A lon-like protease with no ATP-powered unfolding activity

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Liao, Jiahn Haur ^a   Kuo, Chiao I ^a   Huang, Ya Yi ^b   Lin, Yu Ching ^a   Lin, Yen Chen ^c   Yang, Chen Yui ^d   Wu, Wan Ling ^d   Chang, Wei Hau ^e   Liaw, Yen Chywan ^c   Lin, Li Hua ^b   Chang, Chung I ^a,d   Wu, Shih Hsiung ^a,d  

^a INSTITUTE OF BIOLOGICAL CHEMISTRY   (Taiwan)

^b BIODIVERSITY RESEARCH CENTER   (Taiwan)

^c INSTITUTE OF MOLECULAR BIOLOGY   (Taiwan)

^d NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^e INSTITUTE OF CHEMISTRY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

20S PROTEASOME CORE PARTICLE; ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATE; ALPHA CASEIN; ALPHA S1 CASEIN; ALPHA S2 CASEIN; ENDOPEPTIDASE LA; LON LIKE PROTEASE; MAGNESIUM ION; PROTEASOME; PROTEIN LONA; PROTEIN LONB; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYMATIC DEGRADATION; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME BINDING; MEIOTHERMUS TAIWANENSIS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PROTEIN ASSEMBLY; PROTEIN CLEAVAGE; PROTEIN DEGRADATION; PROTEIN UNFOLDING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; THERMOPHILIC BACTERIUM;

ADENOSINE TRIPHOSPHATASES; AMINO ACID SEQUENCE; DEINOCOCCUS; ENZYME ACTIVATION; HYDROLYSIS; MAGNESIUM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEOTIDES; PROTEASE LA; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN UNFOLDING; SEQUENCE ALIGNMENT;

ARCHAEA; MEIOTHERMUS TAIWANENSIS;

EID: 84863652343     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040226     Document Type: Article

References (41)

1. Sauer RT, Baker TA, (2011) AAA+ proteases: ATP-fueled machines of protein destruction. Ann. Review Biochem. 80, 587-612.
2. Neuwald AF, Aravind L, Spouge JL, Koonin EV, (1999) AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 9, 27-43.
3. Tsilibaris V, Maenhaut-Michel G, Van Melderen L, (2006) Biological roles of the Lon ATP-dependent protease. Res. Microbiol. 157, 701-713.
4. Goldberg AL, Moerschell RP, Chung CH, Maurizi MR, (1994) ATP-dependent protease La (lon) from Escherichia coli. Methods Enzymol. 244, 350-375.
5. Amerik A, Antonov VK, Gorbalenya AE, Kotova SA, Rotanova TV, et al. (1991) Site-directed mutagenesis of La protease. A catalytically active serine residue. FEBS. Lett. 287, 211-214.
6. Rotanova TV, Melnikov EE, Khalatova AG, Makhovskaya OV, Botos I, et al. (2004) Classification of ATP-dependent proteases Lon and comparison of the active sites of their proteolytic domains. Eur. J. Biochem. 271, 4865-4871.
7. Fukui T, Eguchi T, Atomi H, Imanaka T, (2002) A membrane-bound archaeal Lon protease displays ATP-independent proteolytic activity towards unfolded proteins and ATP-dependent activity for folded proteins. J. Bacteriol. 184, 3689-3698.
8. Ward DE, Shockley KR, Chang LS, Levy RD, Michel JK, et al. (2002) Proteolysis in hyperthermophilic microorganisms. Archaea 1, 63-74.
9. Maehara T, Hoshino T, Nakamura A, (2008) Characterization of three putative Lon proteases of Thermus thermophilus HB27 and use of their defective mutants as hosts for production of heterologous proteins. Extremophiles 12, 285-296.
10. Chen MY, Lin GH, Lin YT, Tsay SS, (2002) Meiothermus taiwanensis sp. nov., a novel filamentous, thermophilic species isolated in Taiwan. Int. J. Syst. Evol. Microbiol. 52, 1647-1654.
11. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31, 3497-3500.
12. Notredame C, Higgins DG, Heringa J, (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217 doi:10.1006/jmbi.2000.4042.
13. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
14. Botos I, Melnikov EE, Cherry S, Kozlov S, Makhovskaya OV, et al. (2005) Atomic-resolution crystal structure of the proteolytic domain of Archaeoglobus fulgidus lon reveals the conformational variability in the active sites of lon proteases. J. Mol. Biol. 351, 144-157.
15. Botos I, Melnikov EE, Cherry S, Tropea JE, Khalatova AG, et al. (2004) The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site. J. Biol. Chem. 279, 8140-8148.
16. Duman RE, Löwe J, (2010) Crystal Structures of Bacillus subtilis Lon Protease. J. Mol. Biol. 401, 653-670.
17. García-Nafría J, Ondrovičová G, Blagova E, Levdikov VM, Bauer JA, et al. (2010) Structure of the catalytic domain of the human mitochondrial Lon protease: Proposed relation of oligomer formation and activity. Protein Science 19, 987-999.
18. Im YJ, Na Y, Kang GB, Rho SH, Kim MK, et al. (2004) The active site of a lon protease from Methanococcus jannaschii distinctly differs from the canonical catalytic Dyad of Lon proteases. J. Biol. Chem. 279, 53451-53457.
19. Cha SS, An YJ, Lee CR, Lee HS, Kim YG, et al. (2010) Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber. EMBO J. 29, 3520-3530.
20. Park SC, Jia B, Yang JK, Van DL, Shao YG, et al. (2006) Oligomeric structure of the ATP-dependent protease La (Lon) of Escherichia coli. Mol. Cells 21, 129-134.
21. Lee AY, Hsu CH, Wu SH, (2004) Functional domains of Brevibacillus thermoruber lon protease for oligomerization and DNA binding: role of N-terminal and sensor and substrate discrimination domains. J. Biol. Chem. 279, 34903-34912.
22. Lee AY, Tsay SS, Chen MY, Wu SH, (2004) Identification of a gene encoding Lon protease from Brevibacillus thermoruber WR-249 and biochemical characterization of its thermostable recombinant enzyme. Eur. J. Biochem. 271, 834-844.
23. Taylor JS, Vigneron DB, Murphy-Boesch J, Nelson SJ, Kessler HB, et al. (1991) Free magnesium levels in normal human brain and brain tumors: 31P chemical-shift imaging measurements at 1.5 T. Proc. Natl. Acad. Sci. U S A. 88, 6810-6814.
24. Hersch GL, Burton RE, Bolon DN, Baker TA, Sauer RT, (2005) Asymmetric interactions of ATP with the AAA+ ClpX6 unfoldase: allosteric control of a protein machine. Cell 121, 1017-1027.
25. Horwitz AA, Navon A, Groll M, Smith DM, Reis C, et al. (2007) ATP-induced structural transitions in PAN, the proteasome-regulatory ATPase complex in Archaea. J. Biol. Chem. 282, 22921-22929.
26. Yakamavich JA, Baker TA, Sauer RT, (2008) Asymmetric nucleotide transactions of the HslUV protease. J. Mol. Biol. 380, 946-957.
27. Bochtler M, Hartmann C, Song HK, Bourenkov GP, Bartunik HD, et al. (2000) The structures of HsIU and the ATP-dependent protease HsIU-HsIV. Nature 403, 800-805.
28. Glynn SE, Martin A, Nager AR, Baker TA, Sauer RT, (2009) Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Cell 139, 744-756.
29. Waxman L, Goldberg AL, (1985) Protease La, the lon gene product, cleaves specific fluorogenic peptides in an ATP-dependent reaction. J. Biol. Chem. 260, 12022-12028.
30. Gur E, Sauer RT, (2008) Recognition of misfolded proteins by Lon, a AAA(+) protease. Genes Dev. 22, 2267-2277.
31. Nishii W, Suzuki T, Nakada M, Kim YT, Muramatsu T, et al. (2005) Cleavage mechanism of ATP-dependent Lon protease toward ribosomal S2 protein. FEBS Lett. 579, 6846-6850.
32. Goldberg AL, Waxman L, (1985) The role of ATP hydrolysis in the breakdown of proteins and peptides by protease La from Escherichia coli. J. Biol. Chem. 260, 12029-12034.
33. Liao JH, Lin YC, Hsu J, Lee AY, Chen TA, et al. (2010) Binding and cleavage of E. coli HUbeta by the E. coli Lon protease. Biophys. J. 98, 129-137.
34. Nishii W, Maruyama T, Matsuoka R, Muramatsu T, Takahashi K, (2002) The unique sites in SulA protein preferentially cleaved by ATP-dependent Lon protease from Escherichia coli. Eur J Biochem 269, 451-457.
35. Shringarpure R, Grune T, Davies KJ, (2001) Protein oxidation and 20S proteasome-dependent proteolysis in mammalian cells. Cell Mol. Life Sci. 58, 1442-1450.
36. Gur E, Sauer RT, (2009) Degrons in protein substrates program the speed and operating efficiency of the AAA+ Lon proteolytic machine. Proc. Natl. Acad. Sci. USA. 106, 18503-18508.
37. Geiser M, Cebe R, Drewello D, Schmitz R, (2001) Integration of PCR fragments at any specific site within cloning vectors without the use of restriction enzymes and DNA ligase. BioTechniques 31, 88-90, 92.
38. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
39. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739.
40. Mindell JA, Grigorieff N, (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334-347.
41. Schuck P, (2000) Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys. J.78, 1606-1619.