5I5E

Crystal Structure of Transketolase mutants-H66/261C complex with xylulose-5-phoaphate from Pichia Stipitis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1093/protein/gzw036
  • Primary Citation of Related Structures:  

  • 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 d ...

    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 Graduate Institute of Life Science, National Defense Medical Center, Taipei 114, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transketolase
A
697Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545)Mutation(s): 2 
Gene Names: TKT (TKT1)
EC: 2.2.1.1
Find proteins for P34736 (Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545))
Go to Gene View: TKT
Go to UniProtKB:  P34736
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
A
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
5SP
Query on 5SP

Download SDF File 
Download CCD File 
A
5-O-phosphono-D-xylulose
D-xylulose 5-phosphate
C5 H11 O8 P
FNZLKVNUWIIPSJ-RFZPGFLSSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 99.885α = 90.00
b = 182.084β = 90.00
c = 98.263γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references