7E3Z | pdb_00007e3z

Non-Ribosomal Peptide Synthetases, Thioesterase

• PDB DOI: https://doi.org/10.2210/pdb7E3Z/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces sp. SNM55
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-02-09 Released: 2021-12-22 
• Deposition Author(s): Jung, Y.E., Cha, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Unprecedented Noncanonical Features of the Nonlinear Nonribosomal Peptide Synthetase Assembly Line for WS9326A Biosynthesis.

Kim, M.S., Bae, M., Jung, Y.E., Kim, J.M., Hwang, S., Song, M.C., Ban, Y.H., Bae, E.S., Hong, S., Lee, S.K., Cha, S.S., Oh, D.C., Yoon, Y.J.

(2021) Angew Chem Int Ed Engl 60: 19766-19773

• PubMed: 33963654 
• DOI: https://doi.org/10.1002/anie.202103872
• Primary Citation Related Structures: 
  7E3Z


• PubMed Abstract: 
  

  Systematic inactivation of nonribosomal peptide synthetase (NRPS) domains and translocation of the thioesterase (TE) domain revealed several unprecedented nonlinear NRPS assembly processes during the biosynthesis of the cyclodepsipeptide WS9326A in Streptomyces sp. SNM55. First, two sets of type ΙΙ TE (TEΙΙ)-like enzymes mediate the shuttling of activated amino acids between two sets of stand-alone adenylation (A)-thiolation (T) didomain modules and an "A-less" condensation (C)-T module with distinctive specificities and flexibilities. This was confirmed by the elucidation of the affinities of the A-T didomains for the TEΙΙs and its structure. Second, the C-T didomain module operates iteratively and independently from other modules in the same protein to catalyze two chain elongation cycles. Third, this biosynthetic pathway includes the first example of module skipping, where the interpolated C and T domains are required for chain transfer.

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Organizational Affiliation: 
• Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea.
Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.

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

Macromolecule Content 

• Total Structure Weight: 28.67 kDa 
• Atom Count: 2,089 
• Modeled Residue Count: 247 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thioesterase	A	261	Streptomyces sp. SNM55	Mutation(s): 0
UniProt
Find proteins for A0A494V3J7 (Streptomyces fungicidicus) Explore A0A494V3J7  Go to UniProtKB:  A0A494V3J7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.73	α = 90
b = 66.45	β = 98.06
c = 45.29	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Jung, Y.E., Cha, S.S.

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection