Native disulfide bond formation in eukaryotes is dependent on protein-disulfide isomerase (PDI) and its homologs, which contain varying combinations of catalytically active and inactive thioredoxin domains. However, the specific contribution of PDI to the formation of new disulfides versus reduction/rearrangement of non-native disulfides is poorly understood. We analyzed the role of individual PDI domains in disulfide bond formation in a reaction driven by their natural oxidant, Ero1p. We found that Ero1p oxidizes the isolated PDI catalytic thioredoxin domains, A and A at the same rate. In contrast, we found that in the context of full-length PDI, there is an asymmetry in the rate of oxidation of the two active sites. This asymmetry is the result of a dual effect: an enhanced rate of oxidation of the second catalytic (A) domain and the substratemediated inhibition of oxidation of the first catalytic (A) domain. The specific order of thioredoxin domains in PDI is important in establishing the asymmetry in the rate of oxidation of the two active sites thus allowing A and A, two thioredoxin domains that are similar in sequence and structure, to serve opposing functional roles as a disulfide isomerase and disulfide oxidase, respectively. These findings reveal how native disulfide folding is accomplished in the endoplasmic reticulum and provide a context for understanding the proliferation of PDI homologs with combinatorial arrangements of thioredoxin domains.Proteins that traverse the secretory pathway typically contain disulfide bonds that are critical for their correct fold and function. In eukaryotes, the endoplasmic reticulum (ER) 2 is the entry point into the secretory pathway and is the cellular compartment where folding and disulfide bond formation occur (1, 2). Disulfides can form spontaneously in vitro in the presence of an oxidizing agent such as molecular oxygen or oxidized glutathione; however, this process is typically slow and inefficient. In vivo, disulfide bond formation is dependent on cellular machinery to catalyze the formation of new disulfides (oxidation) and the rearrangement of non-native disulfides (isomerization). Both oxidation and isomerization are necessary for allowing the full complement of native disulfide bond formation.Protein-disulfide isomerase (PDI), which was identified more than 40 years ago, plays a critical role in promoting native disulfide bond formation in vivo (3). PDI, an essential enzyme with the ability to catalyze both the oxidation of new disulfides and the isomerization of existing disulfides, is composed of four thioredoxin-like domains (4). The first and last domains (referred to as A and AЈ, respectively) contain Cys-x-x-Cys (CxxC) active sites, whereas the two middle domains (referred to as B and BЈ) are catalytically inactive (5, 6). Oxidation involves the transfer of an active site disulfide from PDI to substrate proteins, while isomerization requires the active site cysteines to be in a reduced form so that they can attack non-native disulfides in substrate ...