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. 1997 Oct;6(10):2043–2058. doi: 10.1002/pro.5560061001

Sequence analysis of the AAA protein family.

A Beyer 1
PMCID: PMC2143574  PMID: 9336829

Abstract

The AAA protein family, a recently recognized group of Walker-type ATPases, has been subjected to an extensive sequence analysis. Multiple sequence alignments revealed the existence of a region of sequence similarity, the so-called AAA cassette. The borders of this cassette were localized and within it, three boxes of a high degree of conservation were identified. Two of these boxes could be assigned to substantial parts of the ATP binding site (namely, to Walker motifs A and B); the third may be a portion of the catalytic center. Phylogenetic trees were calculated to obtain insights into the evolutionary history of the family. Subfamilies with varying degrees of intra-relatedness could be discriminated; these relationships are also supported by analysis of sequences outside the canonical AAA boxes: within the cassette are regions that are strongly conserved within each subfamily, whereas little or even no similarity between different subfamilies can be observed. These regions are well suited to define fingerprints for subfamilies. A secondary structure prediction utilizing all available sequence information was performed and the result was fitted to the general 3D structure of a Walker A/GTPase. The agreement was unexpectedly high and strongly supports the conclusion that the AAA family belongs to the Walker superfamily of A/GTPases.

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Selected References

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  1. Abele U., Schulz G. E. High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer. Protein Sci. 1995 Jul;4(7):1262–1271. doi: 10.1002/pro.5560040702. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  3. Bajaj M., Blundell T. Evolution and the tertiary structure of proteins. Annu Rev Biophys Bioeng. 1984;13:453–492. doi: 10.1146/annurev.bb.13.060184.002321. [DOI] [PubMed] [Google Scholar]
  4. Barinaga M. Molecular evolution. Archaea and eukaryotes grow closer. Science. 1994 May 27;264(5163):1251–1251. doi: 10.1126/science.8191278. [DOI] [PubMed] [Google Scholar]
  5. Cavalier-Smith T. The origin of eukaryotic and archaebacterial cells. Ann N Y Acad Sci. 1987;503:17–54. doi: 10.1111/j.1749-6632.1987.tb40596.x. [DOI] [PubMed] [Google Scholar]
  6. Choi H. S., Seol W., Moore D. D. A component of the 26S proteasome binds on orphan member of the nuclear hormone receptor superfamily. J Steroid Biochem Mol Biol. 1996 Jan;56(1-6):23–30. doi: 10.1016/0960-0760(95)00220-0. [DOI] [PubMed] [Google Scholar]
  7. Chou P. Y., Fasman G. D. Prediction of protein conformation. Biochemistry. 1974 Jan 15;13(2):222–245. doi: 10.1021/bi00699a002. [DOI] [PubMed] [Google Scholar]
  8. Confalonieri F., Duguet M. A 200-amino acid ATPase module in search of a basic function. Bioessays. 1995 Jul;17(7):639–650. doi: 10.1002/bies.950170710. [DOI] [PubMed] [Google Scholar]
  9. Confalonieri F., Marsault J., Duguet M. SAV, an archaebacterial gene with extensive homology to a family of highly conserved eukaryotic ATPases. J Mol Biol. 1994 Jan 7;235(1):396–401. doi: 10.1016/s0022-2836(05)80047-6. [DOI] [PubMed] [Google Scholar]
  10. Dayhoff M. O., Barker W. C., Hunt L. T. Establishing homologies in protein sequences. Methods Enzymol. 1983;91:524–545. doi: 10.1016/s0076-6879(83)91049-2. [DOI] [PubMed] [Google Scholar]
  11. Dubiel W., Ferrell K., Pratt G., Rechsteiner M. Subunit 4 of the 26 S protease is a member of a novel eukaryotic ATPase family. J Biol Chem. 1992 Nov 15;267(32):22699–22702. [PubMed] [Google Scholar]
  12. Eakle K. A., Bernstein M., Emr S. D. Characterization of a component of the yeast secretion machinery: identification of the SEC18 gene product. Mol Cell Biol. 1988 Oct;8(10):4098–4109. doi: 10.1128/mcb.8.10.4098. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Fröhlich K. U., Fries H. W., Peters J. M., Mecke D. The ATPase activity of purified CDC48p from Saccharomyces cerevisiae shows complex dependence on ATP-, ADP-, and NADH-concentrations and is completely inhibited by NEM. Biochim Biophys Acta. 1995 Nov 15;1253(1):25–32. doi: 10.1016/0167-4838(95)00136-i. [DOI] [PubMed] [Google Scholar]
  14. Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 1978 Mar 25;120(1):97–120. doi: 10.1016/0022-2836(78)90297-8. [DOI] [PubMed] [Google Scholar]
  15. Goodman M. Globin evolution was apparently very rapid in early vertebrates: a reasonable case against the rate-constancy hypothesis. J Mol Evol. 1981;17(2):114–120. doi: 10.1007/BF01732683. [DOI] [PubMed] [Google Scholar]
  16. Goyer C., Lee H. S., Malo D., Sonenberg N. Isolation of a yeast gene encoding a protein homologous to the human Tat-binding protein TBP-1. DNA Cell Biol. 1992 Oct;11(8):579–585. doi: 10.1089/dna.1992.11.579. [DOI] [PubMed] [Google Scholar]
  17. Henikoff S. Playing with blocks: some pitfalls of forcing multiple alignments. New Biol. 1991 Dec;3(12):1148–1154. [PubMed] [Google Scholar]
  18. Iwabe N., Kuma K., Hasegawa M., Osawa S., Miyata T. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9355–9359. doi: 10.1073/pnas.86.23.9355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. MacIntyre R. J. Molecular evolution: codes, clocks, genes and genomes. Bioessays. 1994 Sep;16(9):699–703. doi: 10.1002/bies.950160918. [DOI] [PubMed] [Google Scholar]
  20. Makino Y., Yogosawa S., Kanemaki M., Yoshida T., Yamano K., Kishimoto T., Moncollin V., Egly J. M., Muramatsu M., Tamura T. Structures of the rat proteasomal ATPases: determination of highly conserved structural motifs and rules for their spacing. Biochem Biophys Res Commun. 1996 Mar 27;220(3):1049–1054. doi: 10.1006/bbrc.1996.0530. [DOI] [PubMed] [Google Scholar]
  21. Nelson N. Evolution of organellar proton-ATPases. Biochim Biophys Acta. 1992 May 20;1100(2):109–124. doi: 10.1016/0005-2728(92)90072-a. [DOI] [PubMed] [Google Scholar]
  22. Nobrega F. G., Nobrega M. P., Tzagoloff A. BCS1, a novel gene required for the expression of functional Rieske iron-sulfur protein in Saccharomyces cerevisiae. EMBO J. 1992 Nov;11(11):3821–3829. doi: 10.1002/j.1460-2075.1992.tb05474.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Pamilo P., Nei M. Relationships between gene trees and species trees. Mol Biol Evol. 1988 Sep;5(5):568–583. doi: 10.1093/oxfordjournals.molbev.a040517. [DOI] [PubMed] [Google Scholar]
  24. Pearson W. R. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 1990;183:63–98. doi: 10.1016/0076-6879(90)83007-v. [DOI] [PubMed] [Google Scholar]
  25. Rechsteiner M., Hoffman L., Dubiel W. The multicatalytic and 26 S proteases. J Biol Chem. 1993 Mar 25;268(9):6065–6068. [PubMed] [Google Scholar]
  26. Rooman M. J., Wodak S. J. Identification of predictive sequence motifs limited by protein structure data base size. Nature. 1988 Sep 1;335(6185):45–49. doi: 10.1038/335045a0. [DOI] [PubMed] [Google Scholar]
  27. Schnall R., Mannhaupt G., Stucka R., Tauer R., Ehnle S., Schwarzlose C., Vetter I., Feldmann H. Identification of a set of yeast genes coding for a novel family of putative ATPases with high similarity to constituents of the 26S protease complex. Yeast. 1994 Sep;10(9):1141–1155. doi: 10.1002/yea.320100903. [DOI] [PubMed] [Google Scholar]
  28. Sun D., Sathyanarayana U. G., Johnston S. A., Schwartz L. M. A member of the phylogenetically conserved CAD family of transcriptional regulators is dramatically up-regulated during the programmed cell death of skeletal muscle in the tobacco hawkmoth Manduca sexta. Dev Biol. 1996 Feb 1;173(2):499–509. doi: 10.1006/dbio.1996.0043. [DOI] [PubMed] [Google Scholar]
  29. Swaffield J. C., Bromberg J. F., Johnston S. A. Alterations in a yeast protein resembling HIV Tat-binding protein relieve requirement for an acidic activation domain in GAL4. Nature. 1992 Jun 25;357(6380):698–700. doi: 10.1038/357698a0. [DOI] [PubMed] [Google Scholar]
  30. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Walker J. E., Saraste M., Runswick M. J., Gay N. J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982;1(8):945–951. doi: 10.1002/j.1460-2075.1982.tb01276.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. West M. W., Hecht M. H. Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins. Protein Sci. 1995 Oct;4(10):2032–2039. doi: 10.1002/pro.5560041008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Whiteheart S. W., Rossnagel K., Buhrow S. A., Brunner M., Jaenicke R., Rothman J. E. N-ethylmaleimide-sensitive fusion protein: a trimeric ATPase whose hydrolysis of ATP is required for membrane fusion. J Cell Biol. 1994 Aug;126(4):945–954. doi: 10.1083/jcb.126.4.945. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Wilson A. C., Carlson S. S., White T. J. Biochemical evolution. Annu Rev Biochem. 1977;46:573–639. doi: 10.1146/annurev.bi.46.070177.003041. [DOI] [PubMed] [Google Scholar]
  35. Wilson D. W., Wilcox C. A., Flynn G. C., Chen E., Kuang W. J., Henzel W. J., Block M. R., Ullrich A., Rothman J. E. A fusion protein required for vesicle-mediated transport in both mammalian cells and yeast. Nature. 1989 Jun 1;339(6223):355–359. doi: 10.1038/339355a0. [DOI] [PubMed] [Google Scholar]

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