7PXO | pdb_00007pxo

Structure of the Diels Alderase enzyme AbyU, from Micromonospora maris, co-crystallised with a non transformable substrate analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.245 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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This is version 3.0 of the entry. See complete history


Literature

Delineation of the complete reaction cycle of a natural Diels-Alderase.

Maschio, L.Back, C.R.Alnawah, J.Bowen, J.I.Johns, S.T.Mbatha, S.Z.Han, L.C.Lees, N.R.Zorn, K.Stach, J.E.M.Hayes, M.A.van der Kamp, M.W.Pudney, C.R.Burston, S.G.Willis, C.L.Race, P.R.

(2024) Chem Sci 15: 11572-11583

  • DOI: https://doi.org/10.1039/d4sc02908a
  • Primary Citation of Related Structures:  
    7PXO

  • PubMed Abstract: 

    The Diels-Alder reaction is one of the most effective methods for the synthesis of substituted cyclohexenes. The development of protein catalysts for this reaction remains a major priority, affording new sustainable routes to high value target molecules. Whilst a small number of natural enzymes have been shown capable of catalysing [4 + 2] cycloadditions, there is a need for significant mechanistic understanding of how these prospective Diels-Alderases promote catalysis to underpin their development as biocatalysts for use in synthesis. Here we present a molecular description of the complete reaction cycle of the bona fide natural Diels-Alderase AbyU, which catalyses formation of the spirotetronate skeleton of the antibiotic abyssomicin C. This description is derived from X-ray crystallographic studies of AbyU in complex with a non-transformable synthetic substrate analogue, together with transient kinetic analyses of the AbyU catalysed reaction and computational reaction simulations. These studies reveal the mechanistic intricacies of this enzyme system and establish a foundation for the informed reengineering of AbyU and related biocatalysts.


  • Organizational Affiliation
    • School of Biochemistry, University Walk, University of Bristol BS8 1TD UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YD repeat-containing proteinA [auth D],
B [auth A],
C [auth B],
D [auth C]
160Micromonospora maris AB-18-032Mutation(s): 0 
Gene Names: VAB18032_16470
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.245 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.57α = 90
b = 61.56β = 112.96
c = 87.78γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T001968/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M012107/1
Engineering and Physical Sciences Research CouncilUnited KingdomBB/L01386X/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/L016494/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 2.0: 2024-04-24
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 3.0: 2024-12-25
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary