3S1X

Transaldolase from Thermoplasma acidophilum in complex with D-sedoheptulose 7-phosphate Schiff-base intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


This is version 1.4 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:  
    3S0C, 3S1U, 3S1V, 3S1W, 3S1X

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable transaldolaseA, B, C, D, E223Thermoplasma acidophilum DSM 1728Mutation(s): 0 
Gene Names: Ta0616tal
EC: 2.2.1.2
UniProt
Find proteins for Q9HKI3 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q9HKI3 
Go to UniProtKB:  Q9HKI3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.579α = 90
b = 172.802β = 90
c = 100.362γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2011-09-07
    Changes: Database references
  • Version 1.2: 2011-09-14
    Changes: Non-polymer description
  • Version 1.3: 2011-10-05
    Changes: Database references
  • Version 1.4: 2019-09-04
    Changes: Data collection, Derived calculations