8I4Z | pdb_00008i4z

CalA3 with hydrolysis product

• PDB DOI: https://doi.org/10.2210/pdb8I4Z/pdb
• EM Map EMD-35189: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Streptomyces chartreusis NRRL 3882
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-21 Released: 2023-02-22 
• Deposition Author(s): Wang, J., Wang, Z.
• Funding Organization(s): National Science Foundation (NSF, China)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.97 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7WVZ

Literature

C-N bond formation by a polyketide synthase.

Wang, J., Wang, X., Li, X., Kong, L., Du, Z., Li, D., Gou, L., Wu, H., Cao, W., Wang, X., Lin, S., Shi, T., Deng, Z., Wang, Z., Liang, J.

(2023) Nat Commun 14: 1319-1319

• PubMed: 36899013 
• DOI: https://doi.org/10.1038/s41467-023-36989-w
• Primary Citation Related Structures: 
  7WVZ, 8I4Y, 8I4Z


• PubMed Abstract: 
  

  Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the polyketide backbone successively. Here, we present the cryo-EM structure of CalA3, a chain release PKS module without an ACP domain, and its structures with amidation or hydrolysis products. The domain organization reveals a unique "∞"-shaped dimeric architecture with five connected domains. The catalytic region tightly contacts the structural region, resulting in two stabilized chambers with nearly perfect symmetry while the N-terminal docking domain is flexible. The structures of the ketosynthase (KS) domain illustrate how the conserved key residues that canonically catalyze C-C bond formation can be tweaked to mediate C-N bond formation, revealing the engineering adaptability of assembly-line polyketide synthases for the production of novel pharmaceutical agents.

---

Organizational Affiliation: 
• State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Department of Molecular Biology, Shanghai Jikaixing Biotech Inc., Shanghai, 200131, China.
National Facility for Protein Science in Shanghai, Chinese Academy of Sciences, Shanghai, 201204, China.
School of Life Science, North China University of Science and Technology, Tangshan, Hebei, China.
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. [e-mail].
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. [e-mail].
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. [e-mail].
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. [e-mail].
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 357.03 kDa 
• Atom Count: 24,629 
• Modeled Residue Count: 3,374 
• Deposited Residue Count: 3,438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-ketoacyl-acyl-carrier-protein synthase I	A, B	1,719	Streptomyces chartreusis NRRL 3882	Mutation(s): 0  Gene Names: SCNRRL3882_6975 EC: 2.3.1.41
UniProt
Find proteins for A0A2N9BJK0 (Streptomyces chartreusis NRRL 3882) Explore A0A2N9BJK0  Go to UniProtKB:  A0A2N9BJK0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ONF (Subject of Investigation/LOI)	C [auth A]	11-oxidanylidene-11-(1~{H}-pyrrol-2-yl)undecanoic acid C15 H23 N O3 LRVUVJYTRUNASO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.97 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Wang, J., Wang, Z.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	32270033

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2023-04-19
  Changes: Database references
• Version 1.2: 2024-07-03
  Changes: Data collection