1TRK

REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 A resolution.

Nikkola, M.Lindqvist, Y.Schneider, G.

(1994) J.Mol.Biol. 238: 387-404

  • DOI: 10.1006/jmbi.1994.1299
  • Also Cited By: 1GPU

  • PubMed Abstract: 
  • The crystal structure of transketolase from Saccharomyces cerevisiae has been refined to a crystallographic residual of 15.7% at 2.0 A resolution using the program package X-PLOR. The refined model of the transketolase homodimer, corresponding to 135 ...

    The crystal structure of transketolase from Saccharomyces cerevisiae has been refined to a crystallographic residual of 15.7% at 2.0 A resolution using the program package X-PLOR. The refined model of the transketolase homodimer, corresponding to 1356 amino acid residues in the asymmetric unit, consists of 10,396 protein atoms, 1040 solvent molecules, 52 thiamine diphosphate atoms and two calcium ions. All amino acid residues except for the two N-terminal residues of the two subunits are defined in the electron density maps and refined. The estimated root-mean-square (r.m.s.) error of the model is less than 0.2 A as deduced from Luzzati plots. The r.m.s. deviation from ideality is 0.017 A for bond distances and 3.1 degrees for bond angles. The main-chain torsion angles of non-glycine residues lie within the allowed regions of the Ramachandran plots. The model shows a very good fit to the electron density maps. The average B-factor for all protein atoms in the first subunit is 19 A2, and 15A2 in the second. The average B-factor for solvent atoms is 32A2. The two subunits of transketolase were refined independently and have nearly identical structures with an r.m.s. deviation of 0.24 A for C alpha atoms 3 to 680, and slightly less when aligning the individual domains. A few exceptions from the 2-fold symmetry are found, mostly in the surface residues. The thiamine diphosphate cofactors have identical conformations. The cofactor is shielded from solvent except for the C-2 atom of the thiazolium ring. A calcium ion is bound to the diphosphate group of thiamine and protein ligands. The metal binding site and the interactions of thiamine diphosphate with protein residues are described. A network of hydrogen bonds consisting of glutamic acid residues and internal water molecules connects the two thiamine diphosphate molecules. Its structure and possible functional implications are discussed.


    Related Citations: 
    • 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
    • Preliminary Crystallographic Data for Transketolase from Yeast
      Schneider, G.,Sundstrom, M.,Lindqvist, Y.
      (1989) J.Biol.Chem. 264: 21619
    • 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


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Centre, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSKETOLASE
A, B
680Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TKL1
EC: 2.2.1.1
Find proteins for P23254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23254
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.300α = 90.00
b = 113.300β = 90.00
c = 160.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance