Characterization of a new AAA+ protein from archaea

Journal of Structural Biology

Volumn 156, Issue 1, 2006, Pages 120-129

  Summer, Heike ^a   Bruderer, Roland ^a   Weber Ban, Eilika ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

AAA+; Archaea; Archaeoglobus fulgidus; ATA; ATPase; Methanogens

Indexed keywords

ARCHAEA TRIPLE A ATPASE; PROTEIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARCHAEOGLOBUS FULGIDUS; ARTICLE; CONCENTRATION (PARAMETERS); ELECTRON MICROSCOPY; ENZYME ACTIVITY; ENZYME STABILITY; HYDROLYSIS; MICHAELIS CONSTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN PURIFICATION; SEDIMENTATION; SEQUENCE HOMOLOGY; TEMPERATURE;

ADENOSINE TRIPHOSPHATASES; ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; ARCHAEOGLOBUS FULGIDUS; CIRCULAR DICHROISM; ENZYME STABILITY; ESCHERICHIA COLI; HYDROLYSIS; KINETICS; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; PHYLOGENY; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TEMPERATURE;

ARCHAEA; ARCHAEOGLOBUS FULGIDUS; ESCHERICHIA COLI;

EID: 33749239789     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2006.01.010     Document Type: Article

References (43)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
2. Benaroudj N., and Goldberg A.L. PAN, the proteasome-activating nucleotidase from archaebacteria, is a protein-unfolding molecular chaperone. Nat. Cell Biol. 2 (2000) 833-839
3. Besche H., Tamura N., Tamura T., and Zwickl P. Mutational analysis of conserved AAA+ residues in the archaeal Lon protease from Thermoplasma acidophilum. FEBS Lett. 574 (2004) 161-166
4. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., and Thompson J.D. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31 (2003) 3497-3500
5. Coles M., Diercks T., Liermann J., Groger A., Rockel B., Baumeister W., Koretke K.K., Lupas A., Peters J., and Kessler H. The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element. Curr. Biol. 9 (1999) 1158-1168
6. Davey M.J., Jeruzalmi D., Kuriyan J., and O'Donnell M. Motors and switches: AAA+ machines within the replisome. Nat. Rev. Mol. Cell Biol. 3 (2002) 826-835
7. Demeler B., and Saber H. Determination of molecular parameters by fitting sedimentation data to finite-element solutions of the Lamm equation. Biophys. J. 74 (1998) 444-454
8. Dougan D.A., Mogk A., Zeth K., Turgay K., and Bukau B. AAA+ proteins and substrate recognition, it all depends on their partner in crime. FEBS Lett. 529 (2002) 6-10
9. Dougan D.A., Weber-Ban E., and Bukau B. Targeted delivery of an ssrA-tagged substrate by the adaptor protein SspB to its cognate AAA+ protein ClpX. Mol. Cell. 12 (2003) 373-380
10. Elsasser S., and Finley D. Delivery of ubiquitinated substrates to protein-unfolding machines. Nat. Cell Biol. 7 (2005) 742-749
11. Erdmann R., Wiebel F.F., Flessau A., Rytka J., Beyer A., Frohlich K.U., and Kunau W.H. PAS1, a yeast gene required for peroxisome biogenesis, encodes a member of a novel family of putative ATPases. Cell 64 (1991) 499-510
12. Frickey, T., Lupas, A.., 2004. J. Struct. Biol. 146, 2-10.
13. Frohlich K.U., Fries H.W., Peters J.M., and 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 1253 (1995) 25-32
14. Gerega, A., Rockel, B., Peters, J., Tamura, T., Baumeister, W., Zwickl, P.., 2005. VAT, the thermoplasma homolog of mammalian p97/VCP, is an N domain regulated protein unfoldase. J. Biol. Chem.
15. Gouet P., Courcelle E., Stuart D.I., and Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15 (1999) 305-308
16. Groll M., Brandstetter H., Bartunik H., Bourenkow G., and Huber R. Investigations on the maturation and regulation of archaebacterial proteasomes. J. Mol. Biol. 327 (2003) 75-83
17. Guo F., Maurizi M.R., Esser L., and Xia D. Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease. J. Biol. Chem. 277 (2002) 46743-46752
18. van Heel M., Harauz G., Orlova E.V., Schmidt R., and Schatz M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 116 (1996) 17-24
19. Henikoff S., and Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89 (1992) 10915-10919
20. Iyer L.M., Leipe D.D., Koonin E.V., and Aravind L. Evolutionary history and higher order classification of AAA+ ATPases. J. Struct Biol. 146 (2004) 11-31
21. Kihara A., Akiyama Y., and Ito K. Dislocation of membrane proteins in FtsH-mediated proteolysis. EMBO J. 18 (1999) 2970-2981
22. Langer T., Kaser M., Klanner C., and Leonhard K. AAA proteases of mitochondria: quality control of membrane proteins and regulatory functions during mitochondrial biogenesis. Biochem. Soc. Trans. 29 (2001) 431-436
23. Lanzetta P.A., Alvarez L.J., Reinach P.S., and Candia O.A. An improved assay for nanomole amounts of inorganic phosphate. Anal. Biochem. 100 (1979) 95-97
24. Lord J.M., Ceriotti A., and Roberts L.M. ER dislocation: Cdc48p/p97 gets into the AAAct. Curr. Biol. 12 (2002) R182-R184
25. Lupas A.N., and Martin J. AAA proteins. Curr. Opin. Struct. Biol. 12 (2002) 746-753
26. Maupin-Furlow J.A., Gil M.A., Karadzic I.M., Kirkland P.A., and Reuter C.J. Proteasomes: perspectives from the Archaea. Front. Biosci. 9 (2004) 1743-1758
27. Maupin-Furlow J.A., Kaczowka S.J., Ou M.S., and Wilson H.L. Archaeal proteasomes: proteolytic nanocompartments of the cell. Adv. Appl. Microbiol. 50 (2001) 279-338
28. Maupin-Furlow J.A., Wilson H.L., Kaczowka S.J., and Ou M.S. Proteasomes in the archaea: from structure to function. Front. Biosci. 5 (2000) D837-D865
29. Maurizi M.R., and Li C.C. AAA proteins: in search of a common molecular basis. International Meeting on Cellular Functions of AAA Proteins. EMBO Rep. 2 (2001) 980-985
30. Maurizi M.R., and Xia D. Protein binding and disruption by Clp/Hsp100 chaperones. Structure (Camb) 12 (2004) 175-183
31. Notredame C., Higgins D.G., and Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302 (2000) 205-217
32. Ogura T., and Wilkinson A.J. AAA+ superfamily ATPases: common structure-diverse function. Genes Cells 6 (2001) 575-597
33. Pace C.N., Hebert E.J., Shaw K.L., Schell D., Both V., Krajcikova D., Sevcik J., Wilson K.S., Dauter Z., Hartley R.W., and Grimsley G.R. Conformational stability and thermodynamics of folding of ribonucleases Sa, Sa2 and Sa3. J. Mol. Biol. 279 (1998) 271-286
34. Pamnani V., Tamura T., Lupas A., Peters J., Cejka Z., Ashraf W., and Baumeister W. Cloning, sequencing and expression of VAT, a CDC48/p97 ATPase homologue from the archaeon Thermoplasma acidophilum. FEBS Lett. 404 (1997) 263-268
35. Peters J.M., Harris J.R., Lustig A., Muller S., Engel A., Volker S., and Franke W.W. Ubiquitous soluble Mg(2+)-ATPase complex. A structural study. J. Mol. Biol. 223 (1992) 557-571
36. Schuck P. A model for sedimentation in inhomogeneous media. I. Dynamic density gradients from sedimenting co-solutes. Biophys. Chem. 108 (2004) 187-200
37. Shi J., Blundell T.L., and Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310 (2001) 243-257
38. Tatusov R.L., Galperin M.Y., Natale D.A., and Koonin E.V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28 (2000) 33-36
39. Tatusov R.L., Natale D.A., Garkavtsev I.V., Tatusova T.A., Shankavaram U.T., Rao B.S., Kiryutin B., Galperin M.Y., Fedorova N.D., and Koonin E.V. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29 (2001) 22-28
40. Wang Q., Song C., and Li C.C. Molecular perspectives on p97-VCP: progress in understanding its structure and diverse biological functions. J. Struct Biol. 146 (2004) 44-57
41. Wickner S., Maurizi M.R., and Gottesman S. Posttranslational quality control: folding, refolding, and degrading proteins. Science 286 (1999) 1888-1893
42. Ye Y., Meyer H.H., and Rapoport T.A. The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol. Nature 414 (2001) 652-656
43. Zwickl P., Ng D., Woo K.M., Klenk H.P., and Goldberg A.L. An archaebacterial ATPase, homologous to ATPases in the eukaryotic 26 S proteasome, activates protein breakdown by 20 S proteasomes. J. Biol. Chem. 274 (1999) 26008-26014