7FEA

PY14 in complex with Col-D

• PDB DOI:  https://doi.org/10.2210/pdb7FEA/pdb

• Classification: TRANSFERASE
• Organism(s): Massilia sp. YMA4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-19 Released: 2022-07-27 
• Deposition Author(s): Lin, C.C., Ko, T.P., Huang, K.F., Yang, Y.L.
• Funding Organization(s): Academia Sinica (Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.163 
• R-Value Work: 0.146 
• R-Value Observed: 0.146 

Literature

Integrated omics approach to unveil antifungal bacterial polyynes as acetyl-CoA acetyltransferase inhibitors.

Lin, C.C., Hoo, S.Y., Ma, L.T., Lin, C., Huang, K.F., Ho, Y.N., Sun, C.H., Lee, H.J., Chen, P.Y., Shu, L.J., Wang, B.W., Hsu, W.C., Ko, T.P., Yang, Y.L.

(2022) Commun Biol 5: 454-454

• PubMed: 35551233 
• DOI: https://doi.org/10.1038/s42003-022-03409-6
• Primary Citation of Related Structures:  
  7EI3, 7EI4, 7FEA


• PubMed Abstract: 
  

Bacterial polyynes are highly active natural products with a broad spectrum of antimicrobial activities. However, their detailed mechanism of action remains unclear. By integrating comparative genomics, transcriptomics, functional genetics, and metabolomics analysis, we identified a unique polyyne resistance gene, masL (encoding acetyl-CoA acetyltransferase), in the biosynthesis gene cluster of antifungal polyynes (massilin A 1, massilin B 2, collimonin C 3, and collimonin D 4) of Massilia sp. YMA4. Crystallographic analysis indicated that bacterial polyynes serve as covalent inhibitors of acetyl-CoA acetyltransferase. Moreover, we confirmed that the bacterial polyynes disrupted cell membrane integrity and inhibited the cell viability of Candida albicans by targeting ERG10, the homolog of MasL. Thus, this study demonstrated that acetyl-CoA acetyltransferase is a potential target for developing antifungal agents.

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Organizational Affiliation: 

Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 171.53 kDa 
• Atom Count: 13,559 
• Modelled Residue Count: 1,583 
• Deposited Residue Count: 1,628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA C-acyltransferase	A, B, C, D	407	Massilia sp. YMA4	Mutation(s): 0  Gene Names: DPH57_23275
UniProt
Find proteins for A0A7U5Y2I6 (Massilia sp. YMA4) Explore A0A7U5Y2I6  Go to UniProtKB:  A0A7U5Y2I6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3KI (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	(6~{R},7~{R},9~{E})-6,7-bis(oxidanyl)hexadeca-9,15-dien-11,13-diynoic acid C16 H20 O4 JBBDMFIFQBMXHD-FHFZEBMASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.163 
• R-Value Work: 0.146 
• R-Value Observed: 0.146 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.943	α = 70.758
b = 77.741	β = 81.781
c = 98.117	γ = 64.995

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
HKL-2000	data collection
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Lin, C.C., Ko, T.P., Huang, K.F., Yang, Y.L.

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Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	MOST 104-2320-B-001-019-MY2

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2022-10-19
  Changes: Database references