Co-Crystal Structure of ORF2 an Aromatic Prenyl Transferase from Streptomyces sp. strain cl190 complexed with GSPP and 1,6-dihydroxynaphtalene

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

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Structural basis for the promiscuous biosynthetic prenylation of aromatic natural products.

Kuzuyama, T.Noel, J.P.Richard, S.B.

(2005) Nature 435: 983-987

  • DOI: https://doi.org/10.1038/nature03668
  • Primary Citation of Related Structures:  
    1ZB6, 1ZCW, 1ZDW, 1ZDY

  • PubMed Abstract: 

    The anti-oxidant naphterpin is a natural product containing a polyketide-based aromatic core with an attached 10-carbon geranyl group derived from isoprenoid (terpene) metabolism. Hybrid natural products such as naphterpin that contain 5-carbon (dimethylallyl), 10-carbon (geranyl) or 15-carbon (farnesyl) isoprenoid chains possess biological activities distinct from their non-prenylated aromatic precursors. These hybrid natural products represent new anti-microbial, anti-oxidant, anti-inflammatory, anti-viral and anti-cancer compounds. A small number of aromatic prenyltransferases (PTases) responsible for prenyl group attachment have only recently been isolated and characterized. Here we report the gene identification, biochemical characterization and high-resolution X-ray crystal structures of an architecturally novel aromatic PTase, Orf2 from Streptomyces sp. strain CL190, with substrates and substrate analogues bound. In vivo, Orf2 attaches a geranyl group to a 1,3,6,8-tetrahydroxynaphthalene-derived polyketide during naphterpin biosynthesis. In vitro, Orf2 catalyses carbon-carbon-based and carbon-oxygen-based prenylation of a diverse collection of hydroxyl-containing aromatic acceptors of synthetic, microbial and plant origin. These crystal structures, coupled with in vitro assays, provide a basis for understanding and potentially manipulating the regio-specific prenylation of aromatic small molecules using this structurally unique family of aromatic PTases.

  • Organizational Affiliation

    Jack Skirball Chemical Biology and Proteomics Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aromatic prenyltransferase307Streptomyces sp.Mutation(s): 0 
Gene Names: AB187169
Find proteins for Q4R2T2 (Streptomyces sp. (strain CL190))
Explore Q4R2T2 
Go to UniProtKB:  Q4R2T2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4R2T2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.319α = 90
b = 90.243β = 90
c = 47.513γ = 90
Software Package:
Software NamePurpose
XNEMOdata reduction
XDSdata 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: 2005-06-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations