Transketolase from E. coli in complex with substrate D-xylulose-5-phosphate

Experimental Data Snapshot

  • Resolution: 1.47 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

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This is version 1.3 of the entry. See complete history


Strain and near attack conformers in enzymic thiamin catalysis: X-ray crystallographic snapshots of bacterial transketolase in covalent complex with donor ketoses xylulose 5-phosphate and fructose 6-phosphate, and in noncovalent complex with acceptor aldose ribose 5-phosphate.

Asztalos, P.Parthier, C.Golbik, R.Kleinschmidt, M.Hubner, G.Weiss, M.S.Friedemann, R.Wille, G.Tittmann, K.

(2007) Biochemistry 46: 12037-12052

  • DOI: https://doi.org/10.1021/bi700844m
  • Primary Citation of Related Structures:  
    2R8O, 2R8P

  • PubMed Abstract: 

    Transketolase is a prominent thiamin diphosphate-dependent enzyme in sugar metabolism that catalyzes the reversible transfer of a 2-carbon dihydroxyethyl fragment between a donor ketose and an acceptor aldose. The X-ray structures of transketolase from E. coli in a covalent complex with donor ketoses d-xylulose 5-phosphate (X5P) and d-fructose 6-phosphate (F6P) at 1.47 A and 1.65 A resolution reveal significant strain in the tetrahedral cofactor-sugar adducts with a 25-30 degrees out-of-plane distortion of the C2-Calpha bond connecting the substrates' carbonyl with the C2 of the cofactor's thiazolium part. Both intermediates adopt very similar extended conformations in the active site with a perpendicular orientation of the scissile C2-C3 sugar bond relative to the thiazolium ring. The sugar-derived hydroxyl groups of the intermediates form conserved hydrogen bonds with one Asp side chain, with a cluster of His residues and with the N4' of the aminopyrimidine ring of the cofactor. The phosphate moiety is held in place by electrostatic and hydrogen-bonding interactions with Arg, His, and Ser side chains. With the exception of the thiazolium part of the cofactor, no structural changes are observable during intermediate formation indicating that the active site is poised for catalysis. DFT calculations on both X5P-thiamin and X5P-thiazolium models demonstrate that an out-of-plane distortion of the C2-Calpha bond is energetically more favorable than a coplanar bond. The X-ray structure with the acceptor aldose d-ribose 5-phosphate (R5P) noncovalently bound in the active site suggests that the sugar is present in multiple forms: in a strained ring-closed beta-d-furanose form in C2-exo conformation as well as in an extended acyclic aldehyde form, with the reactive C1 aldo function held close to Calpha of the presumably planar carbanion/enamine intermediate. The latter form of R5P may be viewed as a near attack conformation. The R5P binding site overlaps with those of the leaving group moieties of the covalent donor-cofactor adducts, demonstrating that R5P directly competes with the donor-derived products glyceraldehyde 3-phosphate and erythrose 4-phosphate, which are substrates of the reverse reaction, for the same docking site at the active site and reaction with the DHEThDP enamine.

  • Organizational Affiliation

    Institut für Biochemie/Biotechnologie, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transketolase 1
A, B
669Escherichia coli K-12Mutation(s): 0 
Gene Names: tktAtkt
Find proteins for P27302 (Escherichia coli (strain K12))
Explore P27302 
Go to UniProtKB:  P27302
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27302
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on T5X

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thia zol-3-ium-2-yl}-5-O-phosphono-D-xylitol
C17 H30 N4 O15 P3 S
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
H [auth B]
I [auth B]
J [auth B]
K [auth B]
E [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
C2 H6 O2
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.47 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.138α = 90
b = 101.951β = 90
c = 133.258γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Structure summary