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Crystal Structure of Caspase Recruiting Domain (CARD) of Apoptosis Repressor with CARD (ARC) and Its Implication in Inhibition of Apoptosis

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Crystal Structure of Caspase Recruiting Domain (CARD) of Apoptosis Repressor with CARD (ARC) and Its Implication in Inhibition of Apoptosis OPEN Crystal structure of caspase recruiting SUBJECT AREAS: domain (CARD) of apoptosis repressor NANOCRYSTALLOGRAPHY STRUCTURAL BIOLOGY with CARD (ARC) and its implication in inhibition of apoptosis Received 17 November 2014 Tae-ho Jang1*, Seong Hyun Kim1*, Jae-Hee Jeong2*, Sunghwan Kim3 , Yeon-Gil Kim2{ & Hyun Ho Park1{ Accepted 23 March 2015 1Department of Biochemistry, Yeungnam University, Gyeongsan, 712-749, South Korea, 2Pohang Accelerator Laboratory, Pohang 3 Published University of Science and Technology, Pohang, 790-784, South Korea, New Drug Development Center, Daegu-Gyungpook 3 June 2015 Medical Innovation Foundation, Daegu, 701-310, South Korea. Apoptosis repressor with caspase recruiting domain (ARC) is a multifunctional inhibitor of apoptosis that is Correspondence and unusually over-expressed or activated in various cancers and in the state of the pulmonary hypertension. requests for materials Therefore, ARC might be an optimal target for therapeutic intervention. Human ARC is composed of two distinct domains, N-terminal caspase recruiting domain (CARD) and C-terminal P/E (proline and glutamic should be addressed to acid) rich domain. ARC inhibits the extrinsic apoptosis pathway by interfering with DISC formation. ARC H.H.P. (hyunho@ynu. CARD directly interacts with the death domains (DDs) of Fas and FADD, as well as with the death effector ac.kr) or Y.G.K. domains (DEDs) of procaspase-8. Here, we report the first crystal structure of the CARD domain of ARC at (ygkim76@postech. a resolution of 2.4 A˚ . Our structure was a dimer with novel homo-dimerization interfaces that might be ac.kr) critical to its inhibitory function. Interestingly, ARC did not exhibit a typical death domain fold. The sixth helix (H6), which was detected at the typical death domain fold, was not detected in the structure of ARC, * These authors indicating that H6 may be dispensable for the function of the death domain superfamily. contributed equally to this work. ell death and proliferation must be balanced for multi-cellular organisms during developmental stages, as {These authors jointly well as for homeostasis, and cells that present a threat to the integrity of an organism have to be removed. Apoptosis is a well-known mechanism for elimination of cells that maintains tissue homeostasis and supervised this work. C 1,2 protects organisms from accumulation of dangerous cells . Failure to control apoptosis leads to serious diseases, including various cancers3,4. The hallmarks of apoptotic cells are cell shrinkage, cytoplasmic and nuclear con- densation, chromatin condensation, and ordered DNA fragmentation5,6. An intrinsic (mitochondrial) and an extrinsic (cytoplasmic) pathway lead to apoptosis7,8. The extrinsic pathway is triggered through death receptors, which are members of the tumor necrosis factor (TNF) receptor superfamily, whereas the intrinsic pathway leads to the release of cytochrome-c from the mitochondria, thereby activating the death signal8. Both extrinsic and intrinsic pathways ultimately converge, leading to activation of a cascade of cysteine proteases known as caspases, which are a family of cysteine proteases that cleave specifically after aspartic acid residues9,10. Caspases are divided into two classes based on their roles in apoptosis, initiator caspases such as caspase-2, -8, -9, and -10, and effector caspases such as caspases-3 and -7. Initiator caspases are auto-processed upon induction of dimerization by recruitment to oligomeric signaling complexes11. Well-known oligomeric signaling complexes for the activation of initiator caspases include the death-inducing signaling complex (DISC) for caspase-8 activation12, the apopto- some for caspase-9 activation13, and the PIDDosome for caspase-2 activation14,15. Effector caspases are activated upon cleavage by activated initiator caspases10,16. BCL-2 family proteins such as BAX, BAK, BCL-2, BCL-XL, BCL-w, and BCL-B are required for regulation of the intrinsic cell death pathway17. These proteins can trigger both pro-apoptotic (BAX, BAK, BAD and PUMA) and anti-apoptotic (BCL-2, BCL-XL, BCL-w, and BCL-B) pathways. Members of the pro-apoptotic family, BAX and BAK, form pores on the mitochondrial membrane through which apoptotic signals such as cytochrome-c and Smac are released into the cytosol, where they help to activate effector caspases for execution of apoptosis18. Apoptosis repressor with caspase recruiting domain (ARC) is a multifunctional modulator of apoptosis. ARC is predominantly expressed in post-mitotic cells such as cardiomyocytes, neurons, and muscle cells, and unusu- ally over-expressed in various cancers19,20. Involvement of ARC in cancer development is not surprising because SCIENTIFIC REPORTS | 5 : 9847 | DOI: 10.1038/srep09847 1 www.nature.com/scientificreports over-activated anti-apoptotic proteins can render cells insensitive to pathways by sequestering Ca21 in cytosol32. A significant amount of apoptotic signals. Over-activation of ARC has also been detected in Ca21 can bind to the P/E domain of ARC, and Ca21 depletion by ARC pulmonary hypertension21. Additionally, it has been reported that can block the apoptosis process32. Interestingly, it has been reported hypo-activation of ARC causes fulminant liver failure, which is res- that ARC forms a homo-dimer via the CARD domain and that dimer- cued by treatment with ARC protein22. ARC has also recently been ization abolishes the inhibitory activity of ARC.29 reported to be involved in TNFa-induced necroptosis23. Taken To better understand the CARD domain-mediated inhibition together, the results of these previous studies suggest that ARC is mechanism of ARC during apoptosis signaling, we report the first critical to apoptosis and necroptosis, linked to many human diseases, crystal structure of the CARD domain of ARC containing amino and might be a good target for therapeutic intervention. acids 1–95 at a resolution of 2.4 A˚ . Our structure was a dimer and Human ARC contains 208 amino acids and is composed of two revealed novel homo-dimerization interfaces, which might be critical distinct domains, N-terminal caspase recruiting domain (CARD) for the inhibitory function. In addition, the high resolution structure domain and C-terminal P/E (proline and glutamic acid) rich domain revealed similarities and differences with those of other CARD (Fig. 1A). The CARD domain is a protein interaction module belong- domains that may be functionally relevant. Interestingly, ARC did ing to the death domain superfamily that includes the death domain not exhibit a typical death domain fold (the six helix bundle fold; H1– (DD), death effector domain (DED), and pyrin domain (PYD)24-27. H6), and instead contained a five-helix bundle fold. H6 was not ARC exerts its function through multiple protein-protein interactions detected in the structure of ARC, indicating that it is dispensable with apoptosis signaling molecules on both intrinsic and extrinsic for the function of the death domain superfamily. pathways28,29. ARC is a unique apoptosis inhibitor in that it can ant- agonize both the intrinsic and extrinsic pathways. ARC inhibits the Results and Discussion extrinsic pathway by interfering with DISC formation. ARC CARD Crystal structure of ARC CARD. ARC inhibits both the intrinsic and interacts directly with the death domains (DD) of Fas and FADD, as extrinsic apoptosis pathways via interaction with various apoptosis well as with the death effector domains (DEDs) of procaspase-829.Two related proteins, including Fas, FADD, and caspase-8 (Fig. 1A). The different mechanisms for inhibition of the intrinsic pathway by ARC ARC CARD domain is known to interfere with DISC formation have been reported, functional inhibition of pro-apoptotic BAD, through direct interaction with Fas DD, FADD DD, and caspase-8 PUMA, and BAX through direct interaction between the ARC DEDs (Fig. 1A)29. CARD and the C-terminus of BAX and the BH3 motif of BAD and The 2.4 A˚ crystal structure of the CARD domain of ARC (ARC PUMA,30 and functional inhibition of p53 via direct interaction CARD) was solved using a single-wavelength anomalous diffraction 31 between the ARC P/E domain and oligomerization domain of p53 . (SAD) method and refined to an Rwork of 17.0% and an Rfree of 20.0%. ARC also mediates crosstalk between intrinsic and extrinsic apoptosis The high resolution structure of ARC CARD showed that it comprises Figure 1 | Crystal structure of ARC CARD. A. Domain organization and known binding proteins. CARD: caspase recruiting domain. P/E: proline and glutamine rich domain. DD: death domain, DED: death effector domain. B. Ribbon diagram of ARC CARD. The chain from the N- to C-termini is coloured from blue to red. Helices are labelled. The missing H6 at the c-terminus is shown as a red dashed line. C. Two ARC CARD molecules in the asymmetric unit. Chain A and Chain B are shown separately. D. Structure-based sequence alignment of ARC CARD with other CARD domains. Secondary structures (helices H1 to H5) are shown above the sequences. Residues at the hydrophobic core of ARC CARD are blue. Critical residues for the interaction with homo- or hetero- CARD molecules are red. Putative H6 is indicated by a pink box. E. Conserved central hydrophobic core. Hydrophobic residues essential to the formation of this core that stabilize H1 to H6 are shown as blue sticks and labelled. SCIENTIFIC REPORTS | 5 : 9847 | DOI: 10.1038/srep09847 2 www.nature.com/scientificreports five helices, H1 to H5, which is not the typical fold of the DD super- family (Fig. 1B). Interestingly, the sixth helix (H6) was not detected at Table 1 | Data collection and refinement statistics the typical location, indicating that H6 might be flexible in the CARD Data set Wild type domain of ARC or adopt a loop structure instead. There were two X-ray source 5C (SBII) at PAL monomers in the asymmetric unit, chain A and chain B (Fig. 1C). The Space group P65 model of chain A was built from residue 5 to residue 87 and residue 91 Wavelength (A˚ ) 0.97760 to residue 93, while that of chain B was built from residue 5 to residue Resolution (A˚ ) 50.0–2.40 (2.45–2.40) 84.
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