7R0X | pdb_00007r0x

Structure of the branching thioesterase from oocydin biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb7R0X/pdb

• Classification: HYDROLASE
• Organism(s): Serratia
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-02-02 Released: 2022-08-10 
• Deposition Author(s): Fraley, A.E., Piel, J.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.281 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Structure of a Promiscuous Thioesterase Domain Responsible for Branching Acylation in Polyketide Biosynthesis.

Fraley, A.E., Dieterich, C.L., Mabesoone, M.F.J., Minas, H.A., Meoded, R.A., Hemmerling, F., Piel, J.

(2022) Angew Chem Int Ed Engl 61: e202206385-e202206385

• PubMed: 35903999 
• DOI: https://doi.org/10.1002/anie.202206385
• Primary Citation Related Structures: 
  7R0X


• PubMed Abstract: 
  

  Thioesterases (TEs) are fundamentally important enzymes present in all bacteria and eukaryotes, where they have conserved functions in fatty acid biosynthesis and secondary metabolism. This work provides the first structural insights into a functionally distinct group of TEs that perform diverse acylations in polyketide and peptide biosynthesis (TE _B s). Structural analysis of the oocydin (OocS) TE _B domain facilitated identification and engineering of the active site to modulate acyl-group acceptance. In this way, we achieved higher reactivity using a structure-based approach, building a foundation for biocatalytic development of TE _B -mediated O-acylation, a modification known to improve the bioactivity of oocydin-type polyketides. Lastly, the promiscuity of the OocS TE _B motivated us to investigate, and ultimately provide evidence for, the production of longer chain branched oocydins in the native host Serratia plymuthica 4Rx13. This work frames the OocS TE _B and homologs as invaluable synthetic biology tools for polyketide drug development.

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Organizational Affiliation: 
• Department of Biology, Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.

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: 41.1 kDa 
• Atom Count: 2,457 
• Modeled Residue Count: 300 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase	A	364	Serratia	Mutation(s): 0  Gene Names: CT690_01900
UniProt
Find proteins for A0A318P693 (Serratia plymuthica) Explore A0A318P693  Go to UniProtKB:  A0A318P693

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.281 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.818	α = 90
b = 106.818	β = 90
c = 78.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
Aimless	data scaling
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Fraley, A.E., Piel, J.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	742739

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2022-08-31
  Changes: Database references
• Version 1.2: 2022-09-28
  Changes: Database references
• Version 1.3: 2024-11-06
  Changes: Data collection, Structure summary