Volume 17, Issue 2, Pages 172-182 (February 2009) Wheel of Life, Wheel of Death: A Mechanistic Insight into Signaling by STAND Proteins  Olivier Danot, Emélie Marquenet, Dominique Vidal-Ingigliardi, Evelyne Richet  Structure  Volume 17, Issue 2, Pages 172-182 (February 2009) DOI: 10.1016/j.str.2009.01.001 Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 1 Domain Architecture of STAND Proteins (A) Overall primary structure of STAND proteins. The different possible domain architectures are shown. (B) The five STAND clades: representative members. Color coding is the same as in (A), except that the effector domains corresponding to protein recruitment domains, DNA- or RNA-binding domains, and enzymatic domains are represented in dark green, light green, and yellow, respectively. Gray boxes represent domains with unknown functions. Note that the WHD of the MNS clade members is not recognizable by sequence analysis (Leipe et al., 2004), but that the three-dimensional structures of SSO1545 and PAB2304 clearly attest to its existence. BTAD, bacterial transcription activation domain; CARD, caspase recruitment domain; CC, coiled-coil; HisK, histidine kinase; CYA, adenylate cyclase; PYD, pyrin domain; S/T K, serine/threonine kinase; TIR, Toll/interleukin-1 receptor; Rec, response regulator receiver; SUPR, superhelical repeats, a class of TPR-like repeats that characterize the MalT clade (Steegborn et al., 2001). (C) Topology of the NOD module with conserved features. ISM, initiator-specific motif, a motif specific for the STAND class and the AAA+ initiator clade, which comprises the Orc1/Cdc6 subclade; A, Walker A box; B, Walker B box; S-I, sensor I; R-F, arginine finger; H, WHD conserved histidine. Structure 2009 17, 172-182DOI: (10.1016/j.str.2009.01.001) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 2 The STAND Closed Conformation Ribbon representation of the structure of the ADP-bound APAF1 NOD module in crystals of ADP-bound ΔWD40 APAF1 (Riedl et al., 2005). Two hydrogen and ionic bonds stabilizing the structure are indicated (H438 to β-phosphate of ADP, D439 to sensor I [R265], respectively). Color coding is that of Figure 1A: NBD, blue; HD1, cyan; WHD, magenta. Structure 2009 17, 172-182DOI: (10.1016/j.str.2009.01.001) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 3 Comparison of the APAF1, CED4, and SSO1545 NOD Structures (A) Cartoon representation of the structures of the nucleotide-bound NOD modules of APAF1 (PDB ID code 1Z6T), CED4 (PDB ID code 2A5Y), and SSO1545 (PDB ID code 2FNA) in the same orientation, with the AAA+ multimerization interface facing the reader. The arrow represents the viewing axis of Figure 2. The PAB2304 structure (PDB ID code 2QEN), which is very similar to that of SSO1545 (root-mean-square deviation 2.1 Å over 90% of the structure), is not shown. Color coding is as in Figure 2. (B) Close-up of the last helix of HD1 (H8) and the first helix of the WHD (H9) in the three structures. (C) Surface representation of the three structures in the same orientation as in (A). The nucleotides are shown as sticks and spheres. Structure 2009 17, 172-182DOI: (10.1016/j.str.2009.01.001) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 4 Superposition of the SSO1545 and A. pernix Orc2 Structures Structures are aligned along their P loop regions (amino acids 148–159 of PDB ID code 2FNA chain A [SSO1545] and 50–55 and 59–71 of PDB ID code 1W5S chain B [Orc2]). The SSO1545 structure is viewed from the back of Figure 3A. Color coding: SSO1545 as in Figure 2, with ADP colored in blue; Orc2: NBD, green; HD1, light green; WHD, red; ADP, green. Structure 2009 17, 172-182DOI: (10.1016/j.str.2009.01.001) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 5 Active Forms of STAND Proteins (A) Three-dimensional reconstruction of the human apoptosome from electron cryomicroscopy images, reproduced from Yu et al. (2005). (B) Two-dimensional average structure of MalT oligomers derived from electron cryomicroscopy images (Larquet et al., 2004). (C) Surface model of a virtual SSO1545 multimer obtained by repeating the dimer interface present in the ADP-bound SSO1545 crystal. Structure 2009 17, 172-182DOI: (10.1016/j.str.2009.01.001) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 6 The STAND Binary Switch The color code is the same as in Figure 1A. For the sake of clarity, the effector domain is not shown. If the apo form of the sensor domain stabilizes the resting form through an interaction with the NOD module and/or an N-terminal effector domain, removal of this inhibiting effect and inducer binding are predicted to be coupled with the isomerization reaction. If the apo form of the sensor domain prevents nucleotide exchange by inhibiting protein oligomerization, removal of the inhibiting effect and inducer binding would be independent of the isomerization step. The nucleotide-free form should be a transient species; the on rates of ADP and ATP binding are indeed expected to be high, given the nucleotide concentrations prevailing in vivo and the seemingly high affinities of STAND proteins for nucleotides (Nageswara Rao et al., 2007; Richet and Raibaud, 1989; Tameling et al., 2006). Depending on the proteins, the multimeric assemblies correspond to either closed multimers (APAF1) or open homopolymers (MalT, and probably SSO1545). Once ATP is hydrolyzed, the ADP-bound protomer would dissociate because of a low propensity to multimerize (Schreiber and Richet, 1999). Structure 2009 17, 172-182DOI: (10.1016/j.str.2009.01.001) Copyright © 2009 Elsevier Ltd Terms and Conditions