Volume 24, Issue 7, Pages 1120-1129 (July 2016) Structures of Human Peroxiredoxin 3 Suggest Self-Chaperoning Assembly that Maintains Catalytic State  N. Amy Yewdall, Hariprasad Venugopal, Ambroise Desfosses, Vahid Abrishami, Yuliana Yosaatmadja, Mark B. Hampton, Juliet A. Gerrard, David C. Goldstone, Alok K. Mitra, Mazdak Radjainia  Structure  Volume 24, Issue 7, Pages 1120-1129 (July 2016) DOI: 10.1016/j.str.2016.04.013 Copyright © 2016 Elsevier Ltd Terms and Conditions

Structure 2016 24, 1120-1129DOI: (10.1016/j.str.2016.04.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 1 HsPrx3 Crystal Structure with Resolved C Terminus and Fully Folded Active Site (A) The active site showing the peroxidatic cysteine (CP47, in yellow) in a fully folded conformation surrounded by the conserved active-site residues (T44, P40, R123, in purple). The folded C terminus also reveals the resolving cysteine (CR168, in green) from the adjacent monomer (gray). (B) The peroxiredoxin monomer indicating the locations of helices α2 and α6 involved in protein stacking, and the α7 helix, which is part of the C-terminal tail. (C) HsPrx3 homodimers (monomers colored blue and gray) in two orthogonal views. (D) Six copies of the HsPrx3 homodimer showed in (C) organize as a dodecameric ring, under reducing conditions. See also Figures S1 and S2. Structure 2016 24, 1120-1129DOI: (10.1016/j.str.2016.04.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 2 Comparison of Helical Stacking of HsPrx3 (A) The crystal structure of HsPrx3 as three stacked rings viewed from the side. Helices α2 and α6 are highlighted as the main components of the stacking interaction. The azimuthal rotation is 7.3° and the vertical separation 42.2 Å between successive rings arranged as a helix. (B) Analogous view of the cryo-EM reconstruction of HsPrx3 filaments with helices α2 and α6 also highlighted. The rotation angle between successive rings is 8.7° and the vertical separation 42.7 Å. (C) Sections of density volumes rendered at 3.18σ with the fitted pseudo-atomic model, highlighting well-resolved β strands (left) and a blow-up of a section of one β strand (right) showing that bulky residues are easily discernible in the EM density rendered at 2.45σ. See also Figure S4. Structure 2016 24, 1120-1129DOI: (10.1016/j.str.2016.04.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 3 The R Interface of HsPrx3 (A) The R interface as seen in the crystal structure is formed by two adjacent monomers (blue and pink) with important residues highlighted (green, yellow, and gray). Hydrogen bonds (black dotted lines) link residues V64 and Q159 on the same monomer as well as residues N65 and E162 on apposing monomers. T163 residues (gray) from apposing monomers are angled toward one another, creating a hydrophobic pocket that encourages stacking of the rings. (B) PHENIX-refined pseudo-atomic model (Afonine et al., 2012) fitted to the cryo-EM map of the helical filaments at pH 4.0. The density at the R interface rendered at a threshold of 2.0σ suggests a similar hydrogen-bonding pattern as in the crystal structure. (C) Coulombic surface charge at pH 8.5 based on PROPKA-assigned formal charges to the various atoms shows similarly charged C-terminal ends of the α6 and α2 helices (http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/). (D) At pH 4.0, the Coulombic surface charge for the same regions of the α6 and α2 helices are opposite in nature, suggesting a stabilizing attractive interaction. See also Figures S5 and S6. Structure 2016 24, 1120-1129DOI: (10.1016/j.str.2016.04.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 4 Close-Up Details of the Active-Site Cysteines and the C Terminus (A) The active site of the HsPrx3 crystal structure is seen in the fully folded (FF) conformation, whereas the same region with the fitted pseudo-atomic model of cryo-EM structure shows it to be locally unfolded (LU). The density map was rendered at 2.45σ. (B) The C terminus of a monomer in the unsharpened cryo-EM density is seen as partially disordered. The folded C terminus seen in the HsPrx3 crystal structure does not fit into this density map, rendered at 1.8σ. (C) However, the fit of F190L BtPrx3 (PDB: 4MH3) dimer suggests the possibility of a disulfide bond between the C-terminal resolving cysteine (CR) and the peroxidatic cysteine (CP), in the cryo-EM density for the filament. Map rendering is as for (B). See also Figure S2. Structure 2016 24, 1120-1129DOI: (10.1016/j.str.2016.04.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 5 A Postulated Model Depicting that Cellular Stress Induces Prxs to Function as Self-Assembling Chaperones Stacking interactions of Prx proteins can be facilitated by molecular crowding, chemical modifications of the active site (such as CPS mutations or hyperoxidation), or acidification. Prx rings can associate together to form HMW stacks as a means to prevent universal aggregation of protein under these unfavorable conditions. See also Figure S1 and Table S1. Structure 2016 24, 1120-1129DOI: (10.1016/j.str.2016.04.013) Copyright © 2016 Elsevier Ltd Terms and Conditions