6ZS0 | pdb_00006zs0

Crystal structure of 5-dimethylallyltryptophan synthase from Streptomyces coelicolor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.220 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.199 (DCC) 

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

Reprogramming Substrate and Catalytic Promiscuity of Tryptophan Prenyltransferases.

Ostertag, E.Zheng, L.Broger, K.Stehle, T.Li, S.M.Zocher, G.

(2020) J Mol Biology 433: 166726-166726

  • DOI: https://doi.org/10.1016/j.jmb.2020.11.025
  • Primary Citation Related Structures: 
    6ZRX, 6ZRY, 6ZRZ, 6ZS0

  • PubMed Abstract: 

    Prenylation is a process widely prevalent in primary and secondary metabolism, contributing to functionality and chemical diversity in natural systems. Due to their high regio- and chemoselectivities, prenyltransferases are also valuable tools for creation of new compounds by chemoenzymatic synthesis and synthetic biology. Over the last ten years, biochemical and structural investigations shed light on the mechanism and key residues that control the catalytic process, but to date crucial information on how certain prenyltransferases control regioselectivity and chemoselectivity is still lacking. Here, we advance a general understanding of the enzyme family by contributing the first structure of a tryptophan C5-prenyltransferase 5-DMATS. Additinally, the structure of a bacterial tryptophan C6-prenyltransferase 6-DMATS was solved. Analysis and comparison of both substrate-bound complexes led to the identification of key residues for catalysis. Next, site-directed mutagenesis was successfully implemented to not only modify the prenyl donor specificity but also to redirect the prenylation, thereby switching the regioselectivity of 6-DMATS to that of 5-DMATS. The general strategy of structure-guided protein engineering should be applicable to other related prenyltransferases, thus enabling the production of novel prenylated compounds.


  • Organizational Affiliation
    • Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 79.58 kDa 
  • Atom Count: 5,967 
  • Modeled Residue Count: 709 
  • Deposited Residue Count: 740 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DMATS type aromatic prenyltransferaseA [auth AAA],
B [auth BBB]
370Streptomyces coelicolorMutation(s): 0 
Gene Names: FHV93_101284

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.220 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.199 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.88α = 90
b = 70.454β = 92.946
c = 91.145γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB -TR 261

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description