|Gene:||lon||Accession Numbers: EG10542 (MetaCyc), b0439, ECK0433|
Synonyms: capR, deg, dir, lopA, muc, Lon protease
Species: Escherichia coli K-12 substr. MG1655
Subunit composition of DNA-binding, ATP-dependent protease La = [Lon]4
Lon is an ATP-dependent protease responsible for degradation of misfolded proteins as well as a number of rapidly degraded regulatory proteins. Key regulatory proteins that are Lon substrates include the cell division regulator SulA [Schoemaker84, Higashitani97], the capsule synthesis regulator RcsA [TorresCabassa87] and possibly TER components involved in blocking septation sites during the SOS response [Dopazo87]. Lon is required for degradation of misfolded proteins and the prevention of aggregate formation [Chung81, Ryzhavskaia, Laskowska96]. In the absence of Lon function, aggregation triples [Rosen02]. At least some of this degradation of misfolded proteins depends on the chaperone DnaK [Sherman92].
Lon also degrades the lamba phage N and Xis proteins, with degradation of the latter promoting lysogeny over lysis [Maurizi87, Leffers98]. Other substrates included HU1 in the absence of its partner HU2, HemA and DAM methylase [Bonnefoy89, Wang99d, Calmann03].
Lon degrades the antitoxin protein in many toxin/antitoxin protein pairs, including both plasmid and chromosomal versions. Lon proteolysis of the antitoxin protein in plasmid-encoded pairs is required for plasmid maintenance, as the antitoxin has a shorter half life in lon+ cells than the toxin, thus requiring the continued presence of the plasmid for cell survival. Plasmid-encoded antitoxin substrates include CcdA from F plasmid, relBP307 and PasA [Van96a, Van94a, Gronlund99, Smith98a]. Lon proteolyzes chromosomal toxin/antoxin pairs as well, including RelB and YoeB [Christensen01, Christensen04]. This degradation of chromosomal pairs may regulate part of the starvation stress response, as the breakdown of RelB leaves RelE, which suppresses translation [Christensen01]. Starvation-induced transcription of chpA also depends on Lon [Christensen03a].
Lon is an ATP-dependent protease with chymotrypsin-like specificity based on a Serine (679)-Lysine (722) dyad [Charette81, Waxman85, Botos04, Nishii05]. Lon has one proteolytic and four ATP-binding sites, two high affinity, the other two low affinity [Chin88, Menon87]. Detailed kinetic analysis shows that the two types of ATP sites use ATP at different rates as well [Vineyard06]. Lon's protease function depends on its ATPase activity; both require Mg2+, two ATP molecules are used per peptide bond hydrolyzed and loss of ATPase functions leads to concomitant loss of peptidase function [Menon87, Menon87a, Fischer94, Waxman82a]. ATPase activity continues in mutants that are unable to proteolyze [Pohl76]. Though its ATPase activity is required for protein degradation, Lon is capable of breaking down small peptides in the absence of ATP or ATPase function [Goldberg85, Rasulova98]. The isolated ATPase domain undergoes conformational change in response to ADP and ATP binding [Vasilyeva02].
Lon has an independent protein-binding domain in addition to its proteolytic domain. This domain binds unfolded proteins [Chin88]. Protein binding substantially stimulates peptide degradation and ATPase activity, the latter even in mutants incapable of peptidase function [Waxman86, Pohl76].
Lon binds DNA via its DNA-binding domain [Charette81, Chin88]. Addition of DNA, especially denatured DNA, stimulates substrate proteolysis in vitro, as well as stimulating ATPase activity even in the absence of substrate [Chung82, Charette84]. Lon may have specificity for promoter regions, explaining how it targets regulatory proteins [Fu97].
Lon can form a complex with inorganic polyphosphate, allowing subsequent degradation of ribosomal proteins, including S2, L9 and L13 [Kuroda01]. Lon's DNA-binding domain binds polyphosphate with greater affinity than DNA [Nomura04]. Lon complexed with polyphosphate may be an octamer instead of a tetramer [Nishii05].
lon is one of a network of 93 genes believed to play a role in promoting the stress-induced mutagenesis (SIM) response of E. coli K-12 [Al12].
|Map Position: [458,112 -> 460,466]|
Molecular Weight of Polypeptide: 87.438 kD (from nucleotide sequence)
Unification Links: ASAP:ABE-0001521 , CGSC:547 , DIP:DIP-35845N , EchoBASE:EB0537 , EcoGene:EG10542 , EcoliWiki:b0439 , EcoO157Cyc:LON-MONOMER , Mint:MINT-1224190 , ModBase:P0A9M0 , OU-Microarray:b0439 , PortEco:lon , PR:PRO_000023108 , Pride:P0A9M0 , Protein Model Portal:P0A9M0 , RefSeq:NP_414973 , RegulonDB:EG10542 , SMR:P0A9M0 , String:511145.b0439 , UniProt:P0A9M0
Relationship Links: InterPro:IN-FAMILY:IPR003111 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR003959 , InterPro:IN-FAMILY:IPR004815 , InterPro:IN-FAMILY:IPR008268 , InterPro:IN-FAMILY:IPR008269 , InterPro:IN-FAMILY:IPR014721 , InterPro:IN-FAMILY:IPR015947 , InterPro:IN-FAMILY:IPR020568 , InterPro:IN-FAMILY:IPR027065 , InterPro:IN-FAMILY:IPR027417 , InterPro:IN-FAMILY:IPR027543 , Panther:IN-FAMILY:PTHR10046 , PDB:Structure:1QZM , PDB:Structure:1RR9 , PDB:Structure:1RRE , PDB:Structure:2ANE , PDB:Structure:3LJC , Pfam:IN-FAMILY:PF00004 , Pfam:IN-FAMILY:PF02190 , Pfam:IN-FAMILY:PF05362 , Prosite:IN-FAMILY:PS01046 , Smart:IN-FAMILY:SM00382 , Smart:IN-FAMILY:SM00464
|Biological Process:||GO:0006508 - proteolysis
[UniProtGOA11a, GOA01a, Charette81]
GO:0009408 - response to heat [Chuang93]
GO:0006515 - misfolded or incompletely synthesized protein catabolic process [GOA06, Gaudet10]
GO:0030163 - protein catabolic process [GOA01a]
GO:0033554 - cellular response to stress [GOA06]
|Molecular Function:||GO:0003677 - DNA binding
GO:0004176 - ATP-dependent peptidase activity [GOA06, GOA01a, Gaudet10, Rasulova98, Charette81]
GO:0004252 - serine-type endopeptidase activity [GOA06, GOA01a, Rotanova04]
GO:0005515 - protein binding [Redelberger13]
GO:0008233 - peptidase activity [UniProtGOA11a, Rasulova98]
GO:0016887 - ATPase activity [Charette81]
GO:0000166 - nucleotide binding [UniProtGOA11a]
GO:0005524 - ATP binding [UniProtGOA11a, GOA06, GOA01a]
GO:0008236 - serine-type peptidase activity [UniProtGOA11a]
GO:0016787 - hydrolase activity [UniProtGOA11a]
GO:0043565 - sequence-specific DNA binding [GOA06, GOA01a]
|Cellular Component:||GO:0005737 - cytoplasm
[UniProtGOA11, UniProtGOA11a, GOA06, Gaudet10, Fu97]
GO:0005829 - cytosol [DiazMejia09, Ishihama08, LopezCampistrou05]
|MultiFun Terms:||cell processes → cell division|
|extrachromosomal → plasmid related|
|extrachromosomal → prophage genes and phage related functions|
|information transfer → protein related → turnover, degradation|
|metabolism → degradation of macromolecules → proteins/peptides/glycopeptides|
|regulation → type of regulation → posttranscriptional → proteases, cleavage of compounds|
Enzymatic reaction of: serine protease (DNA-binding, ATP-dependent protease La)
EC Number: 188.8.131.52
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.
The reaction is physiologically favored in the direction shown.
This is a serine protease activity with chymotrypsin-like specificity [Charette81, Waxman85, Botos04]. Peptide hydrolysis is ATP independent in vitro, but protein degradation is ATP dependent, requiring 2 ATP per peptide bond hydrolyzed [Menon87a].
|Chain||2 -> 784|
|Conserved-Region||10 -> 201|
|Protein-Segment||211 -> 219|
|Protein-Segment||240 -> 252|
|Protein-Segment||255 -> 270|
|Sequence-Conflict||264 -> 317|
|Nucleotide-Phosphate-Binding-Region||356 -> 363|
|Sequence-Conflict||539 -> 563|
|Sequence-Conflict||779 -> 784|
10/20/97 Gene b0439 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10542; confirmed by SwissProt match.
Al12: Al Mamun AA, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM (2012). "Identity and function of a large gene network underlying mutagenic repair of DNA breaks." Science 338(6112);1344-8. PMID: 23224554
Amerik88: Amerik AIu, Chistiakov LG, Ostroumova NI, Gurevich AI, Antonov VK (1988). "[Cloning, expression and structure of the functionally active shortened lon gene in Escherichia coli]." Bioorg Khim 14(3);408-11. PMID: 3289547
Botos04: Botos I, Melnikov EE, Cherry S, Tropea JE, Khalatova AG, Rasulova F, Dauter Z, Maurizi MR, Rotanova TV, Wlodawer A, Gustchina A (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(9);8140-8. PMID: 14665623
Charette81: Charette MF, Henderson GW, Markovitz A (1981). "ATP hydrolysis-dependent protease activity of the lon (capR) protein of Escherichia coli K-12." Proc Natl Acad Sci U S A 78(8);4728-32. PMID: 6458036
Chin88: Chin DT, Goff SA, Webster T, Smith T, Goldberg AL (1988). "Sequence of the lon gene in Escherichia coli. A heat-shock gene which encodes the ATP-dependent protease La." J Biol Chem 263(24);11718-28. PMID: 3042779
Christensen01: Christensen SK, Mikkelsen M, Pedersen K, Gerdes K (2001). "RelE, a global inhibitor of translation, is activated during nutritional stress." Proc Natl Acad Sci U S A 98(25);14328-33. PMID: 11717402
Christensen03a: Christensen SK, Pedersen K, Hansen FG, Gerdes K (2003). "Toxin-antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA." J Mol Biol 332(4);809-19. PMID: 12972253
Christensen04: Christensen SK, Maenhaut-Michel G, Mine N, Gottesman S, Gerdes K, Van Melderen L (2004). "Overproduction of the Lon protease triggers inhibition of translation in Escherichia coli: involvement of the yefM-yoeB toxin-antitoxin system." Mol Microbiol 51(6);1705-17. PMID: 15009896
Chung82: Chung CH, Goldberg AL (1982). "DNA stimulates ATP-dependent proteolysis and protein-dependent ATPase activity of protease La from Escherichia coli." Proc Natl Acad Sci U S A 79(3);795-9. PMID: 6461007
DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114
Dopazo87: Dopazo A, Tormo A, Aldea M, Vicente M (1987). "Structural inhibition and reactivation of Escherichia coli septation by elements of the SOS and TER pathways." J Bacteriol 169(4);1772-6. PMID: 3031022
Fischer93a: Fischer H, Glockshuber R (1993). "ATP hydrolysis is not stoichiometrically linked with proteolysis in the ATP-dependent protease La from Escherichia coli." J Biol Chem 268(30);22502-7. PMID: 8226758
Fischer94: Fischer H, Glockshuber R (1994). "A point mutation within the ATP-binding site inactivates both catalytic functions of the ATP-dependent protease La (Lon) from Escherichia coli." FEBS Lett 356(1);101-3. PMID: 7988699
Higashitani97: Higashitani A, Ishii Y, Kato Y, Koriuchi K (1997). "Functional dissection of a cell-division inhibitor, SulA, of Escherichia coli and its negative regulation by Lon." Mol Gen Genet 254(4);351-7. PMID: 9180687
Kuroda01: Kuroda A, Nomura K, Ohtomo R, Kato J, Ikeda T, Takiguchi N, Ohtake H, Kornberg A (2001). "Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli." Science 293(5530);705-8. PMID: 11474114
Laskowska96: Laskowska E, Kuczynska-Wisnik D, Skorko-Glonek J, Taylor A (1996). "Degradation by proteases Lon, Clp and HtrA, of Escherichia coli proteins aggregated in vivo by heat shock; HtrA protease action in vivo and in vitro." Mol Microbiol 22(3);555-71. PMID: 8939438
LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532
Nishii05: Nishii W, Suzuki T, Nakada M, Kim YT, Muramatsu T, Takahashi K (2005). "Cleavage mechanism of ATP-dependent Lon protease toward ribosomal S2 protein." FEBS Lett 579(30);6846-50. PMID: 16337203
Nishii15: Nishii W, Kukimoto-Niino M, Terada T, Shirouzu M, Muramatsu T, Kojima M, Kihara H, Yokoyama S (2015). "A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis." Nat Chem Biol 11(1);46-51. PMID: 25383757
Nomura04: Nomura K, Kato J, Takiguchi N, Ohtake H, Kuroda A (2004). "Effects of inorganic polyphosphate on the proteolytic and DNA-binding activities of Lon in Escherichia coli." J Biol Chem 279(33);34406-10. PMID: 15187082
Rasulova98: Rasulova FS, Dergousova NI, Starkova NN, Melnikov EE, Rumsh LD, Ginodman LM, Rotanova TV (1998). "The isolated proteolytic domain of Escherichia coli ATP-dependent protease Lon exhibits the peptidase activity." FEBS Lett 432(3);179-81. PMID: 9720920
Rotanova04: Rotanova TV, Melnikov EE, Khalatova AG, Makhovskaya OV, Botos I, Wlodawer A, Gustchina A (2004). "Classification of ATP-dependent proteases Lon and comparison of the active sites of their proteolytic domains." Eur J Biochem 271(23-24);4865-71. PMID: 15606774
Ryzhavskaia: Ryzhavskaia AS, Kaidalova NV, Anukhin IuM, Kliachko EV, Livshits VA "[Stability of normal, abnormal and recombinant proteins in Escherichia coli strains deficient for intracellular proteinase La--the product of the lon gene]." Mol Biol (Mosk) 22(1);201-8. PMID: 3287135
Schoemaker84: Schoemaker JM, Gayda RC, Markovitz A (1984). "Regulation of cell division in Escherichia coli: SOS induction and cellular location of the sulA protein, a key to lon-associated filamentation and death." J Bacteriol 158(2);551-61. PMID: 6327610
Smith98a: Smith AS, Rawlings DE (1998). "Efficiency of the pTF-FC2 pas poison-antidote stability system in Escherichia coli is affected by the host strain, and antidote degradation requires the lon protease." J Bacteriol 180(20);5458-62. PMID: 9765581
Starkova98: Starkova NN, Koroleva EP, Rumsh LD, Ginodman LM, Rotanova TV (1998). "Mutations in the proteolytic domain of Escherichia coli protease Lon impair the ATPase activity of the enzyme." FEBS Lett 422(2);218-20. PMID: 9490010
Van94a: Van Melderen L, Bernard P, Couturier M (1994). "Lon-dependent proteolysis of CcdA is the key control for activation of CcdB in plasmid-free segregant bacteria." Mol Microbiol 11(6);1151-7. PMID: 8022284
Van96a: Van Melderen L, Thi MH, Lecchi P, Gottesman S, Couturier M, Maurizi MR (1996). "ATP-dependent degradation of CcdA by Lon protease. Effects of secondary structure and heterologous subunit interactions." J Biol Chem 271(44);27730-8. PMID: 8910366
Vasilyeva02: Vasilyeva OV, Kolygo KB, Leonova YF, Potapenko NA, Ovchinnikova TV (2002). "Domain structure and ATP-induced conformational changes in Escherichia coli protease Lon revealed by limited proteolysis and autolysis." FEBS Lett 526(1-3);66-70. PMID: 12208506
Vineyard06: Vineyard D, Zhang X, Lee I (2006). "Transient kinetic experiments demonstrate the existence of a unique catalytic enzyme form in the peptide-stimulated ATPase mechanism of Escherichia coli Lon protease." Biochemistry 45(38);11432-43. PMID: 16981703
Wang99d: Wang L, Elliott M, Elliott T (1999). "Conditional stability of the HemA protein (glutamyl-tRNA reductase) regulates heme biosynthesis in Salmonella typhimurium." J Bacteriol 181(4);1211-9. PMID: 9973348
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