Crystal structure of OE1.3 alkylated with the mechanistic inhibitor 2-bromoacetophenone

  • Classification: HYDROLASE
  • Organism(s): Pyrococcus horikoshii
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-12-13 Released: 2019-06-05 
  • Deposition Author(s): Levy, C.W.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council, European Research Council

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Design and evolution of an enzyme with a non-canonical organocatalytic mechanism.

Burke, A.J.Lovelock, S.L.Frese, A.Crawshaw, R.Ortmayer, M.Dunstan, M.Levy, C.Green, A.P.

(2019) Nature 570: 219-223

  • DOI: https://doi.org/10.1038/s41586-019-1262-8
  • Primary Citation of Related Structures:  
    6Q7N, 6Q7O, 6Q7P, 6Q7Q, 6Q7R

  • PubMed Abstract: 

    The combination of computational design and laboratory evolution is a powerful and potentially versatile strategy for the development of enzymes with new functions 1-4 . However, the limited functionality presented by the genetic code restricts the range of catalytic mechanisms that are accessible in designed active sites. Inspired by mechanistic strategies from small-molecule organocatalysis 5 , here we report the generation of a hydrolytic enzyme that uses N δ -methylhistidine as a non-canonical catalytic nucleophile. Histidine methylation is essential for catalytic function because it prevents the formation of unreactive acyl-enzyme intermediates, which has been a long-standing challenge when using canonical nucleophiles in enzyme design 6-10 . Enzyme performance was optimized using directed evolution protocols adapted to an expanded genetic code, affording a biocatalyst capable of accelerating ester hydrolysis with greater than 9,000-fold increased efficiency over free N δ -methylhistidine in solution. Crystallographic snapshots along the evolutionary trajectory highlight the catalytic devices that are responsible for this increase in efficiency. N δ -methylhistidine can be considered to be a genetically encodable surrogate of the widely employed nucleophilic catalyst dimethylaminopyridine 11 , and its use will create opportunities to design and engineer enzymes for a wealth of valuable chemical transformations.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OE1.3242Pyrococcus horikoshiiMutation(s): 0 
Gene Names: PH0459
Find proteins for O58216 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58216 
Go to UniProtKB:  O58216
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58216
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MHS
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.471α = 90
b = 72.965β = 90
c = 75.168γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

  • Released Date: 2019-06-05 
  • Deposition Author(s): Levy, C.W.

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M027023/1
European Research CouncilUnited Kingdom757991

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description