Structure of the Absent in Melanoma 2 (AIM2) Pyrin Domain Provides Insights into the Mechanisms of AIM2 Autoinhibition and Inflammasome Assembly*

Background: AIM2 binds dsDNA and associates with ASC through their PYDs to form an inflammasome. Results: The AIM2 PYD structure illustrates distinct charge distribution and a unique hydrophobic patch. Conclusion: The AIM2 PYD may bind the ASC PYD and the AIM2 HIN domain through overlapping surface. Significance: These findings provide insights into the mechanisms of AIM2 autoinhibition and inflammasome assembly. Absent in melanoma 2 (AIM2) is a cytosolic double-stranded (dsDNA) sensor essential for innate immune responses against DNA viruses and bacteria such as Francisella and Listeria. Upon dsDNA engagement, the AIM2 amino-terminal pyrin domain (PYD) is responsible for downstream signaling to the adapter protein apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) through homotypic PYD-PYD interactions and the assembly of an inflammasome. Toward a better understanding of the AIM2 signaling mechanism, we determined the crystal structure of the human AIM2 PYD. The structure reveals a death domain fold with a short α3 helix that is buttressed by a highly conserved lysine residue at the α2 helix, which may stabilize the α3 helix for potential interaction with partner domains. The surface of the AIM2 PYD exhibits distinct charge distribution with highly acidic α1-α2 helices and highly basic α5-α6 helices. A prominent solvent-exposed hydrophobic patch formed by residues Phe-27 and Phe-28 at the α2 helix resembles a similar surface involved in the death effector domain homotypic interactions. Docking studies suggest that the AIM2 PYD may bind the AIM2 hematopoietic interferon-inducible nuclear (HIN) domain or ASC PYD using overlapping surface near the α2 helix. This may ensure that AIM2 interacts with the downstream adapter ASC only upon release of the autoinhibition by the dsDNA ligand. Our work thus unveils novel structural features of the AIM2 PYD and provides insights into the potential mechanisms of the PYD-HIN and PYD-PYD interactions important for AIM2 autoinhibition and inflammasome assembly.

[1]  M. Sung,et al.  Crystallographic characterization of mouse AIM2 HIN-200 domain bound to a 15 bp and an 18 bp double-stranded DNA. , 2012, Acta crystallographica. Section F, Structural biology and crystallization communications.

[2]  K. Diederichs,et al.  Structural and Functional Analysis of the NLRP4 Pyrin Domain , 2012, Biochemistry.

[3]  Eva Z. Curley,et al.  The mammalian PYHIN gene family: Phylogeny, evolution and expression , 2012, BMC Evolutionary Biology.

[4]  A. Bowie,et al.  Structures of the HIN domain:DNA complexes reveal ligand binding and activation mechanisms of the AIM2 inflammasome and IFI16 receptor. , 2012, Immunity.

[5]  F. Shao,et al.  Preventing bacterial DNA release and absent in melanoma 2 inflammasome activation by a Legionella effector functioning in membrane trafficking , 2012, Proceedings of the National Academy of Sciences.

[6]  Hong-Gee Kim,et al.  A comprehensive manually curated protein–protein interaction database for the Death Domain superfamily , 2011, Nucleic Acids Res..

[7]  R. Schwarzenbacher,et al.  The NLRP12 pyrin domain: structure, dynamics, and functional insights. , 2011, Journal of molecular biology.

[8]  S. Cusack,et al.  Structural Basis for the Activation of Innate Immune Pattern-Recognition Receptor RIG-I by Viral RNA , 2011, Cell.

[9]  K. Kersse,et al.  The death-fold superfamily of homotypic interaction motifs. , 2011, Trends in biochemical sciences.

[10]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[11]  H. H. Park,et al.  Crystal Structure of NALP3 Protein Pyrin Domain (PYD) and Its Implications in Inflammasome Assembly* , 2011, The Journal of Biological Chemistry.

[12]  V. Hornung,et al.  Cytosolic DNA Triggers Inflammasome Activation in Keratinocytes in Psoriatic Lesions , 2011, Science Translational Medicine.

[13]  Stephen R Comeau,et al.  Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19 , 2010, Proteins.

[14]  A. Bowie,et al.  IFI16 is an innate immune sensor for intracellular DNA , 2010, Nature Immunology.

[15]  David W. Ritchie,et al.  Ultra-fast FFT protein docking on graphics processors , 2010, Bioinform..

[16]  V. Hornung,et al.  Listeria monocytogenes is sensed by the NLRP3 and AIM2 inflammasome , 2010, European journal of immunology.

[17]  J. Sauer,et al.  Listeria monocytogenes triggers AIM2-mediated pyroptosis upon infrequent bacteriolysis in the macrophage cytosol. , 2010, Cell host & microbe.

[18]  Tal Pupko,et al.  ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids , 2010, Nucleic Acids Res..

[19]  Liisa Holm,et al.  Dali server: conservation mapping in 3D , 2010, Nucleic Acids Res..

[20]  Y. Lo,et al.  Helical assembly in the MyD88:IRAK4:IRAK2 complex in TLR/IL-1R signaling , 2010, Nature.

[21]  A. F. Moon,et al.  A synergistic approach to protein crystallization: Combination of a fixed‐arm carrier with surface entropy reduction , 2010, Protein science : a publication of the Protein Society.

[22]  Huilin Li,et al.  Crystal Structure of the Caenorhabditis elegans Apoptosome Reveals an Octameric Assembly of CED-4 , 2010, Cell.

[23]  E. Alnemri,et al.  The AIM2 inflammasome is critical for innate immunity against Francisella tularensis , 2010, Nature Immunology.

[24]  Vincent B. Chen,et al.  PHENIX: a comprehensive Python-based system for macromolecular structure solution , 2010, Acta crystallographica. Section D, Biological crystallography.

[25]  E. de Alba.  Structure and Interdomain Dynamics of Apoptosis-associated Speck-like Protein Containing a CARD (ASC)* , 2009, The Journal of Biological Chemistry.

[26]  G. Superti-Furga,et al.  An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome , 2009, Nature Immunology.

[27]  Jasmyn A. Dunn,et al.  HIN-200 Proteins Regulate Caspase Activation in Response to Foreign Cytoplasmic DNA , 2009, Science.

[28]  E. Alnemri,et al.  AIM2 activates the inflammasome and cell death in response to cytoplasmic DNA , 2009, Nature.

[29]  Daniel R. Caffrey,et al.  AIM2 recognizes cytosolic dsDNA and forms a caspase-1 activating inflammasome with ASC , 2009, Nature.

[30]  D. Armstrong,et al.  Structure of a signal transduction regulator, RACK1, from Arabidopsis thaliana , 2008, Protein science : a publication of the Protein Society.

[31]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[32]  R. Ghose,et al.  Structure and Dynamics of ASC2, a Pyrin Domain-only Protein That Regulates Inflammatory Signaling* , 2006, Journal of Biological Chemistry.

[33]  Liwei Wang,et al.  Crystal structure of MC159 reveals molecular mechanism of DISC assembly and FLIP inhibition. , 2006, Molecular cell.

[34]  R. Johnstone,et al.  The HIN-200 family: more than interferon-inducible genes? , 2005, Experimental cell research.

[35]  Yigong Shi,et al.  Structure of the apoptotic protease-activating factor 1 bound to ADP , 2005, Nature.

[36]  P. Emsley,et al.  Coot: model-building tools for molecular graphics. , 2004, Acta crystallographica. Section D, Biological crystallography.

[37]  Zukang Feng,et al.  Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. , 2004, Acta crystallographica. Section D, Biological crystallography.

[38]  I. Bataronov,et al.  Processing of X-Ray Diffraction Data in Structure Investigations of Amorphous Metal Oxides , 2004 .

[39]  P. Balaram.  Faculty Opinions recommendation of Design of a novel globular protein fold with atomic-level accuracy. , 2003 .

[40]  E. Dahl,et al.  The death-domain fold of the ASC PYRIN domain, presenting a basis for PYRIN/PYRIN recognition. , 2003, Journal of molecular biology.

[41]  G. Wider,et al.  NMR structure of the apoptosis- and inflammation-related NALP1 pyrin domain. , 2003, Structure.

[42]  Peter Briggs,et al.  A graphical user interface to the CCP4 program suite. , 2003, Acta crystallographica. Section D, Biological crystallography.

[43]  F. Martinon,et al.  The inflammasome: a molecular platform triggering activation of inflammatory caspases and processing of proIL-beta. , 2002, Molecular cell.

[44]  Xuejun Jiang,et al.  Three-dimensional structure of the apoptosome: implications for assembly, procaspase-9 binding, and activation. , 2002, Molecular cell.

[45]  V. Dixit,et al.  The PYRIN domain: A member of the death domain‐fold superfamily , 2001, Protein science : a publication of the Protein Society.

[46]  C. Weber,et al.  A docking model of key components of the DISC complex: death domain superfamily interactions redefined , 2001, FEBS letters.

[47]  F. Martinon,et al.  The pyrin domain: a possible member of the death domain-fold family implicated in apoptosis and inflammation , 2001, Current Biology.

[48]  J C Reed,et al.  PAAD - a new protein domain associated with apoptosis, cancer and autoimmune diseases. , 2001, Trends in biochemical sciences.

[49]  E. Dahl,et al.  The DAPIN family: a novel domain links apoptotic and interferon response proteins. , 2001, Trends in biochemical sciences.

[50]  J. Bertin,et al.  The PYRIN domain: a novel motif found in apoptosis and inflammation proteins , 2000, Cell Death and Differentiation.

[51]  S. Sprang,et al.  Three-Dimensional Structure of a Complex between the Death Domains of Pelle and Tube , 1999, Cell.

[52]  Emad S. Alnemri,et al.  Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1 , 1999, Nature.

[53]  Stephen W. Fesik,et al.  NMR structure and mutagenesis of the FADD (Mort1) death-effector domain , 1998, Nature.

[54]  B. Honig,et al.  Classical electrostatics in biology and chemistry. , 1995, Science.

[55]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[56]  K. Diederichs,et al.  Structural and Functional Analysis of the NLRP 4 Pyrin Domain , 2012 .

[57]  Bernhard Rupp,et al.  Correspondence e-mail: , 2000 .

[58]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[59]  Hao Wu,et al.  Serveur Académique Lausannois SERVAL serval.unil.ch , 2022 .

[60]  G. Taylor,et al.  Bmc Structural Biology Crystal Structure of Human Ips-1/mavs/visa/cardif Caspase Activation Recruitment Domain , 2022 .