5DYV

AbyU - wildtype


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Catalytic Mechanism of a Natural Diels-Alderase Revealed in Molecular Detail.

Byrne, M.J.Lees, N.R.Han, L.C.van der Kamp, M.W.Mulholland, A.J.Stach, J.E.Willis, C.L.Race, P.R.

(2016) J.Am.Chem.Soc. 138: 6095-6098

  • DOI: 10.1021/jacs.6b00232
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Diels-Alder reaction, a [4 + 2] cycloaddition of a conjugated diene to a dienophile, is one of the most powerful reactions in synthetic chemistry. Biocatalysts capable of unlocking new and efficient Diels-Alder reactions would have major impact. ...

    The Diels-Alder reaction, a [4 + 2] cycloaddition of a conjugated diene to a dienophile, is one of the most powerful reactions in synthetic chemistry. Biocatalysts capable of unlocking new and efficient Diels-Alder reactions would have major impact. Here we present a molecular-level description of the reaction mechanism of the spirotetronate cyclase AbyU, an enzyme shown here to be a bona fide natural Diels-Alderase. Using enzyme assays, X-ray crystal structures, and simulations of the reaction in the enzyme, we reveal how linear substrate chains are contorted within the AbyU active site to facilitate a transannular pericyclic reaction. This study provides compelling evidence for the existence of a natural enzyme evolved to catalyze a Diels-Alder reaction and shows how catalysis is achieved.


    Organizational Affiliation

    School of Biochemistry, Biomedical Sciences Building, University of Bristol , University Walk, Bristol BS8 1TD, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YD repeat-containing protein
A, B, C, D, E, F, G, H
160Verrucosispora maris (strain AB-18-032)Mutation(s): 0 
Find proteins for F4F7G1 (Verrucosispora maris (strain AB-18-032))
Go to UniProtKB:  F4F7G1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.800α = 112.87
b = 73.590β = 90.04
c = 86.190γ = 89.98
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L01386X/1

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Author supporting evidence