The protein disulfide isomerase (PDI)-related protein Wind is essential inPDI 1 -related proteins are residents of the lumen of the endoplasmic reticulum (ER) with various functions, including redox and chaperone activities, regulation of calcium homeostasis, and regulation of protein export from the ER for degradation. These functions are essential for maintaining a productive folding environment for many secretory proteins within the ER (1, 2) that may be critical for viability of the organism (3, 4). The chaperone function of these proteins, and probably to varying extents redox activity as well, relies on their ability to interact non-covalently with specific peptide sequences or epitopes in substrate proteins (2). However, until recently no concise data on peptide specificity, peptide binding sites, or the molecular basis for the observed substrate selectivity of these proteins were available. Data on such inherently weak interactions would require detailed knowledge of the three-dimensional structure of the protein concerned. Although independent NMR structures of the isolated a-and b-type thioredoxin fold domains (redox-active and redox-inactive domains, respectively) of PDI have been reported (5, 6), no complete structure of a eukaryotic PDI protein was available. Most PDI proteins are redox-active, and the involvement of relatively strong heteromeric disulfide bond formation and reduction in assays aimed at elucidating the nature of weak chaperone interactions poses further problems. Because the bЈ-domain has been identified as the major substrate binding site in PDI (7), much attention has been focused on these redox-inactive domains. However, the lack of suitable substrates of physiological relevance with a maturation process that can be readily monitored has complicated these studies. Thus much could be learned from the study of peptide binding and chaperone activity of a naturally occurring PDI family protein lacking redox properties but having a clearly defined substrate that can be studied both in vivo and in vitro.We recently described the first crystal structure of a complete PDI-related protein of the eukaryotic ER (3). This protein, Wind, is essential in Drosophila melanogaster for dorsal-ventral patterning within the developing embryo, and it is required for ER export of an essential Golgi transmembrane proteoglycan modifying enzyme, Pipe (a 2-O-sulfotransferase) (8). Apart from a b-domain, Wind also has a unique C-terminal domain found only in the PDI-D subclass of PDI-related proteins (1). The function of the D-domain is poorly understood, although in Dictyostelium discoideum PDI-D it was shown to play a role in ER retention (9). Recently, we have shown that the Pipe-processing activity requires both the b-and D-domains of Wind. Although the mammalian Wind orthologue ERp28/29 cannot replace Wind in Pipe processing, the D-domains of both proteins could be exchanged, indicating functional conservation between the proteins (3).Here, we show that Wind binds Pipe directly in vitro, and we map a ...