3AWK | pdb_00003awk

Crystal structure of the polyketide synthase 1 from huperzia serrata


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.234 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Synthesis of unnatural alkaloid scaffolds by exploiting plant polyketide synthase.

Morita, H.Yamashita, M.Shi, S.P.Wakimoto, T.Kondo, S.Kato, R.Sugio, S.Kohno, T.Abe, I.

(2011) Proc Natl Acad Sci U S A 108: 13504-13509

  • DOI: https://doi.org/10.1073/pnas.1107782108
  • Primary Citation Related Structures: 
    3AWJ, 3AWK

  • PubMed Abstract: 

    HsPKS1 from Huperzia serrata is a type III polyketide synthase (PKS) with remarkable substrate tolerance and catalytic potential. Here we present the synthesis of unnatural unique polyketide-alkaloid hybrid molecules by exploiting the enzyme reaction using precursor-directed and structure-based approaches. HsPKS1 produced novel pyridoisoindole (or benzopyridoisoindole) with the 6.5.6-fused (or 6.6.5.6-fused) ring system by the condensation of 2-carbamoylbenzoyl-CoA (or 3-carbamoyl-2-naphthoyl-CoA), a synthetic nitrogen-containing nonphysiological starter substrate, with two molecules of malonyl-CoA. The structure-based S348G mutant not only extended the product chain length but also altered the cyclization mechanism to produce a biologically active, ring-expanded 6.7.6-fused dibenzoazepine, by the condensation of 2-carbamoylbenzoyl-CoA with three malonyl-CoAs. Thus, the basic nitrogen atom and the structure-based mutagenesis enabled additional C─C and C─N bond formation to generate the novel polyketide-alkaloid scaffold.


  • Organizational Affiliation
    • Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 43.94 kDa 
  • Atom Count: 3,119 
  • Modeled Residue Count: 380 
  • Deposited Residue Count: 402 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chalcone synthase-like polyketide synthase402Huperzia serrataMutation(s): 0 
Gene Names: Pks1
UniProt
Find proteins for A3E7Z7 (Huperzia serrata)
Explore A3E7Z7 
Go to UniProtKB:  A3E7Z7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3E7Z7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.234 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.3α = 90
b = 85β = 90
c = 137.7γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary