6KXD

The ishigamide ketosynthase/chain length factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for selectivity in a highly reducing type II polyketide synthase.

Du, D.Katsuyama, Y.Horiuchi, M.Fushinobu, S.Chen, A.Davis, T.D.Burkart, M.D.Ohnishi, Y.

(2020) Nat Chem Biol 16: 776-782

  • DOI: https://doi.org/10.1038/s41589-020-0530-0
  • Primary Citation of Related Structures:  
    6KXD, 6KXE, 6KXF

  • PubMed Abstract: 

    In type II polyketide synthases (PKSs), the ketosynthase-chain length factor (KS-CLF) complex catalyzes polyketide chain elongation with the acyl carrier protein (ACP). Highly reducing type II PKSs, represented by IgaPKS, produce polyene structures instead of the well-known aromatic skeletons. Here, we report the crystal structures of the Iga11-Iga12 (KS-CLF) heterodimer and the covalently cross-linked Iga10=Iga11-Iga12 (ACP=KS-CLF) tripartite complex. The latter structure revealed the molecular basis of the interaction between Iga10 and Iga11-Iga12, which differs from that between the ACP and KS of Escherichia coli fatty acid synthase. Furthermore, the reaction pocket structure and site-directed mutagenesis revealed that the negative charge of Asp 113 of Iga11 prevents further condensation using a β-ketoacyl product as a substrate, which distinguishes IgaPKS from typical type II PKSs. This work will facilitate the future rational design of PKSs.


  • Organizational Affiliation

    Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ketosynthase409Streptomyces sp. MSC090213JE08Mutation(s): 0 
Gene Names: iga11
UniProt
Find proteins for A0A1Y1BW67 (Streptomyces sp. MSC090213JE08)
Explore A0A1Y1BW67 
Go to UniProtKB:  A0A1Y1BW67
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Y1BW67
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ketosynthase378Streptomyces sp. MSC090213JE08Mutation(s): 0 
Gene Names: iga12
UniProt
Find proteins for A0A1Y1BW66 (Streptomyces sp. MSC090213JE08)
Explore A0A1Y1BW66 
Go to UniProtKB:  A0A1Y1BW66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Y1BW66
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.603α = 90
b = 67.603β = 90
c = 261.781γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP25108706

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references
  • Version 1.2: 2020-07-08
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description