5Y84

Hapalindole U and DMSPP Bound AmbP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Two Distinct Substrate Binding Modes for the Normal and Reverse Prenylation of Hapalindoles by the Prenyltransferase AmbP3

Wong, C.P.Awakawa, T.Nakashima, Y.Mori, T.Zhu, Q.Liu, X.Abe, I.

(2018) Angew. Chem. Int. Ed. Engl. 57: 560-563

  • DOI: 10.1002/anie.201710682
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The cyanobacterial prenyltransferase AmbP3 catalyzes the reverse prenylation of the tetracyclic indole alkaloid hapalindole U at its C-2 position. Interestingly, AmbP3 also accepts hapalindole A, a halogenated C-10 epimer of hapalindole U, and cataly ...

    The cyanobacterial prenyltransferase AmbP3 catalyzes the reverse prenylation of the tetracyclic indole alkaloid hapalindole U at its C-2 position. Interestingly, AmbP3 also accepts hapalindole A, a halogenated C-10 epimer of hapalindole U, and catalyzes normal prenylation at its C-2 position. The comparison of the two ternary crystal structures, AmbP3-DMSPP/hapalindole U and AmbP3-DMSPP/hapalindole A, at 1.65-2.00 Å resolution revealed two distinct orientations for the substrate binding that define reverse or normal prenylation. The tolerance of the enzyme for these altered orientations is attributed to the hydrophobicity of the substrate binding pocket and the plasticity of the amino acids surrounding the allyl group of the prenyl donor. This is the first study to provide the intimate structural basis for the normal and reverse prenylations catalyzed by a single enzyme, and it offers novel insight into the engineered biosynthesis of prenylated natural products.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AmbP3
A, B
335Fischerella ambigua UTEX 1903Mutation(s): 0 
Gene Names: ambP3
Find proteins for V5TDY7 (Fischerella ambigua UTEX 1903)
Go to UniProtKB:  V5TDY7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8P6
Query on 8P6

Download SDF File 
Download CCD File 
A, B
Hapalindole U
C21 H24 N2
SLUFHMQYBPOTFZ-ZRRCRCOKSA-N
 Ligand Interaction
DST
Query on DST

Download SDF File 
Download CCD File 
A, B
DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H14 O6 P2 S
UWSFTDFHOGCIEL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.311α = 105.42
b = 54.810β = 106.24
c = 77.087γ = 98.68
Software Package:
Software NamePurpose
XDSdata processing
PHENIXrefinement
PHENIXphasing
Aimlessdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release