Int. J. Mol. Sci. 2004, 5(4), 141-153; doi:10.3390/i5040141
Article

The Mechanism of Phosphoryl Transfer Reaction and the Role of Active Site Residues on the Basis of Ribokinase-Like Kinases

Edyta Dyguda, Borys Szefczyk and W. Andrzej Sokalski*
Molecular Modeling Laboratory, Institute of Physical and Theoretical Chemistry Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
* Author to whom correspondence should be addressed.
Received: 15 December 2003 / Accepted: 11 March 2004 / Published: 1 April 2004
(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)
PDF Full-text Download PDF Full-Text [924 KB, uploaded 28 August 2008 16:06 CEST]
Abstract: The role of ribokinase-like carbohydrate kinases consists in ATP dependent phosphorylation of small molecules containing hydroxymethyl group. Although they differ substantially in structural terms and exhibit a broad substrate specificity, some family-wide conserved features can be distinguished suggesting the common mode of action. 4-methyl-5-β-hydroxyethylthiazole kinase (Thz kinase) was chosen as a representative model and the mechanism proposed in X-ray crystal structure paper provided the basis for calculations. In particular, the possible role of several active site residues (Arg121 and Cys198 among others) and of the two magnesium ions was examined. Static and dynamic catalytic fields for the reaction were generated revealing the most favourable environment for the preferential transition state stabilization. An attempt to model the phosphoryl transfer reaction as well as to investigate the influence of the cysteine residue on the reaction course at the semiempirical PM3 level of theory was undertaken.
Keywords: ribokinase-like carbohydrate kinases; phosphoryl transfer; static and dynamic catalytic fields; enzymatic catalysis

Article Statistics

Click here to load and display the download statistics.

Cite This Article

MDPI and ACS Style

Dyguda, E.; Szefczyk, B.; Sokalski, W.A. The Mechanism of Phosphoryl Transfer Reaction and the Role of Active Site Residues on the Basis of Ribokinase-Like Kinases. Int. J. Mol. Sci. 2004, 5, 141-153.

AMA Style

Dyguda E, Szefczyk B, Sokalski WA. The Mechanism of Phosphoryl Transfer Reaction and the Role of Active Site Residues on the Basis of Ribokinase-Like Kinases. International Journal of Molecular Sciences. 2004; 5(4):141-153.

Chicago/Turabian Style

Dyguda, Edyta; Szefczyk, Borys; Sokalski, W. A. 2004. "The Mechanism of Phosphoryl Transfer Reaction and the Role of Active Site Residues on the Basis of Ribokinase-Like Kinases." Int. J. Mol. Sci. 5, no. 4: 141-153.

Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert