1TKA

SPECIFICITY OF COENZYME BINDING IN THIAMIN DIPHOSPHATE DEPENDENT ENZYMES: CRYSTAL STRUCTURES OF YEAST TRANSKETOLASE IN COMPLEX WITH ANALOGS OF THIAMIN DIPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Specificity of coenzyme binding in thiamin diphosphate-dependent enzymes. Crystal structures of yeast transketolase in complex with analogs of thiamin diphosphate.

Konig, S.Schellenberger, A.Neef, H.Schneider, G.

(1994) J Biol Chem 269: 10879-10882

  • Primary Citation of Related Structures:  
    1TKC, 1TKB, 1TKA

  • PubMed Abstract: 
  • The three-dimensional structures of complexes of yeast apotransketolase with the coenzyme analogs 6'-methyl, N1'-pyridyl, and N3'-pyridyl thiamin diphosphate, respectively, were determined with protein crystallographic methods. All three coenzyme analogs bind to the enzyme in a fashion highly similar to the cofactor thiamin diphosphate ...

    The three-dimensional structures of complexes of yeast apotransketolase with the coenzyme analogs 6'-methyl, N1'-pyridyl, and N3'-pyridyl thiamin diphosphate, respectively, were determined with protein crystallographic methods. All three coenzyme analogs bind to the enzyme in a fashion highly similar to the cofactor thiamin diphosphate. Thus, either one of the hydrogen bonds of the pyrimidine ring nitrogens to the protein is sufficient for proper binding and positioning of the cofactor. The lack of catalytic activity of the N3'-pyridyl analog is not due to incorrect orientation of the pyrimidine ring, but results from the absence of the hydrogen bond between the N1' nitrogen atom and the conserved residue Glu418. The structure analysis provides further evidence for the importance of this conserved interaction for enzymatic thiamin catalysis.


    Related Citations: 
    • Refined Structure of Transketolase from Saccharomyces Cerevisiae at 2.0 Angstrom Resolution
      Nikkola, M., Lindqvist, Y., Schneider, G.
      (1994) J Mol Biol 238: 387
    • Yeast Tkl1 Gene Encodes a Transketolase that is Required for Efficient Glycolysis and Biosynthesis of Aromatic Amino Acids
      Sundstrom, M., Lindqvist, Y., Schneider, G., Hellman, U., Ronne, H.
      (1993) J Biol Chem 268: 24346
    • Three-Dimensional Structure of Transketolase, a Thiamine Diphosphate Dependent Enzyme, at 2.5 Angstroms Resolution
      Lindqvist, Y., Schneider, G., Ermler, U., Sundstrom, M.
      (1992) EMBO J 11: 2373
    • Preliminary Crystallographic Data for Transketolase from Yeast
      Schneider, G., Sundstrom, M., Lindqvist, Y.
      (1989) J Biol Chem 264: 21619

    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSKETOLASEA, B678Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.2.1.1
UniProt
Find proteins for P23254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23254 
Go to UniProtKB:  P23254
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N3T (Subject of Investigation/LOI)
Query on N3T

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]3'-DEAZO-THIAMIN DIPHOSPHATE
C13 H19 N3 O7 P2 S
NWZZJKMZTWGIFE-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
N3T PDBBind:  1TKA Kd: 800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.3α = 90
b = 113.3β = 90
c = 160.9γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-11-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance