6QSR

The Dehydratase Heterocomplex ApeI:P from Xenorhabdus doucetiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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
AMP-dependent synthetase and ligase119Xenorhabdus doucetiaeMutation(s): 0 
Gene Names: XDD1_3466
UniProt
Find proteins for A0A068QWX2 (Xenorhabdus doucetiae)
Explore A0A068QWX2 
Go to UniProtKB:  A0A068QWX2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A068QWX2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase FabA/FabZ180Xenorhabdus doucetiaeMutation(s): 0 
Gene Names: XDD1_3473
EC: 4.2.1
UniProt
Find proteins for A0A068QW34 (Xenorhabdus doucetiae)
Explore A0A068QW34 
Go to UniProtKB:  A0A068QW34
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A068QW34
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.68α = 90
b = 47.77β = 104.65
c = 42.68γ = 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