Catalytic mechanism of the inverting N-acetylglucosaminyltransferase I: DFT quantum mechanical model of the reaction pathway and determination of the transition state structure.
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.
Tvaroska
Igor
I
GlycoDesign, Inc., 480 University Avenue, Suite 900, Toronto, Ontario, Canada, M5G 1V2.
André
Isabelle
I
Carver
Jeremy P
JP
D001665:Binding Sites; D001696:Biomechanical Phenomena; D002384:Catalysis; D018360:Crystallography, X-Ray; D008956:Models, Chemical; D008958:Models, Molecular; D015394:Molecular Structure; D017351:N-Acetylglucosaminyltransferases / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D011789:Quantum Theory; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D017351:N-Acetylglucosaminyltransferases; C024850:alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase I