Alkaline phosphatases (EC 3.1.3.1) (APs) are dimeric metalloenzymes that catalyze the hydrolysis of phosphate monoesters into inorganic phosphate [1] To understand the differences between the rat intestinal alkaline phosphatase isozymes rIAP-I and rIAP-II, we constructed structural models based on the previously determined crystal structure for human placental alkaline phosphatase (hPLAP). Our models of rIAP-I and rIAP-II displayed a typical a ⁄ b topology, but the crown domain of rIAP-I contained an additional b-sheet, while the embracing arm region of rIAP-II lacked the a-helix, when each model was compared to hPLAP. The representations of surface potential in the rIAPs were predominantly positive at the base of the active site. The coordinated metal at the active site was predicted to be a zinc triad in rIAP-I, whereas the typical combination of two zinc atoms and one magnesium atom was proposed for rIAP-II. Using metal-depleted extracts from rat duodenum or jejunum and hPLAP, we performed enzyme assays under restricted metal conditions. With the duodenal and jejunal extract, but not with hPLAP, enzyme activity was restored by the addition of zinc, whereas in nonchelated extracts, the addition of zinc inhibited duodenal IAP and hPLAP, but not jejunal IAP. Western blotting revealed that nearly all of the rIAP in the jejunum extracts was rIAP-I, whereas in duodenum the percentage of rIAP-I (55%) correlated with the degree of AP activation (60% relative to that seen with jejunal extracts). These data are consistent with the presence of a triad of zinc atoms at the active site of rIAP-I, but not rIAP-II or hPLAP. Although no differences in amino acid alignment in the vicinity of metal-binding site 3 were predicted between the rIAPs and hPLAP, the His153 residue of both rIAPs was closer to the metal position than that in hPLAP. Between the rIAPs, a difference was observed at amino acid position 317 that is indirectly related to the coordination of the metal at metal-binding site 3 and water molecules. These findings suggest that the side-chain position of His153, and the alignment of Q317, might be the major determinants for activation of the zinc triad in rIAP-I.Abbreviations AP, alkaline phosphatase; BAC, base of the active site cleft; CB, carbonate-bicarbonate; DM, double mutant; ECAP, Escherichia coli alkaline phosphatase; GCAP, germ cell-type alkaline phosphatase; hPLAP, human placental alkaline phosphatase; IAP, intestinal alkaline phosphatase; M1, metal-binding site 1; M2, metal-binding site 2; M3, metal-binding site 3; PLAP, placental alkaline phosphatase; rIAP, rat intestinal alkaline phosphatase; SAP, shrimp alkaline phosphatase; TNAP, tissue-nonspecific alkaline phosphatase.