4YL7

Crystal structure of the indole prenyltransferase MpnD from Marinactinospora thermotolerans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.601 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Manipulation of prenylation reactions by structure-based engineering of bacterial indolactam prenyltransferases.

Mori, T.Zhang, L.Awakawa, T.Hoshino, S.Okada, M.Morita, H.Abe, I.

(2016) Nat Commun 7: 10849-10849

  • DOI: 10.1038/ncomms10849
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Prenylation reactions play crucial roles in controlling the activities of biomolecules. Bacterial prenyltransferases, TleC from Streptomyces blastmyceticus and MpnD from Marinactinospora thermotolerans, catalyse the 'reverse' prenylation of (-)-indol ...

    Prenylation reactions play crucial roles in controlling the activities of biomolecules. Bacterial prenyltransferases, TleC from Streptomyces blastmyceticus and MpnD from Marinactinospora thermotolerans, catalyse the 'reverse' prenylation of (-)-indolactam V at the C-7 position of the indole ring with geranyl pyrophosphate or dimethylallyl pyrophosphate, to produce lyngbyatoxin or pendolmycin, respectively. Using in vitro analyses, here we show that both TleC and MpnD exhibit relaxed substrate specificities and accept various chain lengths (C5-C25) of the prenyl donors. Comparisons of the crystal structures and their ternary complexes with (-)-indolactam V and dimethylallyl S-thiophosphate revealed the intimate structural details of the enzyme-catalysed 'reverse' prenylation reactions and identified the active-site residues governing the selection of the substrates. Furthermore, structure-based enzyme engineering successfully altered the preference for the prenyl chain length of the substrates, as well as the regio- and stereo-selectivities of the prenylation reactions, to produce a series of unnatural novel indolactams.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Department of Medicinal Resources, Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama 930-0194, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aromatic prenyltransferase
A
382Marinactinospora thermotoleransMutation(s): 0 
Find proteins for I7EIW6 (Marinactinospora thermotolerans)
Go to UniProtKB:  I7EIW6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.601 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.660α = 90.00
b = 53.700β = 90.00
c = 132.680γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-20
    Type: Database references