The vitamin K-dependent ␥-glutamyl carboxylase binds an 18-amino acid sequence usually attached as a propeptide to its substrates. Price and Williamson (Protein Sci. (1993) 2, 1997-1998) noticed that residues 495-513 of the carboxylase shares similarity with the propeptide. They suggested that this internal propeptide could bind intramolecularly to the propeptide binding site of carboxylase, thereby preventing carboxylation of substrates lacking a propeptide recognition sequence. To test Price's hypothesis, we created nine mutant enzyme species that have single or double mutations within this putative internal propeptide. The apparent K d values of these mutant enzymes for human factor IX propeptide varied from 0.5-to 287-fold when compared with that of wild type enzyme. These results are consistent with the internal propeptide hypothesis but could also be explained by these residues participating in propeptide binding site per se. To distinguish between the two alternative hypotheses, we measured the dissociation rates of propeptides from each of the mutant enzymes. Changes in an internal propeptide should not affect the dissociation rates, but changes to a propeptide binding site may affect the dissociation rate. We found that dissociation rates varied in a manner consistent with the apparent K d values measured above. Furthermore, kinetic studies using propeptide-containing substrates demonstrated a correlation between the affinity for propeptide and V max . Taken together, our results indicated that these mutations affected the propeptide binding site rather than a competitive inhibitory internal propeptide sequence. These results agree with our previous observations, indicating that residues in this region are involved in propeptide binding.The vitamin K-dependent ␥-glutamyl carboxylase is a polytopic integral membrane protein that resides in the endoplasmic reticulum (1). It catalyzes the post-translational modification of a number of vitamin K-dependent proteins (e.g. the coagulation proteins prothrombin, factor VII, factor IX, factor X, protein S, protein C, and protein Z) (2, 3). Other known vitamin K-dependent proteins are the bone-related proteins osteocalcin and matrix Gla protein, the growth arrest protein Gas 6, and four proteins of unknown function: proline-rich Gla proteins I and II and TMG proteins 3 and 4 (4 -9). Vitamin K-dependent carboxylase utilizes the substrates: reduced vitamin K, carbon dioxide, oxygen, and a propeptide-containing substrate. Multiple glutamic acid residues of the polypeptide substrate, within about 40 residues of the propeptide, are usually modified to ␥-carboxyglutamate during a single binding event (10).The primary interaction between the vitamin K-dependent carboxylase and its substrates is mediated by the 18-amino acid propeptide sequence (11, 12), which in all known vitamin K-dependent proteins, except for matrix Gla protein, is removed prior to secretion. The role of the substrate's propeptide is to anchor it to the carboxylase for a time sufficient for multiple c...