6QSP

Ketosynthase (ApeO) in Complex with its Chain Length Factor (ApeC) from Xenorhabdus doucetiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An Uncommon Type II PKS Catalyzes Biosynthesis of Aryl Polyene Pigments.

Grammbitter, G.L.C.Schmalhofer, M.Karimi, K.Shi, Y.M.Schoner, T.A.Tobias, N.J.Morgner, N.Groll, M.Bode, H.B.

(2019) J Am Chem Soc 141: 16615-16623

  • DOI: https://doi.org/10.1021/jacs.8b10776
  • Primary Citation of Related Structures:  
    6QSP, 6QSR

  • PubMed Abstract: 

    Aryl polyene (APE) pigments are a widely distributed class of bacterial polyketides. So far, little is known about the biosynthesis of these compounds, which are produced by a novel type II polyketide synthase (PKS). We have identified all enzymes involved in APE biosynthesis and determined their peculiar functions. The biosynthesis was reconstituted in vitro , and ACP-bound intermediates were assigned for each reaction step by HPLC-MS. Native mass spectrometry experiments identified four stable complexes: the acyl-carrier proteins ApeE and ApeF bound to the thioesterase ApeK, the dehydratases ApeI and ApeP, and the ketosynthase ApeO in complex with its chain-length factor ApeC. X-ray structures of the heterodimeric ApeO:ApeC and ApeI:ApeP complexes depict striking protein-protein interactions. Altogether, our study elucidated mechanistic aspects of APE biosynthesis that unifies elements of type II fatty acid and PKS systems, but in addition includes novel enzyme complexes.


  • Organizational Affiliation

    Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt am Main and Buchmann Institute for Molecular Life Sciences (BMLS) , Goethe-Universität Frankfurt , Max-von-Laue-Straße 9 and 15 , 60438 Frankfurt am Main , Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-ketoacyl synthase406Xenorhabdus doucetiaeMutation(s): 0 
Gene Names: XDD1_3472
EC: 2.3.1.41
UniProt
Find proteins for A0A068QVX9 (Xenorhabdus doucetiae)
Explore A0A068QVX9 
Go to UniProtKB:  A0A068QVX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A068QVX9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein239Xenorhabdus doucetiaeMutation(s): 0 
Gene Names: XDD1_3460
UniProt
Find proteins for A0A068QZ94 (Xenorhabdus doucetiae)
Explore A0A068QZ94 
Go to UniProtKB:  A0A068QZ94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A068QZ94
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.95α = 90
b = 88.89β = 108.13
c = 63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description