9D4A | pdb_00009d4a

Atomic model of Ketoacyl Reductase domain and 4 helical bundle of S. cerevisiae Fatty Acid Synthase (FAS) in complex with octanoyl-CoA (in vitro binding)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Allosteric regulation of fungal fatty acid synthesis.

Hasan, S.M.N.Samani, E.K.Keszei, A.F.A.Heydari, M.Mazhab-Jafari, M.T.

(2025) Structure 33: 2041-2048.e4

  • DOI: https://doi.org/10.1016/j.str.2025.09.005
  • Primary Citation of Related Structures:  
    9D47, 9D48, 9D49, 9D4A, 9P4V, 9P4W

  • PubMed Abstract: 

    Mycobiota fatty acid synthases (FASs) catalyze iterative cycles of condensation, dehydration, and reduction to produce saturated fatty acids. Although these multienzymes are attractive antifungal drug targets, no clinically approved small-molecule inhibitors exist, and the regulation of de novo fatty acid synthesis remains poorly understood. Here, we identify an allosteric regulation of the FAS ketoacyl reduction reaction by palmitoyl-CoA. The palmitate moiety binds a distal site on the central wheel of fungal FAS from Saccharomyces cerevisiae and Candida albicans. This site also accommodates shorter acyl chains, but only palmitoyl-CoA suppresses ketoacyl reductase (KR) activity. While no major conformational changes occur in the reductase domain, palmitoyl-CoA binding quenches dynamics in the central disk, improving local resolution and stabilizing structured water molecules. This entropic effect underlies allosteric communication to the reductase site. Our findings uncover a regulatory mechanism of fungal FAS exploitable for antifungal drug design.


  • Organizational Affiliation
    • Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty acid synthase subunit beta2,051Saccharomyces cerevisiaeMutation(s): 2 
EC: 2.3.1.86 (PDB Primary Data), 4.2.1.59 (PDB Primary Data), 1.3.1.9 (PDB Primary Data), 2.3.1.38 (PDB Primary Data), 2.3.1.39 (PDB Primary Data), 3.1.2.14 (PDB Primary Data)
UniProt
Find proteins for P07149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07149 
Go to UniProtKB:  P07149
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07149
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty acid synthase subunit alpha1,887Saccharomyces cerevisiaeMutation(s): 1 
EC: 2.3.1.86 (PDB Primary Data), 1.1.1.100 (PDB Primary Data), 2.3.1.41 (PDB Primary Data)
UniProt
Find proteins for P19097 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P19097 
Go to UniProtKB:  P19097
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19097
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SXO (Subject of Investigation/LOI)
Query on SXO

Download Ideal Coordinates CCD File 
N [auth B]
P [auth F]
R [auth J]
T [auth N]
V [auth R]
N [auth B],
P [auth F],
R [auth J],
T [auth N],
V [auth R],
X [auth V]
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] octanethioate
C19 H37 N2 O8 P S
JIQRMRIKUIPMRV-QGZVFWFLSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
M [auth A]
O [auth E]
Q [auth I]
S [auth M]
U [auth Q]
M [auth A],
O [auth E],
Q [auth I],
S [auth M],
U [auth Q],
W [auth U]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada419240
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2018-06070

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2025-10-15
    Changes: Data collection, Database references
  • Version 1.2: 2025-12-17
    Changes: Data collection, Database references