation of Related Structures:  
  6E6T, 6E6U, 6E6Y


• PubMed Abstract: 
  

  While several bioactive natural products that contain tetramate or pyridone heterocycles have been described, information on the enzymology underpinning these functionalities has been limited. Here we biochemically characterize an off-loading Dieckmann cyclase, NcmC, that installs the tetramate headgroup in nocamycin, a hybrid polyketide/nonribosomal peptide natural product. Crystal structures of the enzyme (1.6 Å) and its covalent complex with the epoxide cerulenin (1.6 Å) guide additional structure-based mutagenesis and product-profile analyses. Our results offer mechanistic insights into how the conserved thioesterase-like scaffold has been adapted to perform a new chemical reaction, namely, heterocyclization. Additional bioinformatics combined with docking and modeling identifies likely candidates for heterocycle formation in underexplored gene clusters and uncovers a modular basis of substrate recognition by the two subdomains of these Dieckmann cyclases.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.27 kDa 
• Atom Count: 4,312 
• Modelled Residue Count: 525 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NcmC	A, B	275	Saccharothrix syringae	Mutation(s): 0
UniProt
Find proteins for A0A1X9WEN9 (Saccharothrix syringae) Explore A0A1X9WEN9  Go to UniProtKB:  A0A1X9WEN9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HVV (Subject of Investigation/LOI)	D [auth A], F [auth B]	(4S,5R)-4,5-dihydroxy-5-[(3E,6E)-octa-3,6-dien-1-yl]pyrrolidin-2-one C12 H19 N O3 VIMHNMLESUAQPL-JFDNTZKISA-N
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.218 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.269	α = 90
b = 80.269	β = 90
c = 77.743	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Cogan, D.P., Nair, S.K.

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2020-02-12
  Changes: Database references
• Version 2.0: 2020-08-05
  Type: Coordinate replacement
  Reason: Real space R-factor
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Experimental preparation, Other, Refinement description, Structure summary
• Version 2.1: 2020-10-21
  Changes: Database references
• Version 2.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description