4EE7

Crystal Structure of the Novel Phenazine Prenyltransferase EpzP in complex with S-thiolodiphosphate (methylated)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based engineering increased the catalytic turnover rate of a novel phenazine prenyltransferase.

Zocher, G.Saleh, O.Heim, J.B.Herbst, D.A.Heide, L.Stehle, T.

(2012) Plos One 7: e48427-e48427

  • DOI: 10.1371/journal.pone.0048427
  • Primary Citation of Related Structures:  4EE6, 4EE8

  • PubMed Abstract: 
  • Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto aromatic substrates in biosynthetic pathways of microbial secondary metabolites. Therefore, these enzymes contribute to the chemical diversity of natural products. ...

    Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto aromatic substrates in biosynthetic pathways of microbial secondary metabolites. Therefore, these enzymes contribute to the chemical diversity of natural products. Prenylation is frequently essential for the pharmacological properties of these metabolites, including their antibiotic and antitumor activities. Recently, the first phenazine PTs, termed EpzP and PpzP, were isolated and biochemically characterized. The two enzymes play a central role in the biosynthesis of endophenazines by catalyzing the regiospecific prenylation of 5,10-dihydrophenazine-1-carboxylic acid (dhPCA) in the secondary metabolism of two different Streptomyces strains. Here we report crystal structures of EpzP in its unliganded state as well as bound to S-thiolodiphosphate (SPP), thus defining the first three-dimensional structures for any phenazine PT. A model of a ternary complex resulted from in silico modeling of dhPCA and site-directed mutagenesis. The structural analysis provides detailed insight into the likely mechanism of phenazine prenylation. The catalytic mechanism suggested by the structure identifies amino acids that are required for catalysis. Inspection of the structures and the model of the ternary complex furthermore allowed us to rationally engineer EpzP variants with up to 14-fold higher catalytic reaction rate compared to the wild-type enzyme. This study therefore provides a solid foundation for additional enzyme modifications that should result in efficient, tailor-made biocatalysts for phenazines production.


    Organizational Affiliation

    Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prenyltransferase
A, B
304Streptomyces cinnamonensisGene Names: epzP
Find proteins for E5KWG9 (Streptomyces cinnamonensis)
Go to UniProtKB:  E5KWG9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PIS
Query on PIS

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A
TRIHYDROGEN THIODIPHOSPHATE
THIOPYROPHOSPHATE
H3 O6 P2 S
HWTUHTNZLQJJEV-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
A, B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.110α = 90.00
b = 97.010β = 90.00
c = 135.860γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-03-28 
  • Released Date: 2012-11-14 
  • Deposition Author(s): Zocher, G., Stehle, T.

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description