Rational design of a novel enzyme - efficient thioester hydrolysis enabled by the incorporation of a single His residue into human glutathione transferase A1-1

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

Starting Model: experimental
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Incorporation of a Single His Residue by Rational Design Enables Thiol-Ester Hydrolysis by Human Glutathione Transferase A1-1

Hederos, S.Broo, K.S.Jakobsson, E.Kleywegt, G.J.Mannervik, B.Baltzer, L.

(2004) Proc Natl Acad Sci U S A 101: 13163

  • DOI: https://doi.org/10.1073/pnas.0403045101
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A strategy for rational enzyme design is reported and illustrated by the engineering of a protein catalyst for thiol-ester hydrolysis. Five mutants of human glutathione (GSH; gamma-Glu-Cys-Gly) transferase A1-1 were designed in the search for a catalyst and to provide a set of proteins from which the reaction mechanism could be elucidated. The single mutant A216H catalyzed the hydrolysis of the S-benzoyl ester of GSH under turnover conditions with a k(cat)/K(M) of 156 M(-1) x min(-1), and a catalytic proficiency of >10(7) M(-1) when compared with the first-order rate constant of the uncatalyzed reaction. The wild-type enzyme did not hydrolyze the substrate, and thus, the introduction of a single histidine residue transformed the wild-type enzyme into a turnover system for thiol-ester hydrolysis. By kinetic analysis of single, double, and triple mutants, as well as from studies of reaction products, it was established that the enzyme A216H catalyzes the hydrolysis of the thiol-ester substrate by a mechanism that includes an acyl intermediate at the side chain of Y9. Kinetic measurements and the crystal structure of the A216H GSH complex provided compelling evidence that H216 acts as a general-base catalyst. The introduction of a single His residue into human GSH transferase A1-1 created an unprecedented enzymatic function, suggesting a strategy that may be of broad applicability in the design of new enzymes. The protein catalyst has the hallmarks of a native enzyme and is expected to catalyze various hydrolytic, as well as transesterification, reactions.

  • Organizational Affiliation

    Department of Chemistry, IFM, Linköping University, SE-581 83 Linköping, Sweden.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
225Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P08263 (Homo sapiens)
Explore P08263 
Go to UniProtKB:  P08263
GTEx:  ENSG00000243955 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08263
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.906α = 90
b = 92.05β = 93.21
c = 51.272γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Advisory, Data collection
  • Version 1.4: 2019-10-09
    Changes: Data collection, Experimental preparation, Other
  • Version 1.5: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description