Fold prediction and evolutionary analysis of the POZ domain: Structural and evolutionary relationship with the potassium channel tetramerization domain

Journal of Molecular Biology

Volumn 285, Issue 4, 1999, Pages 1353-1361

  Aravind, L ^a,b   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Evolutionary analysis; Fold prediction; Potassium channels; POZ domains

Indexed keywords

POTASSIUM CHANNEL; VIRUS PROTEIN; ZINC FINGER PROTEIN;

ARTICLE; CRYSTAL STRUCTURE; DATA BASE; EVOLUTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION;

ANIMALIA; APLYSIA; DNA VIRUSES; EUKARYOTA; POXVIRIDAE;

EID: 0033613909     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2394     Document Type: Article

References (52)

1. Abagyan R. A., Batalov S. Do aligned sequences share the same fold? J. Mol. Biol. 273:1997;355-368.
2. Albagli O., Dhordain P., Deweindt C., Lecocq G., Leprince D. The BTB/POZ domain: a new protein-protein interaction motif common to DNA and actin-binding proteins. Cell Growth Differ. 6:1995;1193-1198.
3. Altschul S. F., Koonin E. V. Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases. Trends Biochem. Sci. 23:1998;in the press.
4. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402.
5. Aravind L., Koonin E. V. A colipase fold in the carboxy-terminal domain of the Wnt antagonists- Dickkpfs. Curr. Biol. 8:1998;R477-478.
6. Aravind L., Galperin M. Y., Koonin E. V. The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold. Trends Biochem. Sci. 23:1998;127-129.
7. Bardwell V. J., Treisman R. The POZ domain: a conserved protein-protein interaction motif. Genes Dev. 8:1994;1664-1677.
8. Bork P. Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally? Proteins: Struct. Funct. Genet. 17:1993;363-374.
9. Bork P., Doolittle R. F. Drosophila kelch motif is derived from a common enzyme fold. J. Mol. Biol. 236:1994;1277-1282.
10. Bork P., Koonin E. V. Predicting functions from protein sequences - where are the bottlenecks? Nature Genet. 18:1998;313-318.
11. Bork P., Sudol M. The WW domain: a signalling site in dystrophin? Trends Biochem. Sci. 19:1994;531-533.
12. Cao H., Glazebrook J., Clarke J. D., Volko S., Dong X. The Atabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats. Cell. 88:1997;57-63.
13. Das A. K., Cohen P. W., Barford D. The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions. EMBO J. 17:1998;1192-1199.
14. David G., Alland L., Hong S. H., Wong C. W., DePinho R. A., Dejean A. Histone deacetylase associated with mSin3A mediates repression by the acute promyelocytic leukemia-associated PLZF protein. Oncogene. 16:1998;2549-2556.
15. Dhordain P., Albagli O., Ansieau S., Koken M. H., Deweindt C., Quief S., Lantoine D., Leutz A., Kerckaert J. P., Leprince D. The BTB/POZ domain targets the LAZ3/BCL6 oncoprotein to nuclear dots and mediates homomerisation in vivo. Oncogene. 11:1995;2689-2697.
16. DiBello P. R., Withers D. A., Bayer C. A., Fristrom J. W., Guild G. M. The Drosophila broad-complex encodes a family of related proteins containing zinc fingers. Genetics. 129:1991;385-397.
17. Eberstadt M., Huang B., Chen Z., Meadows R. P., Ng S. C., Zheng L., Lenardo M. J., Fesik S. W. NMR structure and mutagenesis of the FADD (Mort1) death-effector domain. Nature. 392:1998;941-945.
18. Escalante R., Wessels D., Soll D. R., Loomis W. F. Chemotaxis to cAMP and slug migration in Dictyostelium both depend on migA, a BTB protein. Mol. Biol. Cell. 8:1997;1763-1775.
19. Giniger E., Tietje K., Jan L. Y., Jan Y. N. lola encodes a putative transcription factor required for axon growth and guidance in Drosophila. Development. 120:1994;1385-1398.
20. Godt D., Couderc J. L., Cramton S. E., Laski F. A. Pattern formation in the limbs of Drosophila: bric a brac is expressed in both a gradient and a wave-like pattern and is required for specification and proper segmentation of the tarsus. Development. 119:1993;799-812.
21. Grignani F., DeMatteis S., Nervi C., Tomassoni L., Gelmetti V., Cioce M., Fanelli M., Ruthardt M., Ferrara F. F., Zamir I., Seiser C., Lazar M. A., Minucci S., Pelicci P. G. Fusion proteins of the retinoic acid receptor-alpha recruit histone deacetylase in promyelocytic leukaemia. Nature. 391:1998;815-818.
22. Harrison S. D., Travers A. A. The tramtrack gene encodes a Drosophila finger protein that interacts with the ftz transcriptional regulatory region and shows a novel embryonic expression pattern. EMBO J. 9:1990;207-216.
23. Hofmann K., Bucher P., Tschopp J. The CARD domain: a new apoptotic signalling motif. Trends Biochem. Sci. 22:1997;155-156.
24. Hong S. H., David G., Wong C. W., Dejean A., Privalsky M. L. SMRT corepressor interacts with PLZF and with the PML-retinoic acid receptor alpha (RARalpha) and PLZF-RARalpha oncoproteins associated with acute promyelocytic leukemia. Proc. Natl Acad. Sci. USA. 94:1997;9028-9033.
25. Hu S., Fambrough D., Atashi J. R., Goodman C. S., Crews S. T. The Drosophila abrupt gene encodes a BTB-zinc finger regulatory protein that controls the specificity of neuromuscular connections. Genes Dev. 9:1995;2936-2948.
26. Igarashi K., Hoshino H., Muto A., Suwabe N., Nishikawa S., Nakauchi H., Yamamoto M. Multivalent DNA binding complex generated by small Maf and Bach1 as a possible biochemical basis for beta-globin locus control region complex. J. Biol. Chem. 273:1998;11783-11790.
27. Ito H., Fujitani K., Usui K., Shimizu-Nishikawa K., Tanaka S., Yamamoto D. Sexual orientation in Drosophila is altered by the satori mutation in the sex-determination gene fruitless that encodes a zinc finger protein with a BTB domain. Proc. Natl Acad. Sci. USA. 93:1996;9677-9692.
28. Kajava A. V. Structural diversity of leucine-rich repeat proteins. J. Mol. Biol. 277:1998;519-527.
29. Kim T. A., Lim J., Ota S., Raja S., Rogers R., Rivnay B., Avraham H., Avraham S. NRP/B, a novel nuclear matrix protein, associates with p110(RB) and is involved in neuronal differentiation. J. Cell. Biol. 141:1998;553-566.
30. Koonin E. V., Senkevich T. G., Chernos V. I. A family of DNA virus genes that consists of fused portions of unrelated cellular genes. Trends Biochem. Sci. 17:1992;213-214.
31. Koonin E. V., Tatusov R. L., Rudd K. E. Protein sequence comparison at genome scale. Methods Enzymol. 266:1996;295-322.
32. Kreusch A., Pfaffinger P. J., Stevens C. F., Choe S. Crystal structure of the tetramerization domain of the Shaker potassium channel. Nature. 392:1998;945-948.
33. Kurahashi H., Akagi K., Inazawa J., Ohta T., Niikawa N., Kayatani F., Sano T., Okada S., Nishisho I. Isolation and characterization of a novel gene deleted in DiGeorge syndrome. Hum. Mol. Genet. 4:1995;541-549.
34. Li X., Lopez-Guisa J. M., Ninan N., Weiner E. J., Rauscher F. J. III, Marmorstein R. Overexpression. purification, characterization, and crystallization of the BTB/POZ domain from the PLZF oncoprotein. J. Biol. Chem. 272:1997;27324-27329.
35. Lin R. J., Nagy L., Inoue S., Shao W., Miller W. H. Jr, Evans R. M. Role of the histone deacetylase complex in acute promyelocytic leukaemia. Nature. 391:1998;811-814.
36. Neer E. J., Schmidt C. J., Nambudripad R., Smith T. F. The ancient regulatory-protein family of WD-repeat proteins. Nature. 371:1994;297-300.
37. Ponting C. P., Aravind L. PAS: a multifunctional domain family comes to light. Curr. Biol. 7:1997;R674-677.
38. Robinson D. N., Cooley L. Drosophila kelch is an oligomeric ring canal actin organizer. J. Cell. Biol. 138:1997;799-810.
39. Rost B., Casadio R., Fariselli P., Sander C. Transmembrane helices predicted at 95 % accuracy. Protein Sci. 4:1995;521-533.
40. Saitou N., Nei M. The neighbor-joining method: anew method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
41. Senkevich T. G., Muravnik G. L., Pozdnyakov S. G., Chizhikov V. E., Ryazankina O. L., Shchelkunov S. N., Koonin E. V., Chernos V. I. Nucleotide sequence of Xho I 0 fragment of ectromelia virus DNA reveals significant differences from vaccinia virus. Virus Res. 30:1993;73-88.
42. Shen N. V., Chen X., Boyer M. M., Pfaffinger P. J. Deletion analysis of K+ channel assembly. Neuron. 11:1993;67-76.
43. Stenmark H., Aasland R., Toh B. H., D'Arrigo A. Endosomal localization of the autoantigen EEA1 is mediated by a zinc-binding FYVE finger. J. Biol. Chem. 271:1996;24048-24054.
44. Thompson J. D., Gibson T. J., Plewniak F., Jearmougin F., Higgins D. G. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25:1997;4876-4882.
45. Uren A. G., Vaux D. L. TRAF proteins and meprins share a conserved domain. Trends Biochem. Sci. 21:1996;244-245.
46. Wales M. M., Biel M. A., el Deiry W., Nelkin B. D., Issa J. P., Cavenee W. K., Kuerbitz S. J., Baylin S. B. p53 activates expression of HIC-1, a new candidate tumour suppressor gene on 17p13.3. Nature Med. 1:1995;570-577.
47. Walker D. R., Koonin E. V. SEALS: a system for easy analysis of lots of sequences. Ismb. 5:1997;333-339.
48. Weber U., Siegel V., Mlodzik M. pipsqueak encodes a novel nuclear protein required downstream of seven-up for the development of photoreceptors R3 and R4. EMBO J. 14:1995;6247-6257.
49. Wolf F. W., Marks R. M., Sarma V., Byers M. G., Katz R. W., Shows T. B., Dixit V. M. Characterization of a novel tumor necrosis factor-alpha-induced endothelial primary response gene. J. Biol. Chem. 267:1992;1317-1326.
50. Wootton J. C. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput. Chem. 18:1994;269-285.
51. Wootton J. C., Federhen S. Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266:1996;554-571.
52. Zollman S., Godt D., Prive G. G., Couderc J. L., Laski F. A. The BTB domain, found primarily in zinc finger proteins, defines an evolutionarily conserved family that includes several developmentally regulated genes in Drosophila. Proc. Natl Acad. Sci. USA. 91:1994;10717-10721.