6Z1K | pdb_00006z1k

A de novo Enzyme for the Morita-Baylis-Hillman Reaction BH32.6

  • 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: 1.48 Å
  • R-Value Free: 
    0.177 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6Z1K

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 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.

Macromolecule Content 

  • Total Structure Weight: 27.86 kDa 
  • Atom Count: 2,210 
  • Modeled Residue Count: 231 
  • Deposited Residue Count: 242 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BH32.6 protein242synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free:  0.177 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.69α = 90
b = 71.69β = 90
c = 121.272γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
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