1GPU

Transketolase complex with reaction intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Snapshot of a Key Intermediate in Enzymatic Thiamin Catalysis: Crystal Structure of the Alpha-Carbanion of (Alpha,Beta-Dihydroxyethyl)-Thiamin Diphosphate in the Active Site of Transketolase from Saccharomyces Cerevisiae.

Fiedler, E.Thorell, S.Sandalova, T.Golbik, R.Koenig, S.Schneider, G.

(2002) Proc Natl Acad Sci U S A 99: 591

  • DOI: 10.1073/pnas.022510999
  • Primary Citation of Related Structures:  
    1GPU

  • PubMed Abstract: 
  • Kinetic and spectroscopic data indicated that addition of the donor substrate hydroxypyruvate to the thiamin diphosphate (ThDP)-dependent enzyme transketolase (TK) led to the accumulation of the alpha-carbanion/enamine of (alpha,beta-dihydroxyethyl) ...

    Kinetic and spectroscopic data indicated that addition of the donor substrate hydroxypyruvate to the thiamin diphosphate (ThDP)-dependent enzyme transketolase (TK) led to the accumulation of the alpha-carbanion/enamine of (alpha,beta-dihydroxyethyl) ThDP, the key reaction intermediate in enzymatic thiamin catalysis. The three-dimensional structure of this intermediate trapped in the active site of yeast TK was determined to 1.9-A resolution by using cryocrystallography. The electron density suggests a planar alpha-carbanion/enamine intermediate having the E-configuration. The reaction intermediate is firmly held in place through direct hydrogen bonds to His-103 and His-481 and an indirect hydrogen bond via a water molecule to His-69. The 4-NH(2) group of the amino-pyrimidine ring of ThDP is within 3 A distance to the alpha-hydroxy oxygen atom of the dihydroxyethyl moiety but at an angle unfavorable for a strong hydrogen bond. No structural changes occur in TK on formation of the reaction intermediate, suggesting that the active site is poised for catalysis and conformational changes during the enzyme reaction are not very likely. The intermediate is present with high occupancy in both active sites, arguing against previous proposals of half-of-the-sites reactivity in yeast TK.


    Related Citations: 
    • Identification of Catalytically Important Residues in Yeast Transketolase.
      Wikner, C., Nilsson, U., Meshalkina, L., Udekwu, C., Lindqvist, Y., Schneider, G.
      (1997) Biochemistry 36: 15643
    • Examination of the Thiamin Diphosphate Binding Site in Yeasttransketolase by Site-Directed Mutagenesis
      Meshalkina, L., Nilsson, U., Wikner, C., Kostikowa, T.
      (1997) Eur J Biochem 244: 646
    • How Thiamin Diphosphateis Activated in Enzyme
      Kern, D., Kern, G., Neef, H., Tittmann, K., Killenberg-Jabs, M., Wikner, C., Schneider, G.
      (1997) Science 275: 67
    • Refined Structure of Transketolase from Saccharomyces Cerevisiae at 2.0 Angstroms Resolution
      Nikkola, M., Lindqvist, Y., Schneider, G.
      (1994) J Mol Biol 238: 387

    Organizational Affiliation

    Institute of Biochemistry, Department of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSKETOLASE 1A, B680Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.2.1.1
Find proteins for P23254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23254 
Go to UniProtKB:  P23254
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
THD
Query on THD

Download CCD File 
A, B
2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE
C14 H22 N4 O9 P2 S
LXZUEFPJZTWGEL-SDNWHVSQSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.3α = 90
b = 113.2β = 90
c = 159.4γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-11
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection