4IMP

The missing linker: a dimerization motif located within polyketide synthase modules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

The missing linker: a dimerization motif located within polyketide synthase modules.

Zheng, J.Fage, C.D.Demeler, B.Hoffman, D.W.Keatinge-Clay, A.T.

(2013) ACS Chem Biol 8: 1263-1270

  • DOI: https://doi.org/10.1021/cb400047s
  • Primary Citation of Related Structures:  
    4IMP

  • PubMed Abstract: 

    The dimerization of multimodular polyketide synthases is essential for their function. Motifs that supplement the contacts made by dimeric polyketide synthase enzymes have previously been characterized outside the boundaries of modules, at the N- and C-terminal ends of polyketide synthase subunits. Here we describe a heretofore uncharacterized dimerization motif located within modules. The dimeric state of this dimerization element was elucidated through the 2.6 Å resolution crystal structure of a fragment containing a dimerization element and a ketoreductase. The solution structure of a standalone dimerization element was revealed by nuclear magnetic resonance spectroscopy to be consistent with that of the crystal structure, and its dimerization constant was measured through analytical ultracentrifugation to be ∼20 μM. The dimer buries ∼990 Å(2) at its interface, and its C-terminal helices rigidly connect to ketoreductase domains to constrain their locations within a module. These structural restraints permitted the construction of a common type of polyketide synthase module.


  • Organizational Affiliation

    Department of Chemistry & Biochemistry, The University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyketide synthase extender modules 3-4
A, B, C, D
580Saccharopolyspora spinosaMutation(s): 0 
Gene Names: spnC
UniProt
Find proteins for Q9ALM4 (Saccharopolyspora spinosa)
Explore Q9ALM4 
Go to UniProtKB:  Q9ALM4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ALM4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.815α = 90
b = 211.69β = 95.26
c = 101.742γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-03
    Changes: Structure summary
  • Version 1.2: 2013-11-20
    Changes: Database references
  • Version 1.3: 2014-02-26
    Changes: Database references
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description