Protein fold analysis of the B30.2-like domain

Proteins: Structure, Function and Genetics

Volumn 35, Issue 2, 1999, Pages 235-249

  Seto, Marian H ^a   Liu, Hsiao Lai C ^a   Zajchowski, Deborah A ^a   Whitlow, Marc ^a  

^a BAYER AG   (Germany)

Author keywords

Domain identification; Fold recognition; Secondary structure prediction; SPRY domain; Threading

Indexed keywords

PROTEIN;

ARTICLE; CARBOXY TERMINAL SEQUENCE; MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 0033135464     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990501)35:2<235::AID-PROT9>3.0.CO;2-X     Document Type: Article

References (73)

1. Vernet C, Boretto J, Mattéi M-G, et al. Evolutionary study of multigenic families mapping close to the human MHC class I region. J Mol Evol 1993;37:600-612.
2. Reddy BA, Etkin LD. A unique bipartite cysteine-histidine motif defines a subfamily of potential zinc-finger proteins. Nucleic Acids Res 1991;19:6330.
3. Reddy BA, Etkin LD, Freemont PS. A novel zinc finger coiled-coil domain in a family of nuclear proteins. Trends Biol Sci 1992;17: 344-345.
4. Borden KLB, Lally JM, Martin SR, O'Reilly NJ, Etkin LD, Freemont PS. Novel topology of a zinc-binding domain from a protein involved in regulating early Xenopus development. EMBO 1995;14:5947-5956.
5. Inoue S, Orimo A, Hosoi T, et al. Genomic binding-site cloning reveals an estrogen-responsive gene that encodes a RING finger protein. Proc Natl Acad Sci USA 1993;90:11117-11121.
6. Reddy BA, Kloc M, Etkin L. The cloning and characterization of a maternally expressed novel zinc finger nuclear phosphoprotein (xnf7) in Xenopus laevis. Dev Biol 1991;148:107-116.
7. Tissot C, Mechti N. Molecular cloning of a new interferon-induced factor that represses human immunodeficiency virus type 1 long terminal repeat expression. J Biol Chem 1995;270:14891-14898.
8. Bellini M, Lacroix J-C, Gall GG. A putative zinc-binding protein on lampbrush chromosome loops. EMBO J 1993;12:107-114.
9. Itoh K, Itoh Y, Frank MB. Protein heterogeneity in the human Ro/SSA ribonucleoproteins. The 52- and 60-kD Ro/SSA autoantigens are encoded by separate genes. J Clin Invest 1991;87:177-186.
10. Takahashi M, Inaguma Y, Hiai H, Hirose F. Developmentally regulated expression of a human "finger"-containing gene encoded by the 5' half of the ret transforming gene. Mol Cell Biol 1988;8: 1853-1856.
11. Nagase T, Seki N, Tanaka A, Ishikawa K, Nomura N. Prediction of the coding sequences of unidentified human genes. IV. The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1. DNA Res 1995;2:167-174.
12. Chu TW, Capossela A, Coleman R, Goei VL, Nallur G, Gruen JR. Cloning of a new 'finger' protein gene (ZNF173) within the class I region of the human MHC. Genomics 1995;29:229-239.
13. Henry J, Ribouchon M-T, Depetris D, Matteï M-G, Offer C, Tazi-Ahnini R, Pontarotti P. Cloning, structural analysis, and mapping of the B30 and B7 multigenic families to the major histocompatibility complex (MHC) and other chromosomal regions. Immunogenetics 1997;46:383-395.
14. The International FMF Consortium. Ancient missense mutations in a new member of the RoRet gene family are likely to cause familial Mediterranean fever. Cell 1997;90:797-807.
15. Liu H-L, Golder-Novoselsky E, Seto MH, Webster L, McClary J, Zajchowski DA. The novel estrogen-responsive B box protein (EBBP) gene is tamoxifen-regulated in cells expressing an estrogen receptor DNA-binding domain mutant. Mol Endo 1998;12: 1733-1748.
16. El-Hodiri HM, Che S, Nelman-Gonzalez M, Kuang J, Etkin LD. Mitogen-activated protein kinase and cyclin B/Cdc2 phosphorylate Xenopus nuclear factor7 (xnf7) in extracts from mature oocytes. Implications for regulation of xnf7 subcellular localization. J Biol Chem 1997;272:20463-20470.
17. Miyagawa S, Okada N, Inagaki Y, Kitano Y, Ueki H, Sakamoto K, Steinberg ML. SSA/Ro antigen expression in simian virus 40-transformed human keratinocytes. J Invest Dermatol 1998;90:342-345.
18. Ruddy DA, Kronmal GS, Lee VK, et al. A 1.1-Mb transcript map of the hereditary hemochromatosis locus. Genome Res 1997;7:441-456.
19. Tazi-Ahnini R, Henry J, Offer C, Bouissou-Bouchouata C, Mather IH, Pontarotti P. Cloning, localization, and structure of new members of the butyrophilin gene family in the juxta-telomeric region of the major histocompatibility complex. Immunogenetics 1998;47:55-63.
20. Jack LJW, Mather IH. Cloning and analysis of cDNA encoding bovine butyrophilin, an apical glycoprotein expressed in mammary tissue and secreted in association with the milk-fat globule membrane during lactation. J Biol Chem 1990;265:14481-14486.
21. Ishii T, Aoki N, Noda A, Adachi T, Nakamura R, Matsuda T. Carboxy-terminal cytoplasmic domain of mouse butyrophilin specifically associates with a 150-kDa protein of mammary epithelial cells and milk fat globule membrane. Biochim Biophys Acta 1995;1245:285-292.
22. Banghart LR, Chamberlain CW, Velarde J, Korobko IV, Ogg SL, Jack LJW, Vakharia VN, Mather IH. Butyrophilin is expressed in mammary epithelial cells from a single-sized messenger RNA as a type I membrane glycoprotein. J Biol Chem 1998;273:4171-4179.
23. Taylor MR, Peterson JA, Ceriani RL, Couto JR. Cloning and sequence analysis of human butyrophilin reveals a potential receptor function. Biochim Biophys Acta 1996;1306:1-4.
24. Ghadessy FJ, Jeyaseelan K, Chung MC, Khoo HE, Yuen R. A genomic region encoding stonefish (Synanceja horrida) stonustoxin beta-subunit contains an intron. Toxicon 1994;32:1684-1688.
25. Ghadessy FJ, Chen D, Kini RM, et al. Stonustoxin is a novel lethal factor from stonefish (Synanceja horrida) venom. cDNA cloning and characterization. J Biol Chem 1996;271:25575-25581.
26. Chen D, Kini RM, Yuen R, Khoo HE. Haemolytic activity of stonustoxin from stonefish (Synanceja horrida) venom: pore formation and the role of cationic amino acid residues. Biochem J 1997;325:685-691.
27. Khoo HE, Hon WM, Lee SH, Yuen R. Effects of stonustoxin (lethal factor from Synanceja horrida venom) on platelet aggregation. Toxicon 1995;33:1033-1041.
28. Low KSY, Gwee MCE, Yuen R, Gopalakrishnakone P, Khoo HE. Stonustoxin: a highly potent endothelium-dependent vasorelaxant in the rat. Toxicon 1993;11:1471-1478.
29. Schultz J, Milpetz F, Bork P, Ponting CP. Smart, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci USA 1998;95:5857-5864.
30. Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R. Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 1998;26:320-322.
31. 2+-release channels). Trends Biochem Sci 1997;22: 193-194.
32. Henry J, Ribonuchon M-T, Offer C, Pontarotti P. B30.2-like domain proteins: a growing family. Biochem Biophys Res Commun 1997;235:162-165.
33. Orengo CA, Jones DT, Thornton JM. Protein superfamilies and domain superfolds. Nature 1994;372:631-634.
34. King RD, Sternberg MJE. Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. Protein Sci 1996;5:2298-2310.
35. Rost B, Sander C. Prediction of protein structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
36. Frishman D, Argos P. Seventy-five percent accuracy in protein secondary structure prediction. Proteins 1997;27:329-335.
37. Frishman D, Argos P. Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng 1996;9:133-142.
38. Salamov AA, Solovyev VV. Protein secondary structure prediction using local alignments. J Mol Biol 1997;268:31-36.
39. Salamov AA, Solovyev VV. Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. J Mol Biol 1995;247:11-15.
40. Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
41. Jones D, Thornton J. Protein fold recognition. J. Comput Aided Mol Des 1993;7:439-556.
42. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM, CATH- a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
43. Fischer D, Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci 1996;5:947-955.
44. Gonnet GH, Cohen MA, Benner SA. Exhaustive matching of the entire protein sequence database. Science 1992;256:1443-1445.
45. Bowie JU, Lüthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
46. Zhou GW, Guo J, Huang W, Fletterick RJ, Scanlan TS. Crystal structure of a catalytic antibody with a serine protease active site. Science 1994;265:1059-1064.
47. Bernstein FC, Koetzle TF, Williams GJB, et al. The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
48. Abola EE, Bernstein FC, Bryant SH, Koetzle TF, Weng J. Protein data bank. In: Allen FH, Bergerhoff G, Sievers R, editors. Crystallographic databases-information content, software systems, scientific applications. Bonn/Cambridge/Chester: Data Commission of the International Union of Crystallography; 1987. p 107-132.
49. Braden BC, Souchon H, Eisele JL, et al. Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody. J Mol Biol 1994;243:767-781.
50. Deisenhofer J. Crystallograhic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-Å resolution. Biochemistry 1981;20:2361-2370.
51. Eigenbrot C, Gonzalez T, Mayeda J, et al. X-ray structures of fragments from binding and nonbinding versions of a humanized anti-CD18 antibody: structural indications of the key role of VH residues 59 to 65. Proteins 1994;18:49-62.
52. Satow Y, Cohen GH, Padlan EA, Davies DR. Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 Å. J Mol Biol 1986;190:593-604.
53. Pflugrath JW, Wiegand G, Huber R, Vertesy L. Crystal structure determination, refinement and the molecular model of the alpha-amylase inhibitor Hoe-467 A. J Mol Biol 1986;189:383-386.
54. Lescar J, Pellegrini M, Souchon H, et al. Crystal structure of a cross-reaction complex between Fab F9.13.7 and guinea fowl lysozyme. J Biol Chem 1995;270:18067-18076.
55. Lüthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992;356:83-85.
56. Sander C, Schneider R. Database of homology-derived protein structures and structural meaning of sequence alignment. Proteins 1991;9:56-68.
57. Hobohm U, Scharf M, Schneider R, Sander C. Selection of representative protein data sets. Protein Sci 1992;1:409-417.
58. Norledge BV, Hay RE, Bateman OA, Slingsby C, Driessen HP. Towards a molecular understanding of phase separation in the lens: a comparison of the X-ray structures of two high Tc gamma-crystallins, gammaE and gammaF, with two low Tc gamma-crystallins, gammaB and gammaD. Exp Eye Res 1997;65:609-630.
59. Wistow G, Turnell B, Summers L, et al. X-ray analysis of the eye lens protein gamma-II crystallin at 1.9 Å resolution. J Mol Biol 1983;170:175-202.
60. Bamborough P, Hedgecock CJ, Richards WG. The interleukin-2 and interleukin-4 receptors studied by molecular modelling. Structure 1994;2:839-851.
61. Adman ET, Godden JW, Turley S. The structure of copper-nitrite reductase from Achrombacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted. J Biol Chem 1995;270:27458-27474.
62. Van Roey P, Beerman TA. Crystal structure analysis of auromomycin apoprotein (macromomycin) shows importance of protein side chains to chromophore binding selectivley. Proc Natl Acad Sci USA 1989;86:6587-6591.
63. Bentley GA, Boulot G, Karjalainen K, Mariuzza RA. Crystal structure of the beta chain of a T cell antigen receptor. Science 1995;267:1984-1987.
64. DeVos AM, Ultsch M, Kossiakoff AA. Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science 1992;255:306-312.
65. Bork P, Holm L, Sander C. The immunoglobulin fold. Structural classification, sequence patterns and common core. J Mol Biol 1994;242:309-320.
66. Gugolya Z, Dosztányi Zs, Simon I. Interresidue interactions in protein classes. Proteins 1997;27:360-366.
67. Ghosh G, van Duyne G, Ghosh S, Sigler PB. Structure of NF-κB p50 homodimer bound to a κB site. Nature 1995;373:303-310.
68. Müller CW, Rey FA, Sodeoka M, Verdine GL, Harrison SC. Structure of the NF-κB p50 homodimer bound to DNA. Nature 1995;373:311-317.
69. v, the variable domain of a human immunoglobulin κ light chain. Fold Des 1996;1:431-440.
70. Proba K, Arne W, Honegger A, Plückthun A. Antibody scFV fragments without disulfide bonds made by molecular evolution. J Mol Biol 1998;275:245-253.
71. Martin AC, MacArthur MW, Thornton JM. Assessment of comparative modeling in CASP2. Proteins Suppl 1997;1:14-28.
72. Chen X, Whitmire D, Bowen JP. Xylanase homology modeling using the inverse protein folding approach. Protein Sci 1996;5:705-708.
73. Banner DW, D'Arcy A, Chène C, et al. The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Nature 1996;380:41-46.