This research was to study the structure-function relationships and catalytic mechanisms of maize starch synthase IIa (SSIIa). Chemical modification of maize SSIIa showed that pyridoxal-5-phosphate, which specifically modifies lysine residues, inactivated maize SSIIa activity in a time and concentration dependent manner. Substrate ADP-glucose completely protected SSIIa from inactivation by pyridoxal-5-phosphate, indicating that lysine residue(s) is important for ADP-glucose binding of maize SSIIa. To identify lysine residues possibly involved in substrate ADP-glucose binding, site-directed mutagenesis was used to generate mutants at conserved lysine sites. Lysine-193 located at the conserved KTGGL domain has been widely suggested as a putative ADP-glucose binding site in plants based on the study of E. coli glycogen synthase. In contrast with E. coli glycogen synthase (GS), the mutations at the conserved lysine-193 did not change the ADP-glucose affinity of maize SSIIa. It suggests that the epsilon-amino group of lysine-193 is not involved in the binding of ADP-glucose in maize SSIIa. However, the mutations at lysine-193 influenced enzyme activity of maize SSIIa, suggesting that lysine-193 is involved in catalysis of maize SSIIa. The functional difference in the conserved K-T-G-G motif between E. coli GS and maize SSIIa is not related to the N-terminal extension of SSIIa, a structural difference between the two enzymes. Kinetic characterization of mutants at lysine-497 has shown that K497Q, K497N, and K497E resulted in a significant increase in Km for ADP-glucose over wild type enzyme. The kinetic changes are not caused by a global conformational change, as shown by Circular Dichroism spectra. This suggests that the conserved lysine-497 may be the ADP-glucose binding site of maize SSIIa. A three-dimensional structure model of maize SSIIa has been proposed based on protein threading and site-directed mutagenesis. In this model, the likely scenario of catalysis and substrate binding in maize SSIIa is that lysine-193 is involved in catalysis, and lysine-497 and aspartic acid 199 participate in substrate ADP-glucose binding of SSIIa. Furthermore, my research also showed that citrate not only increased primer affinity to the enzyme, but also affected catalytic chain elongation specificity of maize SSIIa. These findings may lead to generating improved starch synthases through protein engineering. Subsequent transformation of these enzymes in commercial crops may improve starch quantity and quality.