5XPS

Crystal Structure of Transketolase in complex with erythrose-4-phosphate from Pichia Stipitis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.119 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Evidence of Diradicals Involved in the Yeast Transketolase Catalyzed Keto-Transferring Reactions.

Hsu, N.S.Wang, Y.L.Lin, K.H.Chang, C.F.Ke, S.C.Lyu, S.Y.Hsu, L.J.Li, Y.S.Chen, S.C.Wang, K.C.Li, T.L.

(2018) Chembiochem 19: 2395-2402

  • DOI: 10.1002/cbic.201800378
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transketolase (TK) catalyzes a reversible transfer of a two-carbon (C <sub>2 </sub> ) unit between phosphoketose donors and phosphoaldose acceptors, for which the group-transfer reaction that follows a one- or two-electron mechanism and the force tha ...

    Transketolase (TK) catalyzes a reversible transfer of a two-carbon (C 2 ) unit between phosphoketose donors and phosphoaldose acceptors, for which the group-transfer reaction that follows a one- or two-electron mechanism and the force that breaks the C2"-C3" bond of the ketose donors remain unresolved. Herein, we report ultrahigh-resolution crystal structures of a TK (TKps) from Pichia stipitis in previously undiscovered intermediate states and support a diradical mechanism for a reversible group-transfer reaction. In conjunction with MS, NMR spectroscopy, EPR and computational analyses, it is concluded that the enzyme-catalyzed non-Kekulé diradical cofactor brings about the C2"-C3" bond cleavage/formation for the C 2 -unit transfer reaction, for which suppression of activation energy and activation and destabilization of enzymatic intermediates are facilitated.


    Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.,Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan.,Department of Physics, National Dong Hwa University, Hualien, 974, 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): 0 
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 4 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
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
E4P
Query on E4P

Download SDF File 
Download CCD File 
A
ERYTHOSE-4-PHOSPHATE
C4 H9 O7 P
NGHMDNPXVRFFGS-IUYQGCFVSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.119 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 101.149α = 90.00
b = 185.246β = 90.00
c = 98.710γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-12-19
    Type: Data collection, Database references