Comprehensive Analysis of a Novel Ketoreductase for Pentangular Polyphenol Biosynthesis

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Comprehensive Analysis of a Novel Ketoreductase for Pentangular Polyphenol Biosynthesis.

Valentic, T.R.Jackson, D.R.Brady, S.F.Tsai, S.C.

(2016) ACS Chem Biol 11: 3421-3430

  • DOI: https://doi.org/10.1021/acschembio.6b00658
  • Primary Citation of Related Structures:  
    5THQ, 5TII

  • PubMed Abstract: 

    Arixanthomycins are pentangular polyphenols (PP) with potent antiproliferative activities that were discovered through the heterologous expression of environmental DNA-derived gene clusters. The biosynthesis of arixanthomycin and other PPs is unusual because it requires several novel type II polyketide synthase (PKS) enzymes for its complete maturation. Most type II PKSs contain a ketoreductase (KR) that mediates the C7-C12 first ring cyclization and C-9 reduction. In contrast, based on previous studies of product analysis and genome mining, the arixanthomycin (ARX) gene cluster harbors a C-11 reducing KR (ARX 27), a C9-C14 first-ring aromatase/cyclase (ARX 19), and an unprecedented C-17 and C-19 reducing KR (ARX 21). While bioinformatics is useful for predicting novel enzymes, the functions of ARX 19, ARX 21, and ARX 27 have yet to be confirmed. Further, the structural features that predispose the ARX biosynthetic enzymes to process atypical poly-β-ketone scaffolds remain unknown. We report the crystal structure of ARX 21, the first structure of an enzyme involved in PP biosynthesis and likely a C-17 and C-19 reducing-KR, which is structurally similar to C-15 reducing KRs. Structural comparison of ARX 21 and other C-9 reducing KRs revealed a difference in the enzyme active site that may enlighten the molecular basis of KR substrate specificity. In addition, we report the successful in vitro reconstitution of ARX 19. The structural characterization of ARX 21 in conjunction with the in vitro results of ARX 19 lays the groundwork toward a complete in vitro and structural characterization of type II PKS enzymes involved in PP biogenesis.

  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxoacyl-ACP reductase272uncultured bacteriumMutation(s): 0 
Gene Names: arx21
Find proteins for A0A023PKG5 (uncultured bacterium)
Explore A0A023PKG5 
Go to UniProtKB:  A0A023PKG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A023PKG5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.38α = 90
b = 86.65β = 108.97
c = 107.32γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description