8I6M | pdb_00008i6m

Acyl-ACP synthetase structure bound to AMP-C18:1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8I6M

This is version 1.3 of the entry. See complete history

Literature

Structure and catalytic mechanism of exogenous fatty acid recycling by AasS, a versatile acyl-ACP synthetase.

Huang, H.Wang, C.Chang, S.Cui, T.Xu, Y.Huang, M.Zhang, H.Zhou, C.Zhang, X.Feng, Y.

(2025) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01464-7
  • Primary Citation Related Structures: 
    8I35, 8I3I, 8I49, 8I51, 8I6M, 8I8D, 8I8E

  • PubMed Abstract: 

    Fatty acids (FAs) are essential building blocks for all the domains of life, of which bacterial de novo synthesis, called type II FA synthesis (FAS II), is energetically expensive. The recycling of exogenous FAs (eFAs) partially relieves the FAS II demand and, therefore, compromises the efficacy of FAS II-directed antimicrobials. The versatile acyl-acyl carrier protein (ACP) synthetase, AasS, enables bacterial channeling of diverse eFA nutrients through holo-ACP, an activated form of ACP. However, the molecular mechanism for AasS catalysis is not fully understood. Here we report a series of cryo-electron microscopy structures of AasS from the bioluminescent bacterium Vibrio harveyi to provide insights into the catalytic cycle. AasS forms a ring-shaped hexamer, with each protomer folding into two distinct domains. Biochemical and structural analysis suggests that AasS accommodates distinct eFA substrates and the conserved W230 residue has a gating role. Adenosine triphosphate and Mg 2+ binding converts the AasS hexamer to a tetramer, which is likely needed for the acyl adenylate intermediate formation. Afterward, AasS reverts to the hexamer conformation in adaption to acyl-ACP production. The complete landscape for eFA scavenging lays a foundation for exploiting the versatility of AasS in biopharmaceuticals.


  • 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, China.

Macromolecule Content 

  • Total Structure Weight: 366.9 kDa 
  • Atom Count: 25,464 
  • Modeled Residue Count: 3,168 
  • Deposited Residue Count: 3,198 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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 F]
N [auth D]
Q [auth C]
T [auth B]
H [auth A],
K [auth F],
N [auth D],
Q [auth C],
T [auth B],
W [auth E]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
OLA
(Subject of Investigation/LOI)

Query on OLA



Download:Ideal Coordinates CCD File
G [auth A]
J [auth F]
M [auth D]
P [auth C]
S [auth B]
G [auth A],
J [auth F],
M [auth D],
P [auth C],
S [auth B],
V [auth E]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
I [auth A]
L [auth F]
O [auth D]
R [auth C]
U [auth B]
I [auth A],
L [auth F],
O [auth D],
R [auth C],
U [auth B],
X [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 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: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Database references, Structure summary
  • Version 1.2: 2025-01-15
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2025-01-22
    Changes: Data collection, Database references