Crystal structure of dienelactone hydrolase B-4 variant (Q35H, F38L, Y64H, Q76L, Q110L, C123S, Y137C, A141V, Y145C, N154D, E199G, S208G, G211D, S233G and 237Q) at 1.80 A resolution

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report

This is version 1.7 of the entry. See complete history


Directed evolution of new and improved enzyme functions using an evolutionary intermediate and multidirectional search.

Porter, J.L.Boon, P.L.Murray, T.P.Huber, T.Collyer, C.A.Ollis, D.L.

(2015) ACS Chem Biol 10: 611-621

  • DOI: https://doi.org/10.1021/cb500809f
  • Primary Citation of Related Structures:  
    4U2B, 4U2C, 4U2D, 4U2E, 4U2F, 4U2G

  • PubMed Abstract: 

    The ease with which enzymes can be adapted from their native roles and engineered to function specifically for industrial or commercial applications is crucial to enabling enzyme technology to advance beyond its current state. Directed evolution is a powerful tool for engineering enzymes with improved physical and catalytic properties and can be used to evolve enzymes where lack of structural information may thwart the use of rational design. In this study, we take the versatile and diverse α/β hydrolase fold framework, in the form of dienelactone hydrolase, and evolve it over three unique sequential evolutions with a total of 14 rounds of screening to generate a series of enzyme variants. The native enzyme has a low level of promiscuous activity toward p-nitrophenyl acetate but almost undetectable activity toward larger p-nitrophenyl esters. Using p-nitrophenyl acetate as an evolutionary intermediate, we have generated variants with altered specificity and catalytic activity up to 3 orders of magnitude higher than the native enzyme toward the larger nonphysiological p-nitrophenyl ester substrates. Several variants also possess increased stability resulting from the multidimensional approach to screening. Crystal structure analysis and substrate docking show how the enzyme active site changes over the course of the evolutions as either a direct or an indirect result of mutations.

  • Organizational Affiliation

    Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxymethylenebutenolidase237Pseudomonas knackmussiiMutation(s): 14 
Gene Names: clcD
Find proteins for P0A115 (Pseudomonas knackmussii (strain DSM 6978 / LMG 23759 / B13))
Explore P0A115 
Go to UniProtKB:  P0A115
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A115
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.796α = 90
b = 70.106β = 90
c = 73.806γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP120104262

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Derived calculations
  • Version 1.2: 2015-03-04
    Changes: Database references
  • Version 1.3: 2015-08-26
    Changes: Source and taxonomy
  • Version 1.4: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.5: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.6: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.7: 2023-12-27
    Changes: Data collection, Database references