9GLF | pdb_00009glf

Anthraquinone Pigment Production Regulated by Cinnamic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.181 (Depositor), 0.181 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.147 (DCC) 
  • R-Value Observed: 
    0.149 (Depositor) 

Starting Model: experimental
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Literature

The Isopropylstilbene Precursor Cinnamic Acid Inhibits Anthraquinone Pigment Production by Targeting AntI.

Su, L.Schmalhofer, M.Grammbitter, G.L.C.Paczia, N.Glatter, T.Groll, M.Bode, H.B.

(2025) J Am Chem Soc 147: 20246-20250

  • DOI: https://doi.org/10.1021/jacs.5c07388
  • Primary Citation of Related Structures:  
    9GLF

  • PubMed Abstract: 

    Photorhabdus strains, Gram-negative bacteria pathogenic to insect larvae, produce two signature compounds: the multifunctional isopropylstilbene (IPS), known for its antibiotic, insecticidal, and immunosuppressive activities, and orange-to-red pigmented anthraquinones (AQs), which attenuate oxidative stress. Here, we demonstrate an inverse correlation between the production of AQs and cinnamic acid (CA), the primary precursor for IPS formation in the model strain P. laumondii TTO1. Metabolic and proteomic analyses following CA treatment show that CA inhibits AntI, a key enzyme in the final step of AQ-256 biosynthesis. The crystal structure of AntI in complex with CA reveals that cinnamic acid functions as a competitive inhibitor by inducing specific structural rearrangements in the lyase, resulting in noncovalent, reversible inhibition. These findings provide atomic insights into the intricate regulatory control of pigment biosynthesis and the production of bioactive compounds.


  • Organizational Affiliation

    Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AntI399Photorhabdus luminescensMutation(s): 0 
Gene Names: plu4186
UniProt
Find proteins for Q7MZT8 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01))
Explore Q7MZT8 
Go to UniProtKB:  Q7MZT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MZT8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
G [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
TCA (Subject of Investigation/LOI)
Query on TCA

Download Ideal Coordinates CCD File 
B [auth A]PHENYLETHYLENECARBOXYLIC ACID
C9 H8 O2
WBYWAXJHAXSJNI-VOTSOKGWSA-N
PEG
Query on PEG

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F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

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H [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.181 (Depositor), 0.181 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.147 (DCC) 
  • R-Value Observed: 0.149 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.38α = 90
b = 154.46β = 90
c = 91.06γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB1309

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release