9IYW | pdb_00009iyw

Crystal structure of chimeric KSQ-AT didomain

• PDB DOI: https://doi.org/10.2210/pdb9IYW/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces graminofaciens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-31 Released: 2025-08-06 
• Deposition Author(s): Chisuga, T., Miyanaga, A.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.246 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: in silico

Literature

Ancestral sequence reconstruction as a tool for structural analysis of modular polyketide synthases.

Chisuga, T., Takinami, S., Liao, Z., Karasawa, M., Adachi, N., Kawasaki, M., Moriya, T., Senda, T., Terada, T., Kudo, F., Eguchi, T., Nakano, S., Ito, S., Miyanaga, A.

(2025) Nat Commun 16: 6847-6847

• PubMed: 40715098 
• DOI: https://doi.org/10.1038/s41467-025-62168-0
• Primary Citation Related Structures: 
  9IYW, 9JJ9, 9JJB


• PubMed Abstract: 
  

  Modular polyketide synthases (PKSs) are large multi-domain enzymes critical for the biosynthesis of polyketide antibiotics. However, challenges with structural analysis limits our mechanistic understanding of modular PKSs. In this report, we explore the potential of ancestral sequence reconstruction (ASR) for structure analysis of target proteins. As a model, we focus on the FD-891 PKS loading module composed of ketosynthase-like decarboxylase (KS _Q ), acyltransferase (AT) and acyl carrier protein (ACP) domains. We construct a KS _Q AncAT chimeric didomain by replacing the native AT with an ancestral AT (AncAT) using ASR. After confirming that KS _Q AncAT chimeric didomain retains similar enzymatic function to the native KS _Q AT didomain, we successfully determine a high-resolution crystal structure of the KS _Q AncAT chimeric didomain and cryo-EM structures of the KS _Q -ACP complex. These cryo-EM structures, which could not be determined for the native protein, exemplify the utility of ASR to enable cryo-EM single-particle analysis. Our findings demonstrate that integrating ASR with structural analysis provides deeper mechanistic insight into modular PKSs. Furthermore, applying ASR to a partial region of the targeted multi-domain proteins could expand the potential of ASR and may serve as a valuable framework for investigating the structure and function of various multi-domain proteins.

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Organizational Affiliation: 
• Graduate School of Integrated Pharmaceutical and Nutritional Science, University of Shizuoka, Shizuoka, Japan.
Department of Chemistry, Tokyo Institute of Technology (Institute of Science Tokyo), Tokyo, Japan.
Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan.
California Institute for Quantitative Biosciences/Department of Molecular and Cell Biology/Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.
Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Ibaraki, Japan.
Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Ibaraki, Japan.
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
Faculty of Chemistry and Biochemistry, Kanagawa University, Yokohama, Japan.
Graduate School of Integrated Pharmaceutical and Nutritional Science, University of Shizuoka, Shizuoka, Japan. [e-mail].
PREST, Japan Science and Technology Agency, Saitama, Japan. [e-mail].
Graduate School of Integrated Pharmaceutical and Nutritional Science, University of Shizuoka, Shizuoka, Japan. [e-mail].
Department of Chemistry, Tokyo Institute of Technology (Institute of Science Tokyo), Tokyo, Japan. [e-mail].
Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan. [e-mail].
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
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: 96.15 kDa 
• Atom Count: 6,371 
• Modeled Residue Count: 834 
• Deposited Residue Count: 922 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase,GfsA KSQ-AncAT chimeric protein	A	922	Streptomyces graminofaciens, synthetic construct	Mutation(s): 0  Gene Names: gfsA EC: 2.3.1 (UniProt), 4.1.1 (UniProt)
UniProt
Find proteins for E0D202 (Streptomyces halstedii) Explore E0D202  Go to UniProtKB:  E0D202

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.246 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.065	α = 90
b = 76.065	β = 90
c = 352.97	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Chisuga, T., Miyanaga, A.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20H02911

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release
  
• Version 1.1: 2025-08-13
  Changes: Database references