6DC1

Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 25 round 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

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:  
    6DKV, 6DNJ, 6C7H, 6C8B, 6C7T, 6CT3, 6CAI, 6DC1, 6C7V, 6C7M

  • 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 enzymes c ...

    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. colin.jackson@anu.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kemp eliminase KE07ABCDEFGHABCDEFGHIJKL
264synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download Ideal Coordinates CCD File 
A, C
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
6VP
Query on 6VP

Download Ideal Coordinates CCD File 
A, B, H, K
5-nitro-2-oxidanyl-benzenecarbonitrile
C7 H4 N2 O3
MPQNPFJBRPRBFF-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
L
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C, G
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.033α = 90
b = 111.033β = 90
c = 257.739γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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