6Z1L

A de novo Enzyme for the Morita-Baylis-Hillman Reaction BH32.12

  • Classification: BIOSYNTHETIC PROTEIN
  • Organism(s): synthetic construct
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-05-13 Released: 2021-08-25 
  • Deposition Author(s): Levy, C.W.
  • Funding Organization(s): European Research Council (ERC), Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Engineering an efficient and enantioselective enzyme for the Morita-Baylis-Hillman reaction.

Crawshaw, R.Crossley, A.E.Johannissen, L.Burke, A.J.Hay, S.Levy, C.Baker, D.Lovelock, S.L.Green, A.P.

(2022) Nat Chem 14: 313-320

  • DOI: https://doi.org/10.1038/s41557-021-00833-9
  • Primary Citation of Related Structures:  
    6Z1K, 6Z1L, 7O1D

  • PubMed Abstract: 

    The combination of computational design and directed evolution could offer a general strategy to create enzymes with new functions. So far, this approach has delivered enzymes for a handful of model reactions. Here we show that new catalytic mechanisms can be engineered into proteins to accelerate more challenging chemical transformations. Evolutionary optimization of a primitive design afforded an efficient and enantioselective enzyme (BH32.14) for the Morita-Baylis-Hillman (MBH) reaction. BH32.14 is suitable for preparative-scale transformations, accepts a broad range of aldehyde and enone coupling partners and is able to promote selective monofunctionalizations of dialdehydes. Crystallographic, biochemical and computational studies reveal that BH32.14 operates via a sophisticated catalytic mechanism comprising a His23 nucleophile paired with a judiciously positioned Arg124. This catalytic arginine shuttles between conformational states to stabilize multiple oxyanion intermediates and serves as a genetically encoded surrogate of privileged bidentate hydrogen-bonding catalysts (for example, thioureas). This study demonstrates that elaborate catalytic devices can be built from scratch to promote demanding multi-step processes not observed in nature.


  • Organizational Affiliation

    Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BH32.12 protein242synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.967α = 90
b = 70.967β = 90
c = 118.768γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2021-08-25 
  • Deposition Author(s): Levy, C.W.

Funding OrganizationLocationGrant Number
European Research Council (ERC)United Kingdom757991
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M027023/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references
  • Version 1.2: 2022-03-16
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description