we described the molecular cloning, recombinant expression, and preliminary biochemical characterization of the heparin/heparan sulfate 2-O-sulfatase from Flavobacterium heparinum. In this paper, we extend our structure-function investigation of the 2-O-sulfatase. First, we have constructed a homology-based structural model of the enzyme active site, using as a framework the available crystallographic data for three highly related arylsulfatases. In this model, we have identified important structural parameters within the enzyme active site relevant to enzyme function, especially as they relate to its substrate specificity. By docking various disaccharide substrates, we identified potential structural determinants present within these substrates that would complement this unique active site architecture. These determinants included the position and number of sulfates present on the glucosamine, oligosaccharide chain length, the presence of a ⌬4,5-unsaturated double bond, and the exolytic versus endolytic potential of the enzyme. The predictions made from our model provided a structural basis of substrate specificity originally interpreted from the biochemical and kinetic data. Our modeling approach was further complemented experimentally using peptide mapping in tandem with mass spectrometry and site-directed mutagenesis to physically demonstrate the presence of a covalently modified cysteine (formylglycine) within the active site. This combinatorial approach of structure modeling and biochemical studies provides insight into the molecular basis of enzyme function.Heparin and heparin sulfate glycosaminoglycans (HSGAGs) 1 are structurally complex linear polysaccharides (1, 2) composed of repeating disaccharides of uronic acid (␣-L-iduronic or -Dglucuronic) linked 134 to ␣-D-glucosamine. This structural complexity derives principally from the variable chemical modifications made to the polysaccharide chain. Such modifications include acetylation or sulfation at the N-position of the glucosamine, epimerization of glucuronic acid to iduronic acid, and additional O-sulfation at the 2-O-position of the uronic acid in addition to the 3-O, 6-O-position of the adjoining glucosamine. It is a highly variable sulfation pattern, in particular, which ascribes to each GAG chain a unique structural signature. In turn, this signature dictates specific GAG-protein interactions underlying critical biological processes related to cell and tissue function. Given this critical structure-function relationship of GAG sulfation, enzymes that can hydrolyze these sulfates in a structurally specific manner are important tools for the determination of GAG fine structure to better ascertain these structure-function relationships. In the previous paper (21), we described the cloning, recombinant expression, and biochemical characterization of one such sulfatase, the 2-O-sulfatase from Flavobacterium heparinum.As members of a large enzyme family, the sulfatases hydrolyze a wide array of sulfate esters (for a review, see Refs. 3 and 4). Their ...