5HYV

Crystal Structure of Transketolase with ThDP from Pichia Stipitis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.116 
  • R-Value Work: 0.106 
  • R-Value Observed: 0.106 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural and biochemical interrogation on transketolase from Pichia stipitis for new functionality

Hsu, L.J.Hsu, N.S.Wang, Y.L.Wu, C.J.Li, T.L.

(2016) Protein Eng Des Sel 

  • DOI: https://doi.org/10.1093/protein/gzw036
  • Primary Citation of Related Structures:  
    5HGX, 5HJE, 5HYV, 5I4I, 5I51, 5I5E, 5I5G

  • PubMed Abstract: 

    In the development of new functionalities of transketolase for the industrial strain Pichia stipitis (TKps) the structural information of TKps would allow us to gain insight into the enzyme's reaction mechanisms, substrates selectivity and reaction directionality to help reach the goal. We here report seven TKps crystal structures of wild type (WT) and mutants in complex with various physiological ligands. These complexes were refined to resolutions at 1.6-1.03 Å. Both biochemical and mutagenic analyses concluded that residues His27, His66, His100, His261, His478, Asp473, Arg356 and Arg525 play important roles in coenzyme binding and substrates recognition. In general, His66 and His261 hold thiamine diphosphate in place; Arg356 and Arg525 serve as gatekeepers interacting with the terminal phosphate group of sugar-phosphates. His27, His66, His100, His478 and Asp473 are critical for sugars recognition/binding, in which His27 is relatively more important in interaction with sedoheptulose-7-phosphate (S7P) than xylulose-5-phosphate (X5P) in terms of molecular recognition/binding affinity. Kinetically, the reactions with X5P (forward) which were catalyzed by WT or H27A are indistinguishable, while in the reactions with S7P (backward) H27A exhibits weaker activity relative to WT. As a result, given TKps(H27A) as the biocatalyst the overall reactivity reverses from the backward reaction preference to forward, thus facilitating net xylose assimilation.


  • Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transketolase697Scheffersomyces stipitis CBS 6054Mutation(s): 0 
Gene Names: TKTTKT1PICST_67105
EC: 2.2.1.1
UniProt
Find proteins for P34736 (Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545))
Explore P34736 
Go to UniProtKB:  P34736
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34736
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.116 
  • R-Value Work: 0.106 
  • R-Value Observed: 0.106 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.762α = 90
b = 183.83β = 90
c = 98.986γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description