6E6Y | pdb_00006e6y

Dieckmann cyclase, NcmC

• PDB DOI: https://doi.org/10.2210/pdb6E6Y/pdb

• Classification: BIOSYNTHETIC PROTEIN
• 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: 
  0.204 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

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 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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.82 kDa 
• Atom Count: 4,474 
• Modeled Residue Count: 536 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dieckmann cyclase, 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [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:  0.204 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.435	α = 90
b = 80.435	β = 90
c = 77.923	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data scaling
AutoSol	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 1.2: 2020-10-21
  Changes: Database references, Refinement description
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references