Three-Dimensional Structure of Human NLRP10/PYNOD Pyrin Domain Reveals a Homotypic Interaction Site Distinct from Its Mouse Homologue

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Su, Ming Yuan ^a,b   Kuo, Chiao I ^a   Chang, Chi Fon ^c   Chang, Chung I ^a,b  

^a INSTITUTE OF BIOLOGICAL CHEMISTRY   (Taiwan)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^c GENOMICS RESEARCH CENTER   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

PATTERN RECOGNITION RECEPTOR; PROTEIN NLRP10; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CELL AGGREGATION; CONFORMATIONAL TRANSITION; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NONHUMAN; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; ANIMALS; CARRIER PROTEINS; CYTOSKELETAL PROTEINS; ESCHERICHIA COLI; GUANOSINE TRIPHOSPHATE; HUMANS; HYDROLYSIS; MICE; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY;

EID: 84879816463     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067843     Document Type: Article

References (34)

1. Franchi L, Eigenbrod T, Munoz-Planillo R, Nunez G, (2009) The inflammasome: a caspase-1-activation platform that regulates immune responses and disease pathogenesis. Nat Immunol 10: 241-247.
2. Chang CI, Deisenhofer J, (2007) The peptidoglycan recognition proteins LCa and LCx. Cellular and molecular life sciences: CMLS 64: 1395-1402.
3. Medzhitov R, (2001) Toll-like receptors and innate immunity. Nat Rev Immunol 1: 135-145.
4. Kersse K, Bertrand MJ, Lamkanfi M, Vandenabeele P, (2011) NOD-like receptors and the innate immune system: coping with danger, damage and death. Cytokine Growth Factor Rev 22: 257-276.
5. Ting JP, Lovering RC, Alnemri ES, Bertin J, Boss JM, et al. (2008) The NLR gene family: a standard nomenclature. Immunity 28: 285-287.
6. Shaw MH, Reimer T, Kim YG, Nunez G, (2008) NOD-like receptors (NLRs): bona fide intracellular microbial sensors. Current opinion in immunology 20: 377-382.
7. Eibl C, Grigoriu S, Hessenberger M, Wenger J, Puehringer S, et al. (2012) Structural and functional analysis of the NLRP4 pyrin domain. Biochemistry 51: 7330-7341.
8. Pinheiro AS, Eibl C, Ekman-Vural Z, Schwarzenbacher R, Peti W, (2011) The NLRP12 pyrin domain: structure, dynamics, and functional insights. Journal of molecular biology 413: 790-803.
9. Bae JY, Park HH, (2011) Crystal structure of NALP3 protein pyrin domain (PYD) and its implications in inflammasome assembly. The Journal of biological chemistry 286: 39528-39536.
10. Pinheiro AS, Proell M, Eibl C, Page R, Schwarzenbacher R, et al. (2010) Three-dimensional structure of the NLRP7 pyrin domain: insight into pyrin-pyrin-mediated effector domain signaling in innate immunity. The Journal of biological chemistry 285: 27402-27410.
11. Natarajan A, Ghose R, Hill JM, (2006) Structure and dynamics of ASC2, a pyrin domain-only protein that regulates inflammatory signaling. The Journal of biological chemistry 281: 31863-31875.
12. Liepinsh E, Barbals R, Dahl E, Sharipo A, Staub E, et al. (2003) The death-domain fold of the ASC PYRIN domain, presenting a basis for PYRIN/PYRIN recognition. Journal of molecular biology 332: 1155-1163.
13. Hiller S, Kohl A, Fiorito F, Herrmann T, Wider G, et al. (2003) NMR structure of the apoptosis- and inflammation-related NALP1 pyrin domain. Structure 11: 1199-1205.
14. Imamura R, Wang Y, Kinoshita T, Suzuki M, Noda T, et al. (2010) Anti-inflammatory activity of PYNOD and its mechanism in humans and mice. Journal of immunology 184: 5874-5884.
15. Wang Y, Hasegawa M, Imamura R, Kinoshita T, Kondo C, et al. (2004) PYNOD, a novel Apaf-1/CED4-like protein is an inhibitor of ASC and caspase-1. International immunology 16: 777-786.
16. Eisenbarth SC, Williams A, Colegio OR, Meng H, Strowig T, et al. (2012) NLRP10 is a NOD-like receptor essential to initiate adaptive immunity by dendritic cells. Nature 484: 510-513.
17. Su MY, Chang CI, Chang CF (2012) (1)H, (13)C and (15)N resonance assignments of the pyrin domain from human PYNOD. Biomolecular NMR assignments.
18. Cogan EB, Birrell GB, Griffith OH, (1999) A robotics-based automated assay for inorganic and organic phosphates. Analytical biochemistry 271: 29-35.
19. Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, et al. (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. Journal of biomolecular NMR 12: 1-23.
20. Florence Cordier AJD, Stephan Grzesiek, (1999) A doublet-separated sensitivity-enhanced HSQC for the determination of scalar and dipolar one-bond J-couplings. Journal of Biomolecular NMR 13: 175-180.
21. Güntert P (2004) Automated NMR Structure Calculation With CYANA. In: Downing AK, editor. Protein NMR Techniques: Humana Press. 353-378.
22. Herrmann T, Güntert P, Wüthrich K, (2002) Protein NMR Structure Determination with Automated NOE Assignment Using the New Software CANDID and the Torsion Angle Dynamics Algorithm DYANA. Journal of Molecular Biology 319: 209-227.
23. Gabriel Cornilescu FD, Ad Bax, (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. Journal of Biomolecular NMR 13: 289-302.
24. Kozakov D, Hall DR, Beglov D, Brenke R, Comeau SR, et al. (2010) Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19. Proteins 78: 3124-3130.
25. Arnold K, Bordoli L, Kopp J, Schwede T, (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22: 195-201.
26. Laskowski RARJ, MacArthur MW, Kaptein R, Thornton JM, (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8: 477-486.
27. de Alba E, (2009) Structure and interdomain dynamics of apoptosis-associated speck-like protein containing a CARD (ASC). The Journal of biological chemistry 284: 32932-32941.
28. Holm L, Rosenstrom P, (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38: W545-549.
29. Saito K, Koshiba S, Inoue M, Kigawa T, Yokoyama S Solution structure of the Pyrin/PAAD-DAPIN domain in mouse NALP10 (NACHT, leucine rich repeat and PYD containing 10). Unpublished PDB entry.
30. Vajjhala PR, Mirams RE, Hill JM, (2012) Multiple binding sites on the pyrin domain of ASC protein allow self-association and interaction with NLRP3 protein. The Journal of biological chemistry 287: 41732-41743.
31. Srimathi T, Robbins SL, Dubas RL, Chang H, Cheng H, et al. (2008) Mapping of POP1-binding site on pyrin domain of ASC. The Journal of biological chemistry 283: 15390-15398.
32. Chang CI, Ihara K, Chelliah Y, Mengin-Lecreulx D, Wakatsuki S, et al. (2005) Structure of the ectodomain of Drosophila peptidoglycan-recognition protein LCa suggests a molecular mechanism for pattern recognition. Proc Natl Acad Sci U S A 102: 10279-10284.
33. Chang CI, Chelliah Y, Borek D, Mengin-Lecreulx D, Deisenhofer J, (2006) Structure of tracheal cytotoxin in complex with a heterodimeric pattern-recognition receptor. Science 311: 1761-1764.
34. Kersse K, Verspurten J, Vanden Berghe T, Vandenabeele P, (2011) The death-fold superfamily of homotypic interaction motifs. Trends Biochem Sci 36: 541-552.