Glycobiology Advance Access originally published online on April 2, 2003
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Glycobiology, 2003, Vol. 13, No. 8 559-566
© 2003 Oxford University Press
Catalytic mechanism of the inverting N-acetylglucosaminyltransferase I: DFT quantum mechanical model of the reaction pathway and determination of the transition state structure
ka2,3
2 GlycoDesign, Inc., 480 University Avenue, Suite 900, Toronto, Ontario, Canada, M5G 1V2
3 Institute of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava, Slovak Republic
Received on January 6, 2003; revised on March 4, 2003; accepted on March 10, 2003
The complex N-glycan structures on glycoproteins play important roles in cell adhesion and recognition events in metazoan organisms. A critical step in the biosynthetic pathway leading from high mannose to these complex structures includes the transfer of N-acetylglucosamine (GlcNAc) to a mannose residue by the inverting N-acetylglucosaminyltransferase I (GnT-I). The catalytic mechanism of this enzymatic reaction is explored herein using DFT quantum chemical methods. The computational model used to follow the reaction is based on the X-ray crystallographic structure of GnT-I and contains 127 atoms that represent fragments of residues critical for the substrate binding and catalysis. The mechanism of the catalytic reaction was monitored by means of a 2D potential energy map calculated as a function of predefined reaction coordinates at the B3LYP/6-31G** level. This potential energy surface revealed one transition state associated with a reaction pathway following a concerted mechanism. The reaction barrier was estimated, and the structure of the transition state was characterized at the B3LYP/6-311++G**// B3LYP/6-31G** level.
1 To whom correspondence should be addressed; e-mail: isabelle{at}glycodesign.com