8JYU | pdb_00008jyu

Acyl-ACP Synthetase structure bound to Decanoyl-AMP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An inhibitory mechanism of AasS, an exogenous fatty acid scavenger: Implications for re-sensitization of FAS II antimicrobials.

Huang, H.Chang, S.Cui, T.Huang, M.Qu, J.Zhang, H.Lu, T.Zhang, X.Zhou, C.Feng, Y.

(2024) PLoS Pathog 20: e1012376-e1012376

  • DOI: https://doi.org/10.1371/journal.ppat.1012376
  • Primary Citation of Related Structures:  
    8HSY, 8JYL, 8JYU

  • PubMed Abstract: 

    Antimicrobial resistance is an ongoing "one health" challenge of global concern. The acyl-ACP synthetase (termed AasS) of the zoonotic pathogen Vibrio harveyi recycles exogenous fatty acid (eFA), bypassing the requirement of type II fatty acid synthesis (FAS II), a druggable pathway. A growing body of bacterial AasS-type isoenzymes compromises the clinical efficacy of FAS II-directed antimicrobials, like cerulenin. Very recently, an acyl adenylate mimic, C10-AMS, was proposed as a lead compound against AasS activity. However, the underlying mechanism remains poorly understood. Here we present two high-resolution cryo-EM structures of AasS liganded with C10-AMS inhibitor (2.33 Å) and C10-AMP intermediate (2.19 Å) in addition to its apo form (2.53 Å). Apart from our measurements for C10-AMS' Ki value of around 0.6 μM, structural and functional analyses explained how this inhibitor interacts with AasS enzyme. Unlike an open state of AasS, ready for C10-AMP formation, a closed conformation is trapped by the C10-AMS inhibitor. Tight binding of C10-AMS blocks fatty acyl substrate entry, and therefore inhibits AasS action. Additionally, this intermediate analog C10-AMS appears to be a mixed-type AasS inhibitor. In summary, our results provide the proof of principle that inhibiting salvage of eFA by AasS reverses the FAS II bypass. This facilitates the development of next-generation anti-bacterial therapeutics, esp. the dual therapy consisting of C10-AMS scaffold derivatives combined with certain FAS II inhibitors.


  • Organizational Affiliation
    • Key Laboratory of Multiple Organ Failure, Ministry of Education; Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-acyl carrier protein synthetase533Vibrio harveyiMutation(s): 0 
Gene Names: aasSAL538_21690
UniProt
Find proteins for Q00IB3 (Vibrio harveyi)
Explore Q00IB3 
Go to UniProtKB:  Q00IB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00IB3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
H [auth A]
K [auth D]
N [auth B]
Q [auth C]
T [auth E]
H [auth A],
K [auth D],
N [auth B],
Q [auth C],
T [auth E],
W [auth F]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
DKA (Subject of Investigation/LOI)
Query on DKA

Download Ideal Coordinates CCD File 
I [auth A]
L [auth D]
O [auth B]
R [auth C]
U [auth E]
I [auth A],
L [auth D],
O [auth B],
R [auth C],
U [auth E],
X [auth F]
DECANOIC ACID
C10 H20 O2
GHVNFZFCNZKVNT-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]
J [auth D]
M [auth B]
P [auth C]
S [auth E]
G [auth A],
J [auth D],
M [auth B],
P [auth C],
S [auth E],
V [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32125003

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Data collection, Database references, Structure summary