6DKV

Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 21 round 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The evolution of multiple active site configurations in a designed enzyme.

Hong, N.S.Petrovic, D.Lee, R.Gryn'ova, G.Purg, M.Saunders, J.Bauer, P.Carr, P.D.Lin, C.Y.Mabbitt, P.D.Zhang, W.Altamore, T.Easton, C.Coote, M.L.Kamerlin, S.C.L.Jackson, C.J.

(2018) Nat Commun 9: 3900-3900

  • DOI: 10.1038/s41467-018-06305-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzym ...

    Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.


    Organizational Affiliation

    Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.,Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.,Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia. colin.jackson@anu.edu.au.,Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden. lynn.kamerlin@kemi.uu.se.,Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kemp eliminase KE07
A
264N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6VP
Query on 6VP

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Download CCD File 
A
5-nitro-2-oxidanyl-benzenecarbonitrile
2-hydroxy-5-nitrobenzonitrile
C7 H4 N2 O3
MPQNPFJBRPRBFF-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.188 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 96.266α = 90.00
b = 96.266β = 90.00
c = 155.010γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2020-01-22
    Type: Author supporting evidence
  • Version 1.2: 2020-02-12
    Type: Database references