6FIJ

Structure of the loading/condensing region (SAT-KS-MAT) of the cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1

• PDB DOI:  https://doi.org/10.2210/pdb6FIJ/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Cercospora nicotianae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-01-18 Released: 2018-03-21 
• Deposition Author(s): Herbst, D.A., Jakob, R.P., Townsend, C.A., Maier, T.
• Funding Organization(s): Swiss National Science Foundation, National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.240 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

The structural organization of substrate loading in iterative polyketide synthases.

Herbst, D.A., Huitt-Roehl, C.R., Jakob, R.P., Kravetz, J.M., Storm, P.A., Alley, J.R., Townsend, C.A., Maier, T.

(2018) Nat Chem Biol 14: 474-479

• PubMed: 29610486 
• DOI: https://doi.org/10.1038/s41589-018-0026-3
• Primary Citation of Related Structures:  
  6FIJ, 6FIK


• PubMed Abstract: 
  

Polyketide synthases (PKSs) are microbial multienzymes for the biosynthesis of biologically potent secondary metabolites. Polyketide production is initiated by the loading of a starter unit onto an integral acyl carrier protein (ACP) and its subsequent transfer to the ketosynthase (KS). Initial substrate loading is achieved either by multidomain loading modules or by the integration of designated loading domains, such as starter unit acyltransferases (SAT), whose structural integration into PKS remains unresolved. A crystal structure of the loading/condensing region of the nonreducing PKS CTB1 demonstrates the ordered insertion of a pseudodimeric SAT into the condensing region, which is aided by the SAT-KS linker. Cryo-electron microscopy of the post-loading state trapped by mechanism-based crosslinking of ACP to KS reveals asymmetry across the CTB1 loading/-condensing region, in accord with preferential 1:2 binding stoichiometry. These results are critical for re-engineering the loading step in polyketide biosynthesis and support functional relevance of asymmetric conformations of PKSs.

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Organizational Affiliation: 

Department of Biozentrum, University of Basel, Basel, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
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: 281.71 kDa 
• Atom Count: 19,867 
• Modelled Residue Count: 2,550 
• Deposited Residue Count: 2,608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase	A, B	1,304	Cercospora nicotianae	Mutation(s): 1  Gene Names: CTB1 EC: 2.3.1
UniProt
Find proteins for Q6DQW3 (Cercospora nicotianae) Explore Q6DQW3  Go to UniProtKB:  Q6DQW3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTT	R [auth B]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
GOL	I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.240 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.05	α = 90
b = 230.2	β = 90
c = 253.8	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Herbst, D.A., Jakob, R.P., Townsend, C.A., Maier, T.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	159696
Swiss National Science Foundation	Switzerland	145023
Swiss National Science Foundation	Switzerland	164074
Swiss National Science Foundation	Switzerland	138262
National Institutes of Health	United States	ES001670

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2018-04-11
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2018-04-25
  Changes: Data collection, Database references, Derived calculations, Structure summary