2Y6Z

Crystallographic structure of GM23 an example of Catalytic migration from TIM to thiamin phosphate synthase.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.191 

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


Literature

Evolutionary Walk between (Beta/Alpha)(8) Barrels: Catalytic Migration from Triosephosphate Isomerase to Thiamin Phosphate Synthase.

Saab-Rincon, G.Olvera, L.Olvera, M.Rudino-Pinera, E.Benites, E.Soberon, X.Morett, E.

(2012) J Mol Biol 416: 255

  • DOI: https://doi.org/10.1016/j.jmb.2011.12.042
  • Primary Citation of Related Structures:  
    2Y6Z, 2Y70

  • PubMed Abstract: 

    The functionally versatile (β/α)(8) barrel scaffold was used to migrate triosephosphate isomerase (TPI) to thiamin phosphate synthase (TPS) activity, two enzymes that share the same fold but catalyze unrelated reactions through different mechanisms. The high sensitivity of the selection methodology was determinant to succeed in finding proteins with the desired activity. A combination of rational design and random mutagenesis was used to achieve the desired catalytic migration. One of the parallel directed evolution strategies followed resulted in TPI derivatives able to complement the thiamin phosphate auxotrophy phenotype of an Escherichia coli strain deleted of thiE, the gene that codes for TPS. Successive rounds of directed evolution resulted in better complementing TPI variants. Biochemical characterization of some of the evolved TPI clones demonstrated that the K(m) for the TPS substrates was similar to that of the native TPS; however and in agreement with the very slow complementation phenotype, the k(cat) was 4 orders of magnitude lower, indicating that substrate binding played a major role on selection. Interestingly, the crystal structure of the most proficient variant showed a slightly modified TPI active site occupied by a thiamin-phosphate-like molecule. Substitution of key residues in this region reduced TPS activity, strongly suggesting that this is also the catalytic site for the evolved TPS activity. The presence of the TPS reaction product at the active site explains the fast inactivation of the enzyme observed. In conclusion, by combining rational design, random mutagenesis and a very sensitive selection, it is possible to achieve enzymatic activity migration.


  • Organizational Affiliation

    Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, AP 510-3, CP 62250, Cuernavaca, Morelos, México. gsaab@ibt.unam.mx


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRIOSE-PHOSPHATE ISOMERASE256Trypanosoma brucei bruceiMutation(s): 21 
EC: 5.3.1.1
UniProt
Find proteins for P04789 (Trypanosoma brucei brucei)
Explore P04789 
Go to UniProtKB:  P04789
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04789
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.191 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.3α = 90
b = 126.3β = 90
c = 107.29γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
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: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-01-25
    Changes: Other
  • Version 1.2: 2012-02-08
    Changes: Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary