6KXF

The ishigamide ketosynthase/chain length factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

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Ligand Structure Quality Assessment 

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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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ketosynthase409Streptomyces sp. MSC090213JE08Mutation(s): 0 
Gene Names: iga11
EC: 2.3.1.41
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
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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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ACP83Streptomyces sp. MSC090213JE08Mutation(s): 0 
Gene Names: iga10
UniProt
Find proteins for A0A1Y1BWQ0 (Streptomyces sp. MSC090213JE08)
Explore A0A1Y1BWQ0 
Go to UniProtKB:  A0A1Y1BWQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Y1BWQ0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DYF (Subject of Investigation/LOI)
Query on DYF

Download Ideal Coordinates CCD File 
D [auth C][(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate
C19 H36 N3 O8 P
KFHBREMVHHVYJE-IJDCCNJMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.872α = 90
b = 104.411β = 90
c = 114.706γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DYFClick on this verticalbar to view details

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: 2024-11-13
    Changes: Data collection, Database references, Structure summary