Structure of the third catalytic domain of the protein disulfide isomerase ERp46

Abstract

PDB Reference: third catalytic domain of ERp46, 3uvt.Protein disulfide isomerases are responsible for catalyzing the proper oxidation and isomerization of disulfide bonds of newly synthesized proteins in the endoplasmic reticulum. Here, the crystal structure of the third catalytic domain of protein disulfide isomerase ERp46 (also known as protein disulfide isomerase A5 and TXNDC5) was determined to 2.0 Å resolution. The structure shows a typical thioredoxin-like fold, but also identifies regions of high structural variability. In particular, the loop between helix 2 and strand 3 adopts strikingly different conformations among the five chains of the asymmetric unit. Cys381 and Cys388 form a structural disulfide and its absence in one of the molecules leads to dramatic conformational changes. The tryptophan residue Trp349 of this molecule inserts into the cavity formed by helices 1 and 3 of a neighbouring molecule, potentially mimicking the interactions of ERp46 with misfolded substrates.

Structure of the Non-Catalytic Domain of the Protein Disulfide Isomerase-Related Protein (PDIR) Reveals Function in Protein Binding

“…These hydrophobic contacts are reminiscent of the b'x structure of human PDIA1, where a tryptophan residue of the x linker between the b' and a' domains inserts into the substrate-binding site on the non-catalytic b' domain [23]. A similar interaction was observed in the recent structure of the third catalytic domain of ERp46 [22]. Importantly, the site of these interactions is different, as the substrate-binding pocket is located between helices α1 and α3 of PDIA1.…”

“…These cysteines are strictly conserved in PDIR which suggests a structural requirement for the disulfide. A similar disulfide bridge is implicated in the stability of the third catalytic domain of ERp46 [22]. Secondly, analysis of crystal contacts identified a putative substrate-binding site in the non-catalytic domain.…”

“…The highest structural similarity was to the N-terminal, catalytic domain a of human ERp57 (PDB entry 3f8u; Z-score of 14.7)[20] and the corresponding domain of yeast PDI (PDB entry 2b5e; Z-score of 14.2)[21]. These hits were followed by several thioredoxins and the third catalytic domain of ERp46 (PDB entry 3uvt; Z-score of 14.0)[22].…”

Hyperoxidized peroxiredoxin 2 interacts with the protein disulfide- isomerase ERp46

“…The remaining cysteine residues of ERp46 are not known to be involved in catalytic activity, but they may have structural roles [34]. ERp46 has 12 cysteine residues, with three pairs of thioredoxin-like domains characteristic of PDIs that catalyse the formation of disulfide bonds during protein synthesis.…”

“…The beads were sequentially eluted with DTT to isolate disulfide-linked Prx2 interactors, followed by glycine, pH 3, to elute non-covalently bound proteins (Figure 2b). ERp46 contains 12 cysteine residues, including three pairs of thioredoxin-like domains, and contributes to disulfide bond formation in the ER (endoplasmic reticulum) [34]. This protein was identified by MS of the trypsin-digested silver-stained SDS/PAGE band and subsequently confirmed by immunoblotting as the PDI ERp46.…”