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Insights into the Thiamine Diphosphate Enzyme Activation Mechanism: Computational Model for Transketolase Using a Quantum Mechanical/Molecular Mechanical Method.
- Source :
-
Biochemistry [Biochemistry] 2016 Apr 12; Vol. 55 (14), pp. 2144-52. Date of Electronic Publication: 2016 Mar 31. - Publication Year :
- 2016
-
Abstract
- We propose the first computational model for transketolase (TK), a thiamine diphosphate (ThDP)-dependent enzyme, using a quantum mechanical/molecular mechanical method on the basis of crystallographic TK structures from yeast and Escherichia coli, together with experimental kinetic data reported in the literature with wild-type and mutant TK. This model allowed us to define a new route for ThDP activation in the enzyme environment. We evidenced a strong interaction between ThDP and Glu418B of the TK active site, itself stabilized by Glu162A. The crucial point highlighted here is that deprotonation of ThDP C2 is not performed by ThDP N4' as reported in the literature, but by His481B, involving a HOH688A molecule bridge. Thus, ThDP N4' is converted from an amino form to an iminium form, ensuring the stabilization of the C2 carbanion or carbene. Finally, ThDP activation proceeds via an intermolecular process and not by an intramolecular one as reported in the literature. More generally, this proposed ThDP activation mechanism can be applied to some other ThDP-dependent enzymes and used to define the entire TK mechanism with donor and acceptor substrates more accurately.
- Subjects :
- Amino Acid Substitution
Binding Sites
Biocatalysis
Catalytic Domain
Computational Biology
Databases, Protein
Dimerization
Energy Transfer
Enzyme Activation
Escherichia coli Proteins chemistry
Escherichia coli Proteins genetics
Escherichia coli Proteins metabolism
Molecular Conformation
Molecular Dynamics Simulation
Mutation
Quantum Theory
Saccharomyces cerevisiae Proteins genetics
Saccharomyces cerevisiae Proteins metabolism
Structural Homology, Protein
Thermodynamics
Thiamine Pyrophosphate metabolism
Transketolase genetics
Transketolase metabolism
Vitamin B Complex metabolism
Models, Molecular
Saccharomyces cerevisiae Proteins chemistry
Thiamine Pyrophosphate chemistry
Transketolase chemistry
Vitamin B Complex chemistry
Subjects
Details
- Language :
- English
- ISSN :
- 1520-4995
- Volume :
- 55
- Issue :
- 14
- Database :
- MEDLINE
- Journal :
- Biochemistry
- Publication Type :
- Academic Journal
- Accession number :
- 26998737
- Full Text :
- https://doi.org/10.1021/acs.biochem.5b00787