Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2

FEBS Letters

Volumn 554, Issue 3, 2003, Pages 520-528

  Albrecht, Mario ^a   Domingues, Francisco S ^a   Schreiber, Stefan ^b   Lengauer, Thomas ^a  

^a MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^b UNIVERSITY OF KIEL   (Germany)

Author keywords

Inflammation; Leucine rich repeat; NACHT domain; PYD CARD containing protein; Structural modeling

Indexed keywords

GENE PRODUCT; NUCLEOTIDE BINDING OLIGOMERIZATION DOMAIN PROTEIN 2; PYRIN CONTAINING APOPTOTIC PROTEASE ACTIVATING FACTOR 1 LIKE PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; GENETIC VARIABILITY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

EID: 0242626505     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0014-5793(03)01222-5     Document Type: Article

References (123)

1. Inohara N., Núñez G. Oncogene. 20:2001;6473-6481.
2. Girardin S.E., Sansonetti P.J., Philpott D.J. Trends Microbiol. 10:2002;193-199.
3. Gumucio D.L., Diaz A., Schaner P., Richards N., Babcock C., Schaller M., Cesena T. Clin. Exp. Rheumatol. 20:2002;S45-53.
4. Harton J.A., Linhoff M.W., Zhang J., Ting J.P. J. Immunol. 169:2002;4088-4093.
5. Inohara N., Ogura Y., Núñez G. Curr. Opin. Microbiol. 5:2002;76-80.
6. McDermott M.F. Trends Mol. Med. 8:2002;550-554.
7. Chamaillard M., Girardin S.E., Viala J., Philpott D.J. Cell Microbiol. 5:2003;581-592.
8. Hull K.M., Shoham N., Chae J.J., Aksentijevich I., Kastner D.L. Curr. Opin. Rheumatol. 15:2003;61-69.
9. Inohara N., Núñez G. Nat. Rev. Immunol. 3:2003;371-382.
10. Reed J.C., et al. Genome Res. 13:2003;1376-1388.
11. Tschopp J., Martinon F., Burns K. Nat. Rev. Mol. Cell Biol. 4:2003;95-104.
12. Doctor K.S., Reed J.C., Godzik A., Bourne P.E. Cell Death Differ. 10:2003;621-633.
13. Sarrauste de Menthière C., Tèrriere S., Pugnère D., Ruiz M., Demaille J., Touitou I. Nucleic Acids Res. 31:2003;282-285.
14. Hoffman H.M., Mueller J.L., Broide D.H., Wanderer A.A., Kolodner R.D. Nat. Genet. 29:2001;301-305.
15. Aganna E., et al. Arthritis Rheum. 46:2002;2445-2452.
16. Aksentijevich I., et al. Arthritis Rheum. 46:2002;3340-3348.
17. Dodé C., et al. Am. J. Hum. Genet. 70:2002;1498-1506.
18. Feldmann J., Prieur A.M., Quartier P., Berquin P., Certain S., Cortis E., Teillac-Hamel D., Fischer A., de Saint Basile G. Am. J. Hum. Genet. 71:2002;198-203.
19. Hoffman H.M., Gregory S.G., Mueller J.L., Tresierras M., Broide D.H., Wanderer A.A., Kolodner R.D. Hum. Genet. 112:2003;209-216.
20. Rösen-Wolff A., Quietzsch J., Schröder H., Lehmann R., Gahr M., Roesler J. Eur. J. Haematol. 71:2003;214-219.
21. Miceli-Richard C., Lesage S., Rybojad M., Prieur A.M., Manouvrier-Hanu S., Häfner R., Chamaillard M., Zouali H., Thomas G., Hugot J.P. Nat. Genet. 29:2001;19-20.
22. Wang X., Kuivaniemi H., Bonavita G., Mutkus L., Mau U., Blau E., Inohara N., Núñez G., Tromp G., Williams C.J. Arthritis Rheum. 46:2002;3041-3045.
23. Hampe J., et al. Lancet. 357:2001;1925-1928.
24. Hugot J.P., et al. Nature. 411:2001;599-603.
25. Ogura Y., et al. Nature. 411:2001;603-606.
26. Lesage S., et al. Am. J. Hum. Genet. 70:2002;845-857.
27. Bouma G., Strober W. Nat. Rev. Immunol. 3:2003;521-533.
28. Schölmerich J. Eur. J. Gastroenterol. Hepatol. 15:2003;585-586.
29. Adams J.M., Cory S. Curr. Opin. Cell Biol. 14:2002;715-720.
30. van der Biezen E.A., Jones J.D. Curr. Biol. 8:1998;R226-227.
31. Aravind L., Dixit V.M., Koonin E.V. Trends Biochem. Sci. 24:1999;47-53.
32. Koonin E.V., Aravind L. Trends Biochem. Sci. 25:2000;223-224.
33. Albrecht M., Domingues F.S., Schreiber S., Lengauer T. FEBS Lett. 538:2003;173-177.
34. The international FMF consortium (1997) Cell 90, 797-807.
35. Centola M., Aksentijevich I., Kastner D.L. Hum. Mol. Genet. 7:1998;1581-1588.
36. Bertin J., DiStefano P.S. Cell Death Differ. 7:2000;1273-1274.
37. Fairbrother W.J., Gordon N.C., Humke E.W., O'Rourke K.M., Starovasnik M.A., Yin J.P., Dixit V.M. Protein Sci. 10:2001;1911-1918.
38. Martinon F., Hofmann K., Tschopp J. Curr. Biol. 11:2001;R118-120.
39. Pawlowski K., Pio F., Chu Z., Reed J.C., Godzik A. Trends Biochem. Sci. 26:2001;85-87.
40. Staub E., Dahl E., Rosenthal A. Trends Biochem. Sci. 26:2001;83-85.
41. Hofmann K., Bucher P., Tschopp J. Trends Biochem. Sci. 22:1997;155-156.
42. Weber C.H., Vincenz C. Trends Biochem. Sci. 26:2001;475-481.
43. Liepinsh E., Barbals R., Dahl E., Sharipo A., Staub E., Otting G. J. Mol. Biol. 332:2003;1155-1163.
44. Manji G.A., et al. J. Biol. Chem. 277:2002;11570-11575.
45. Srinivasula S.M., Poyet J.L., Razmara M., Datta P., Zhang Z., Alnemri E.S. J. Biol. Chem. 277:2002;21119-21122.
46. Espagne E., Balhadere P., Begueret J., Turcq B. Mol. Gen. Genet. 256:1997;620-627.
47. Harton J.A., Cressman D.E., Chin K.C., Der C.J., Ting J.P. Science. 285:1999;1402-1405.
48. Accolla R.S., De Lerma Barbaro A., Mazza S., Casoli C., De Maria A., Tosi G. Trends Immunol. 22:2001;560-563.
49. Ting, J.P. and Trowsdale, J. (2002) Cell 109 Suppl., S21-33.
50. Nickerson K., Sisk T.J., Inohara N., Yee C.S., Kennell J., Cho M.C., Yannie P.J. II, Núñez G., Chang C.H. J. Biol. Chem. 276:2001;19089-19093.
51. Steimle V., Otten L.A., Zufferey M., Mach B. Cell. 75:1993;135-146.
52. Bontron S., Steimle V., Ucla C., Eibl M.M., Mach B. Hum. Genet. 99:1997;541-546.
53. Cressman D.E., Chin K.C., Taxman D.J., Ting J.P. Immunity. 10:1999;163-171.
54. Quan V., Towey M., Sacks S., Kelly A.P. Immunogenetics. 49:1999;957-963.
55. Wiszniewski W., et al. J. Immunol. 167:2001;1787-1794.
56. Dziembowska M., et al. Immunogenetics. 53:2002;821-829.
57. Patarroyo J.C., Stuve O., Piskurich J.F., Hauser S.L., Oksenberg J.R., Zamvil S.S. Genes Immun. 3:2002;34-37.
58. Chamaillard M., et al. Proc. Natl. Acad. Sci. USA. 100:2003;3455-3460.
59. Girardin S.E., Travassos L.H., Hérve M., Blanot D., Boneca I.G., Philpott D.J., Sansonetti P.J., Mengin-Lecreulx D. J. Biol. Chem. 278:2003;41702-41708.
60. Underhill D.M. Eur. J. Immunol. 33:2003;1767-1775.
61. Armant M.A., Fenton M.J. Genome Biol. 3:2002;3011.1-3011.6.
62. Dunne, A. and O'Neill, L.A. (2003) Sci. STKE 171, re3.1-re3.17.
63. Akira S. Curr. Opin. Immunol. 15:2003;5-11.
64. Ellis J., Jones D. Curr. Opin. Plant. Biol. 1:1998;288-293.
65. Dixon M.S., Golstein C., Thomas C.M., van Der Biezen E.A., Jones J.D. Proc. Natl. Acad. Sci. USA. 97:2000;8807-8814.
66. Shirasu K., Schulze-Lefert P. Plant Mol. Biol. 44:2000;371-385.
67. Young N.D. Curr. Opin. Plant Biol. 3:2000;285-290.
68. Menezes H., Jared C. Comp. Biochem. Physiol. C. Toxicol. Pharmacol. 132:2002;1-7.
69. Nürnberger T., Brunner F. Curr. Opin. Plant. Biol. 5:2002;318-324.
70. Holt B.F., Hubert D.A., Dangl J.L. Curr. Opin. Immunol. 15:2003;20-25.
71. Boeckmann B., et al. Nucleic Acids Res. 31:2003;365-370.
72. Westbrook J., Feng Z., Chen L., Yang H., Berman H.M. Nucleic Acids Res. 31:2003;489-491.
73. Lo Conte L., Brenner S.E., Hubbard T.J., Chothia C., Murzin A.G. Nucleic Acids Res. 30:2002;264-267.
74. Kabsch W., Sander C. Biopolymers. 22:1983;2577-2637.
75. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. J. Mol. Biol. 215:1990;403-410.
76. McGuffin L.J., Bryson K., Jones D.T. Bioinformatics. 16:2000;404-405.
77. Rost B., Eyrich V.A. Proteins. 45:(Suppl. 5):2001;192-199.
78. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., Thompson J.D. Nucleic Acids Res. 31:2003;3497-3500.
79. Shindyalov I.N., Bourne P.E. Protein Eng. 11:1998;739-747.
80. Lackner P., Koppensteiner W.A., Sippl M.J., Domingues F.S. Protein Eng. 13:2000;745-752.
81. Bujnicki J.M., Elofsson A., Fischer D., Rychlewski L. Bioinformatics. 17:2001;750-751.
82. Ginalski K., Rychlewski L. Nucleic Acids Res. 31:2003;3291-3292.
83. Sommer I., Zien A., von Öhsen N., Zimmer R., Lengauer T. Bioinformatics. 18:2002;802-812.
84. von Öhsen, N., Sommer, I. and Zimmer, R. (2003) Pac. Symp. Biocomput., 252-263.
85. Rodriguez R., Chinea G., Lopez N., Pons T., Vriend G. Bioinformatics. 14:1998;523-528.
86. Bower M.J., Cohen F.E., Dunbrack R.L. Jr. J. Mol. Biol. 267:1997;1268-1282.
87. Bates P.A., Kelley L.A., MacCallum R.M., Sternberg M.J. Proteins. 45:(Suppl. 5):2001;39-46.
88. Galtier N., Gouy M., Gautier C. Comput. Appl. Biosci. 12:1996;543-548.
89. Gouet P., Robert X., Courcelle E. Nucleic Acids Res. 31:2003;3320-3323.
90. Liu J., Smith C.L., DeRyckere D., DeAngelis K., Martin G.S., Berger J.M. Mol. Cell. 6:2000;637-648.
91. Zhang X., et al. Mol. Cell. 6:2000;1473-1484.
92. Guo F., Maurizi M.R., Esser L., Xia D. J. Biol. Chem. 277:2002;46743-46752.
93. Li J., Sha B. J. Mol. Biol. 318:2002;1127-1137.
94. Abrahams J.P., Leslie A.G., Lutter R., Walker J.E. Nature. 370:1994;621-628.
95. Bourne H.R., Sanders D.A., McCormick F. Nature. 349:1991;117-127.
96. Beyer A. Protein Sci. 6:1997;2043-2058.
97. Neuwald A.F., Aravind L., Spouge J.L., Koonin E.V. Genome Res. 9:1999;27-43.
98. Patel S.S., Picha K.M. Annu. Rev. Biochem. 69:2000;651-697.
99. Vale R.D. J. Cell Biol. 150:2000;F13-19.
100. Geourjon C., Orelle C., Steinfels E., Blanchet C., Deléage G., Di Pietro A., Jault J.M. Trends Biochem. Sci. 26:2001;539-544.
101. Ogura T., Wilkinson A.J. Genes Cells. 6:2001;575-597.
102. Caruthers J.M., McKay D.B. Curr. Opin. Struct. Biol. 12:2002;123-133.
103. Dougan D.A., Mogk A., Zeth K., Turgay K., Bukau B. FEBS Lett. 529:2002;6-10.
104. Leipe D.D., Wolf Y.I., Koonin E.V., Aravind L. J. Mol. Biol. 317:2002;41-72.
105. Lupas A.N., Martin J. Curr. Opin. Struct. Biol. 12:2002;746-753.
106. Ramakrishnan C., Dani V.S., Ramasarma T. Protein Eng. 15:2002;783-798.
107. Schmitt L., Tampé R. Curr. Opin. Struct. Biol. 12:2002;754-760.
108. Hopfner K.P., Tainer J.A. Curr. Opin. Struct. Biol. 13:2003;249-255.
109. Walker J.E., Saraste M., Runswick M.J., Gay N.J. EMBO J. 1:1982;945-951.
110. Cardozo T.J., Abagyan R. J. Mol. Model. 4:1998;83-93.
111. Jaroszewski L., Rychlewski L., Reed J.C., Godzik A. Proteins. 39:2000;197-203.
112. Muneyuki E., Noji H., Amano T., Masaike T., Yoshida M. Biochim. Biophys. Acta. 1458:2000;467-481.
113. Granel B., et al. Dermatology. 206:2003;257-259.
114. Kobe B., Kajava A.V. Curr. Opin. Struct. Biol. 11:2001;725-732.
115. Kobe B., Deisenhofer J. J. Mol. Biol. 264:1996;1028-1043.
116. Papageorgiou A.C., Shapiro R., Acharya K.R. EMBO J. 16:1997;5162-5177.
117. Aloy P., Ceulemans H., Stark A., Russell R.B. J. Mol. Biol. 332:2003;989-998.
118. Linhoff M.W., Harton J.A., Cressman D.E., Martin B.K., Ting J.P. Mol. Cell Biol. 21:2001;3001-3011.
119. Seewald M.J., Körner C., Wittinghofer A., Vetter I.R. Nature. 415:2002;662-666.
120. Hake S.B., Masternak K., Kammerbauer C., Janzen C., Reith W., Steimle V. Mol. Cell Biol. 20:2000;7716-7725.
121. Harton J.A., O'Connor W. Jr., Conti B.J., Linhoff M.W., Ting J.P. Hum. Immunol. 63:2002;588-601.
122. Wilke-Mounts S., Pagan J., Senior A.E. Arch. Biochem. Biophys. 324:1995;153-158.
123. Schnizer R.A., Schuster S.M. Arch. Biochem. Biophys. 326:1996;126-136.