A molecular model of the full-length human NOD-like receptor family CARD domain containing 5 (NLRC5) protein

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Mótyán, János A ^a   Bagossi, Péter ^a   Benko, Szilvia ^a   Tozsér, József ^a  

^a UNIVERSITY OF DEBRECEN   (Hungary)

Author keywords

LRR protein; Molecular modeling; NLRC5; NOD like receptor

Indexed keywords

CONSENSUS PATTERNS; LEUCINE-RICH REPEATS; LRR PROTEINS; MOLECULAR PATTERNS; NLRC5; NOD-LIKE RECEPTORS; PATTERN RECOGNITION RECEPTORS; TEMPLATE STRUCTURES;

AMINO ACIDS; MOLECULAR MODELING; PATTERN RECOGNITION;

PROTEINS;

VERTEBRATA;

NLRC5 PROTEIN, HUMAN; SIGNAL PEPTIDE;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HUMAN; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; ANIMALS; HUMANS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

EID: 84883870339     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-275     Document Type: Article

References (33)

1. Lee MS, Kim YJ. Pattern-recognition receptor signaling initiated from extracellular, membrane, and cytoplasmic space. Mol Cells 2007, 23:1-10.
2. Ting JP, Davis BK. Caterpiller: a novel gene family important in immunity, cell death, and diseases. Annu Rev Immunol 2005, 23:387-414. 10.1146/annurev.immunol.23.021704.115616, 15771576.
3. Kanneganti TD, Lamkanfi M, Núñez G. Intracellular NOD-like receptors in host defense and disease. Immunity 2007, 27:549-559. 10.1016/j.immuni.2007.10.002, 17967410.
4. Proell M, Riedl SJ, Fritz JH, Rojas AM, Schwarzenbacher R. The Nod-like receptor (NLR) family: a tale of similarities and differences. Plos One 2008, 3:e2119. 10.1371/journal.pone.0002119, 2323615, 18446235.
5. Meissner TB, Li A, Liu YJ, Gagnon E, Kobayashi KS. The nucleotide-binding domain of NLRC5 is critical for nuclear import and transactivation activity. Biochem Biophys Res Commun 2012, 418:786-791. 10.1016/j.bbrc.2012.01.104, 3289513, 22310711.
6. Benko{double acute} S, Magalhaes JG, Philpott DJ, Girardin SE. NLRC5 limits the activation of inflammatory pathways. J Immunol 2010, 185:1681-1691. 10.4049/jimmunol.0903900, 20610642.
7. Wilmanski JM, Petnicki-Ocwieja T, Kobayashi KS. NLR proteins: integral members of innate immunity and mediators of inflammatory diseases. J Leukoc Biol 2008, 83:13-30. 3256237, 17875812.
8. Istomin AY, Godzik A. Understanding diversity of human innate immunity receptors: analysis of surface features of leucine-rich repeat domains in NLRs and TLRs. BMC Immunol 2009, 10:48. 10.1186/1471-2172-10-48, 2747839, 19728889.
9. Kobe B, Kajava AV. The leucine-rich repeat as a protein recognition motif. Curr Opin Struct Biol 2001, 11:725-732. 10.1016/S0959-440X(01)00266-4, 11751054.
10. Bella J, Hindle KL, McEwan PA, Lovell SC. The leucine-rich repeat structure. Cell Mol Life Sci 2008, 65:2307-2333. 10.1007/s00018-008-8019-0, 18408889.
11. Kobe B, Deisenhofer J. Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A. J Mol Biol 1996, 264:1028-1043. 10.1006/jmbi.1996.0694, 9000628.
12. Neerincx A, Lautz K, Menning M, Kremmer E, Zigrino P, Hösel M, Büning H, Schwarzenbacher R, Kufer TA. A role for the human nucleotide-binding domain, leucine-rich repeat-containing family member NLRC5 in antiviral responses. J Biol Chem 2010, 285:26223-26232. 10.1074/jbc.M110.109736, 2924034, 20538593.
13. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
14. The UniProt Consortium Reorganizing the protein space at the universal protein resource (UniProt). Nucleic Acids Res 2012, 40:D71-D75. 3245120, 22102590, The UniProt Consortium.
15. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. ClustalW and ClustalX version 2. Bioinformatics 2007, 23:2947-2948. 10.1093/bioinformatics/btm404, 17846036.
16. Wei T, Gong J, Jamitzky F, Heckl WM, Stark RW, Rössle SC. LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs). BMC Struct Biol 2008, 8:47. 10.1186/1472-6807-8-47, 2645405, 18986514.
17. Offord V, Werling D. LRRfinder2.0: a webserver for the prediction of leucine-rich repeats. Innate Immun 19:398-402.
18. Helft L, Reddy V, Chen X, Koller T, Federici L, Fernández-Recio J, Gupta R, Bent A. LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains. PLoS One 2011, 6:e21614. 10.1371/journal.pone.0021614, 3138743, 21789174.
19. Rost B, Yachdav G, Liu J. The PredictProtein server. Nucleic Acids Res 2004, 32(Web Server issue):W321-W326. 441515, 15215403.
20. Šali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993, 234:779-815. 10.1006/jmbi.1993.1626, 8254673.
21. Porollo A, Meller J. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D. BMC Bioinformatics 2007, 8:316. 10.1186/1471-2105-8-316, 1978507, 17727718.
22. Kuenzel S, Till A, Winkler M, Häsler R, Lipinski S, Jung S, Grötzinger J, Fickenscher H, Schreiber S, Rosenstiel P. The nucleotide-binding oligomerization domain-like receptor NLRC5 is involved in IFN-dependent antiviral immune responses. J Immunol 2010, 184:1990-2000. 10.4049/jimmunol.0900557, 20061403.
23. Kajava AV. Structural diversity of leucine-rich repeat proteins. J Mol Biol 1998, 277:519-527. 10.1006/jmbi.1998.1643, 9533877.
24. Lamkanfi M, Kanneganti TD. Regulation of immune pathways by the NOD-like receptor NLRC5. Immunobiology 2012, 217:13-16. 10.1016/j.imbio.2011.08.011, 3225722, 22024701.
25. Dosztányi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 2005, 21:3433-3434. 10.1093/bioinformatics/bti541, 15955779.
26. Dosztányi Z, Mészáros B, Simon I. ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics 2009, 25:2745-2746. 10.1093/bioinformatics/btp518, 2759549, 19717576.
27. Stumpp MT, Forrer P, Binz HK, Plückthun A. Designing repeat proteins: modular leucine-rich repeat protein libraries based on the mammalian ribonuclease inhibitor family. J Mol Biol 2003, 332:471-487. 10.1016/S0022-2836(03)00897-0, 12948496.
28. Matsushima N, Tanaka T, Enkhbayar P, Mikami T, Taga M, Yamada K, Kuroki Y. Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors. BMC Genomics 2007, 8:124. 10.1186/1471-2164-8-124, 1899181, 17517123.
29. Johnson RJ, McCoy JG, Bingman CA, Phillips GN, Raines RT. Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein. J Mol Biol 2007, 368:434-449. 10.1016/j.jmb.2007.02.005, 1993901, 17350650.
30. Riedl SJ, Li W, Chao Y, Schwarzenbacher R, Shi Y. Structure of the apoptotic protease-activating factor 1 bound to ADP. Nature 2005, 434:926-933. 10.1038/nature03465, 15829969.
31. Yuan S, Yu X, Topf M, Ludtke SJ, Wang X, Akey CW. Structure of an apoptosome-procaspase-9 CARD complex. Structure 2010, 18:571-583. 10.1016/j.str.2010.04.001, 2874686, 20462491.
32. Martinon F, Tschopp J. NLRs join TLRs as innate sensors of pathogens. Trends Immunol 2005, 26:447-454. 10.1016/j.it.2005.06.004, 15967716.
33. Cui J, Zhu L, Xia X, Wang HY, Legras X, Hong J, Ji J, Shen P, Zheng S, Chen ZJ, Wang RF. NLRC5 negatively regulates the NF-kappaB and type I interferon signaling pathways. Cell 2010, 141:483-496. 10.1016/j.cell.2010.03.040, 3150216, 20434986.