3S1V

Transaldolase from Thermoplasma acidophilum in complex with D-fructose 6-phosphate Schiff-base intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Twisted Schiff base intermediates and substrate locale revise transaldolase mechanism.

Lehwess-Litzmann, A.Neumann, P.Parthier, C.Ludtke, S.Golbik, R.Ficner, R.Tittmann, K.

(2011) Nat.Chem.Biol. 7: 678-684

  • DOI: 10.1038/nchembio.633
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We examined the catalytic cycle of transaldolase (TAL) from Thermoplasma acidophilum by cryocrystallography and were able to structurally characterize--for the first time, to our knowledge--different genuine TAL reaction intermediates. These include ...

    We examined the catalytic cycle of transaldolase (TAL) from Thermoplasma acidophilum by cryocrystallography and were able to structurally characterize--for the first time, to our knowledge--different genuine TAL reaction intermediates. These include the Schiff base adducts formed between the catalytic lysine and the donor ketose substrates fructose-6-phosphate and sedoheptulose-7-phosphate as well as the Michaelis complex with acceptor aldose erythrose-4-phosphate. These structural snapshots necessitate a revision of the accepted reaction mechanism with respect to functional roles of active site residues, and they further reveal fundamental insights into the general structural features of enzymatic Schiff base intermediates and the role of conformational dynamics in enzyme catalysis, substrate binding and discrimination. A nonplanar arrangement of the substituents around the Schiff base double bond was observed, suggesting that a structurally encoded reactant-state destabilization is a driving force of catalysis. Protein dynamics and the intrinsic hydrogen-bonding pattern appear to be crucial for selective recognition and binding of ketose as first substrate.


    Organizational Affiliation

    Albrecht-von-Haller-Institut and Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable transaldolase
A, B, C, D, E
223Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)Mutation(s): 0 
Gene Names: tal
EC: 2.2.1.2
Find proteins for Q9HKI3 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Go to UniProtKB:  Q9HKI3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
F6R
Query on F6R

Download SDF File 
Download CCD File 
A, B, C, D, E
FRUCTOSE -6-PHOSPHATE
C6 H13 O9 P
GSXOAOHZAIYLCY-HSUXUTPPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 148.617α = 90.00
b = 172.535β = 90.00
c = 100.277γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXphasing
MAR345dtbdata collection
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2011-09-07
    Type: Database references
  • Version 1.2: 2011-10-05
    Type: Database references
  • Version 1.3: 2019-09-04
    Type: Data collection, Derived calculations