4B0N

Crystal structure of PKS-I from the brown algae Ectocarpus siliculosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

Starting Model: experimental
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This is version 1.10 of the entry. See complete history


Literature

Structure/Function Analysis of a Type III Polyketide Synthase in the Brown Alga Ectocarpus Siliculosus Reveals a Biochemical Pathway in Phlorotannin Monomer Biosynthesis.

Meslet-Cladiere, L.Delage, L.J-J Leroux, C.Goulitquer, S.Leblanc, C.Creis, E.Gall, E.A.Stiger-Pouvreau, V.Czjzek, M.Potin, P.

(2013) Plant Cell 25: 3089

  • DOI: https://doi.org/10.1105/tpc.113.111336
  • Primary Citation of Related Structures:  
    4B0N

  • PubMed Abstract: 

    Brown algal phlorotannins are structural analogs of condensed tannins in terrestrial plants and, like plant phenols, they have numerous biological functions. Despite their importance in brown algae, phlorotannin biosynthetic pathways have been poorly characterized at the molecular level. We found that a predicted type III polyketide synthase in the genome of the brown alga Ectocarpus siliculosus, PKS1, catalyzes a major step in the biosynthetic pathway of phlorotannins (i.e., the synthesis of phloroglucinol monomers from malonyl-CoA). The crystal structure of PKS1 at 2.85-Å resolution provided a good quality electron density map showing a modified Cys residue, likely connected to a long chain acyl group. An additional pocket not found in other known type III PKSs contains a reaction product that might correspond to a phloroglucinol precursor. In vivo, we also found a positive correlation between the phloroglucinol content and the PKS III gene expression level in cells of a strain of Ectocarpus adapted to freshwater during its reacclimation to seawater. The evolution of the type III PKS gene family in Stramenopiles suggests a lateral gene transfer event from an actinobacterium.


  • Organizational Affiliation

    Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Station Biologique de Roscoff, 29688 Roscoff cedex, Brittany, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POLYKETIDE SYNTHASE III
A, B
414Ectocarpus siliculosusMutation(s): 0 
EC: 2.3.1
UniProt
Find proteins for D8LJ35 (Ectocarpus siliculosus)
Explore D8LJ35 
Go to UniProtKB:  D8LJ35
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD8LJ35
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.32α = 90
b = 83.395β = 90
c = 152.729γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Other
  • Version 1.2: 2013-09-11
    Changes: Database references
  • Version 1.3: 2013-10-09
    Changes: Database references
  • Version 1.4: 2014-03-12
    Changes: Source and taxonomy
  • Version 1.5: 2015-04-22
    Changes: Non-polymer description
  • Version 1.6: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.7: 2019-05-15
    Changes: Data collection, Experimental preparation
  • Version 1.8: 2020-11-18
    Changes: Derived calculations, Other, Structure summary
  • Version 1.9: 2023-12-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.10: 2024-10-16
    Changes: Structure summary