6NW4

Evolution of a computationally designed Kemp eliminase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.192 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Emergence of a Negative Activation Heat Capacity during Evolution of a Designed Enzyme.

Bunzel, H.A.Kries, H.Marchetti, L.Zeymer, C.Mittl, P.R.E.Mulholland, A.J.Hilvert, D.

(2019) J Am Chem Soc 141: 11745-11748

  • DOI: https://doi.org/10.1021/jacs.9b02731
  • Primary Citation of Related Structures:  
    6NW4

  • PubMed Abstract: 

    Temperature influences the reaction kinetics and evolvability of all enzymes. To understand how evolution shapes the thermodynamic drivers of catalysis, we optimized the modest activity of a computationally designed enzyme for an elementary proton-transfer reaction by nearly 4 orders of magnitude over 9 rounds of mutagenesis and screening. As theorized for primordial enzymes, the catalytic effects of the original design were almost entirely enthalpic in origin, as were the rate enhancements achieved by laboratory evolution. However, the large reductions in Δ H were partially offset by a decrease in T Δ S and unexpectedly accompanied by a negative activation heat capacity, signaling strong adaptation to the operating temperature. These findings echo reports of temperature-dependent activation parameters for highly evolved natural enzymes and are relevant to explanations of enzymatic catalysis and adaptation to changing thermal environments.


  • Organizational Affiliation

    Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Indole-3-glycerol phosphate synthase247Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: trpCSSO0895
EC: 4.1.1.48
UniProt
Find proteins for Q06121 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q06121 
Go to UniProtKB:  Q06121
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06121
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.304α = 90
b = 61.304β = 90
c = 121.278γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Other
  • Version 1.3: 2020-04-22
    Changes: Database references
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Refinement description