In an accompanying paper [J. R. Myette, Z. Shriver, J. Liu, G. Venkataraman, and R. Sasisekharan (2002) Biochem. Biophys. Res. Commun. 290, 1206-1213], we described the purification and biochemical characterization of a soluble, recombinantly expressed form of the human heparan sulfate 3-O-sulfotransferase (3-OST-1). Such an important first step enables detailed structure-function studies for this class of enzymes. Herein, we describe a complimentary, structure-based homology modeling approach for predicting 3-OST-1 structure. This approach employs a variety of structural analysis and molecular modeling tools used in conjunction with protein crystallographic studies of related enzymes. In this manner, we describe important motifs within the predicted three-dimensional structure of the enzyme and identify specific amino acids that are likely important for enzymatic function. (C) 2002 Elsevier Science (USA).