6Q7N

Crystal structure of BH32 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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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 ...

    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. anthony.green@manchester.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BH32A242Pyrococcus horikoshiiMutation(s): 0 
Gene Names: PH0459
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AC0
Query on AC0

Download Ideal Coordinates CCD File 
B [auth A]1-PHENYLETHANONE
C8 H8 O
KWOLFJPFCHCOCG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.571α = 90
b = 70.549β = 103.484
c = 53.004γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

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