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Escherichia coli K-12 substr. MG1655 Enzyme: ClpP serine protease



Gene: clpP Accession Numbers: EG10158 (EcoCyc), b0437, ECK0431

Synonyms: lopP, heat shock protein F21.5

Regulation Summary Diagram: ?

Component of:
ClpAXP (summary available)
ClpXP (extended summary available)
ClpAP (extended summary available)

Subunit composition of ClpP serine protease = [ClpP]14

Summary:
ClpP is a serine protease with a chymotrypsin-like activity that is a part of the ClpAP, ClpAPX and ClpXP protease complexes [Arribas93, Wang97a].

The ClpP protease is a tetradecamer, consisting of two heptamers of ClpP subunits stacked head-to-head [Kessel95, Shin96]. ClpP has an axial pore large enough to accept unfolded polypeptide chains, leading into a central cavity that contains fourteen serine protease active sites [Flanagan95, Wang98b]. This ring structure is required for proper protease function [Thompson98]. Serine-111 and histidine-136 are also required for protease function [Maurizi90]. The interface between the two heptameric rings can switch between two different conformations; limiting this switching via crosslinking slows substrate release [Sprangers05].

Translocation of polypeptide substrates into ClpP is directional, with the carboxy-terminus going first [Reid01].

ClpP degrades the antitoxin proteins Phd and MazE from the toxin/antitoxin pairs phd-doc (from plasmid prophage P1) and mazEF (from the rel plasmid). The lysogenically expressed lambda protein lambdarexB inhibits this proteolysis [EngelbergKulka98].

Lambda protein gpW mutants with hydrophobic tails are degraded in a ClpP-dependent manner [Maxwell00].

ClpP is required for normal adaptation to and extended viability in stationary phase, and for growth in SDS [Weichart03, Rajagopal02].

ClpP is a heat shock protein expressed in a sigma 32-dependent manner [Kroh90]. It has a 14-amino acid leader peptide which is cleaved intermolecularly by another ClpP without any requirement for associated ClpA [Maurizi90a, Maurizi90].

Review: [Alexopoulos12]

Gene Citations: [Gottesman93, Li00a]

Locations: cytosol, membrane

Map Position: [455,901 -> 456,524] (9.83 centisomes)
Length: 624 bp / 207 aa

Molecular Weight of Polypeptide: 23.187 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001515 , CGSC:31280 , DIP:DIP-31838N , EchoBASE:EB0156 , EcoGene:EG10158 , EcoliWiki:b0437 , ModBase:P0A6G7 , OU-Microarray:b0437 , PortEco:clpP , PR:PRO_000022298 , Pride:P0A6G7 , Protein Model Portal:P0A6G7 , RefSeq:NP_414971 , RegulonDB:EG10158 , SMR:P0A6G7 , String:511145.b0437 , UniProt:P0A6G7

Relationship Links: InterPro:IN-FAMILY:IPR001907 , InterPro:IN-FAMILY:IPR018215 , InterPro:IN-FAMILY:IPR023562 , Panther:IN-FAMILY:PTHR10381 , PDB:Structure:1TYF , PDB:Structure:1YG6 , PDB:Structure:1YG8 , PDB:Structure:2FZS , PDB:Structure:3HLN , PDB:Structure:3MT6 , Pfam:IN-FAMILY:PF00574 , Prints:IN-FAMILY:PR00127 , Prosite:IN-FAMILY:PS00381 , Prosite:IN-FAMILY:PS00382

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006515 - misfolded or incompletely synthesized protein catabolic process Inferred from experiment [Andresen00]
GO:0009266 - response to temperature stimulus Inferred from experiment [Kroh90]
GO:0009408 - response to heat Inferred from experiment [Chuang93a]
GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01]
GO:0006950 - response to stress Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008236 - serine-type peptidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Arribas93]
GO:0042802 - identical protein binding Inferred from experiment [Hauser14, Rajagopala14, Lasserre06]
GO:0004252 - serine-type endopeptidase activity Inferred by computational analysis [GOA06, GOA01]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: cell processes adaptations temperature extremes
information transfer protein related turnover, degradation
metabolism degradation of macromolecules proteins/peptides/glycopeptides
regulation type of regulation posttranscriptional proteases, cleavage of compounds

Essentiality data for clpP knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Revised 25-May-2011 by Brito D


Enzymatic reaction of: serine protease

EC Number: 3.4.21.92

a protein + H2O <=> a peptide + a peptide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

pH(opt): 7 [BRENDA14, Maurizi94], 7.5 [BRENDA14, Maurizi94]


Subunit of: ClpAXP

Synonyms: ATP-dependent endopeptidase Clp, ATP-dependent protease Clp

Subunit composition of ClpAXP = [(ClpP)14][(ClpA)6][(ClpX)6]
         ClpP serine protease = (ClpP)14 (extended summary available)
         ClpA ATP-dependent protease specificity component and chaperone = (ClpA)6
         ClpX ATP-dependent protease specificity component and chaperone = (ClpX)6 (extended summary available)

Summary:
Hybrid complexes can form in vitro, consisting of a ClpP tetradecamer capped at one end with ClpA and at the other with ClpX. These complexes are translocation competent. Stoichiometry in vivo suggests heterocomplexes may form there, as well [Ortega04].


Enzymatic reaction of: ATP-dependent Clp protease (ClpAXP)

Synonyms: ATP-binding Clp protease, ATP-dependent Clp endopeptidase

EC Number: 3.4.21.92

a protein + H2O <=> a peptide + a peptide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.


Subunit of: ClpXP

Subunit composition of ClpXP = [(ClpP)14][(ClpX)6]2
         ClpP serine protease = (ClpP)14 (extended summary available)
         ClpX ATP-dependent protease specificity component and chaperone = (ClpX)6 (extended summary available)

Summary:
ClpXP is a serine protease complex responsible for the ATP-dependent degradation of a wide range of proteins [Gottesman93, Wojtkowiak93].

ClpXP degrades the altered Mu immunity repressor, Vir. When Vir is present, the normal immunity repressor, Rep, becomes more vulnerable to ClpXP-mediated degradation as well [Welty97]. ClpXP can also degrade MuA, although it does not degrade it all, allowing ClpX to act in its chaperone capacity to assist MuA function [Jones98, MhammediAlaoui94].

ClpXP is partially responsible for degradation of proteins with the SsrA degradation tag, including SsrA-tagged lambda repressor [Bohn02, Gottesman98]. ClpXP degrades stably folded SsrA proteins efficiently, but only poorly degrades proteins bearing SsrA tags artificially attached in the middle of their sequences via cysteine linkages [Kenniston04].

ClpXP can degrade DNA-bound lambda O protein when transcription is possible, otherwise, it is stable [Zylicz98]. ClpXP-mediated degradation of lambda O protein can affect the lysis/lysogeny decision under certain growth conditions [Wojtkowiak93, Czyz01].

ClpXP is also required for degradation of the starvation-induced proteins Dps and sigma S during exponential growth [Stephani03, Schweder96].

Several other ClpXP substrates have been discovered. ClpXP degrades variants of the restriction enzyme EcoKI that have impaired enzymatic function, the mutagenically active protein UmuD' when it is in a heterodimer with unmodified UmuD and the antitoxin Phd from the Doc-Phd toxin/antitoxin pair (from plasmid prophage P1) [ONeill01, Frank96, Lehnherr95].

Putative ClpXP substrates were found by trapping with inactivated ClpP. Potential substrates included some with SsrA-like tails (crl, dksA, fnr, iscR, rplJ, rplU, gcp, pepB, katE, nrdH, tpx, chew, cysA, exbB, acnB, aldA, glpD, glyA, IldD and ycbW), MuA-like carboxy-terminal motifs (paaA, pncB, ribB, ybaQ), novel amino-terminal binding motifs (crl, dksA, fnr, lexA, rpoS, rplE, rplJ, rplK, rplS, rplU, tufB, dps, katE, nrdH, tpx, insH, chew, cysA, gatA, ompA, secA, aceA, atpD, cysD, dada, fabB, gapA, gatY, gatZ, glcB, glyA, iscS, lipA, moaA, pncB, tnaA, udp, ybaQ and ycbW) and no specific binding motifs (rseA, rplN, lon, clpX, dnaK, groEL, ftsZ, iscU, yebO and ygaT) [Flynn03].

SspB binds to SsrA-tagged proteins via its amino-terminal domain and enhances their degradation by ClpXP through carboxy-terminal binding to ClpXP [Levchenko00, Wah03]. SspB alone is sufficient to allow interaction with ClpXP. A protein that has been covalently linked to SspB becomes a ClpXP substrate even in the absence of an SsrA tag [Bolon04]. ClpX and SspB bind to overlapping parts of the SsrA tag, weakening the direct SsrA-ClpX interaction. The SspB-ClpX interaction overcomes this weakening effect [Hersch04]. Trapping experiments based on SspB show that RseA, which is cleaved from the membrane and binds to sigma E as an inhibitor during stress interacts with SspB and is degraded by ClpXP, thus releasing sigma E [Flynn04]. Sigma S degradation by ClpXP requires the adaptor RssB, which binds to Region 2.5 of sigma S, allowing binding of ClpX at the amino-terminus and subsequent degradation by ClpXP [Muffler96, Zhou01a, Studemann03]. Each ClpX hexamer has three SspB binding domains to match up with two ClpXP binding domains per SspB dimer, so only one SspB dimer can function with a given ClpX hexamer at a time [Bolon04a]. UmuD operates in a manner similar to SspB, binding to the ClpX amino-terminus and serving as a substrate tether for UmuD' [Neher03].

ClpXP consists of a ClpP tetradecamer capped at one or both ends by ClpX hexamers [Grimaud98].

Substrates bind to the distal surface of ClpX, and then are passed off to the inner cavity of ClpP to be degraded, in a process that is driven by ATP and modulated by ClpXP protease specificity-enhancing factor [Ortega00, Thibault06]. This process involves both static and dynamic contacts between ClpX and ClpP [Martin07]. The initial ClpX-mediated denaturation of substrate is the rate-limiting step in degradation of a well-folded protein, such as SsrA-tagged GFP [Kim00a]. ClpXP uses mechanical force to unfold its protein substrate. Substrate translocation occurs in phases - a dwell phase when there is no movement followed by a burst phase during which ClpXP almost instantaneously translocates a portion of the substrate [Maillard11, AubinTam11, Sen13].

ClpXP is required for limitation of lambda phage early DNA replication during slow growth [Wegrzyn].

ClpXP is required for acquisition of the genes encoding the restriction enzymes EcoKI and EcoAI by conjugation or transformation [Makovets98].

Despite lambda O initiator protein being a ClpXP substrate, lambda replication does not depend on ClpXP levels [Szalewska94].

Reviews: [Baker12]
Comments: [AlegreCebollada11, Maurizi13]

Credits:
Last-Curated ? 09-Jan-2006 by Shearer A , SRI International


Enzymatic reaction of: protease (ClpXP)

EC Number: 3.4.21.92

a protein + H2O <=> a peptide + a peptide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.


Subunit of: ClpAP

Subunit composition of ClpAP = [(ClpP)14][(ClpA)6]2
         ClpP serine protease = (ClpP)14 (extended summary available)
         ClpA ATP-dependent protease specificity component and chaperone = (ClpA)6

Summary:
ClpAP is a serine protease complex responsible for the ATP-dependent degradation of a number of proteins [Katayama88]. Substrates for ClpAP include the plasmid P1 replication intiator RepA, HemA and a number of carbon starvation proteins [Wickner94, Wang99b, Damerau93]. ClpAP is also one of the proteases responsible for degradation of proteins tagged with the SsrA degradation marker, including tagged lambda repressor and tagged GFP (the latter substrate indicating that ClpAP can unfold stable, native protein in an ATP-dependent manner) [Gottesman98, WeberBan99]. ClpAP degrades a number of substrates that are not degraded by ClpXP [Gottesman93]. ClpAP is also responsible for rapid degradation of N-end rule substrates, which are marked for degradation by the identity of their amino-terminal residue (arginine, lysine, leucine, phenylalanine, tyrosine and tryptophan all mark a protein for N-end rule degradation) [Tobias91].

ClpAP consists of a ClpP tetradecamer capped at one or both ends by ClpA hexamers [Kessel95, Ishikawa]. The formation of this complex requires ATP binding and hydrolysis [Thompson94, Seol95, Maurizi98]. ATP is also required for degradation of larger polypeptide substrates by ClpAP [Thompson94]. ClpAP remains together as a complex through repeated rounds of degradation [Singh99]. ClpAP substrates interact with an allosteric site on ClpA prior to proteolysis by ClpP [Thompson94a].

A putative internal translation site variant of ClpA inhibits the interaction of full-length ClpA with ClpP, preventing formation of ClpAP [Seol94].

ClpS binds to the amino-terminal domain of ClpA, inhibiting degradation of SsrA-tagged proteins and of ClpA but accelerating disaggregation and degradation of heat-aggregated proteins in vitro [Dougan02, Zeth02].

ClpA levels increase during late exponential and early stationary phase, resulting in an increase in ClpAP activity [Katayama90].

ClpAP is required to maintain translation of the DNA protection protein Dps during starvation [Stephani03].


Enzymatic reaction of: ClpAP

EC Number: 3.4.21.92

a protein + H2O <=> a peptide + a peptide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.


Sequence Features

Feature Class Location Citations Comment
Propeptide 1 -> 14
[UniProt10a]
Signal-Sequence 1 -> 14
[Maurizi90a]
 
Chain 15 -> 207
[UniProt09]
UniProt: ATP-dependent Clp protease proteolytic subunit;
Active-Site 111
[UniProt10]
UniProt: Non-Experimental Qualifier: probable;
Active-Site 136
[UniProt10]
UniProt: Non-Experimental Qualifier: probable;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0437 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10158; confirmed by SwissProt match.


References

AlegreCebollada11: Alegre-Cebollada J, Kosuri P, Fernandez JM (2011). "Protease power strokes force proteins to unfold." Cell 145(3);339-40. PMID: 21529709

Alexopoulos12: Alexopoulos JA, Guarne A, Ortega J (2012). "ClpP: a structurally dynamic protease regulated by AAA+ proteins." J Struct Biol 179(2);202-10. PMID: 22595189

Andresen00: Andresen BS, Corydon TJ, Wilsbech M, Bross P, Schroeder LD, Hindkjaer TF, Bolund L, Gregersen N (2000). "Characterization of mouse Clpp protease cDNA, gene, and protein." Mamm Genome 11(4);275-80. PMID: 10754102

Arribas93: Arribas J, Castano JG (1993). "A comparative study of the chymotrypsin-like activity of the rat liver multicatalytic proteinase and the ClpP from Escherichia coli." J Biol Chem 268(28);21165-71. PMID: 8407953

AubinTam11: Aubin-Tam ME, Olivares AO, Sauer RT, Baker TA, Lang MJ (2011). "Single-molecule protein unfolding and translocation by an ATP-fueled proteolytic machine." Cell 145(2);257-67. PMID: 21496645

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Baker12: Baker TA, Sauer RT (2012). "ClpXP, an ATP-powered unfolding and protein-degradation machine." Biochim Biophys Acta 1823(1);15-28. PMID: 21736903

Bohn02: Bohn C, Binet E, Bouloc P (2002). "Screening for stabilization of proteins with a trans-translation signature in Escherichia coli selects for inactivation of the ClpXP protease." Mol Genet Genomics 266(5);827-31. PMID: 11810257

Bolon04: Bolon DN, Grant RA, Baker TA, Sauer RT (2004). "Nucleotide-dependent substrate handoff from the SspB adaptor to the AAA+ ClpXP protease." Mol Cell 16(3);343-50. PMID: 15525508

Bolon04a: Bolon DN, Wah DA, Hersch GL, Baker TA, Sauer RT (2004). "Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery: a protein-design study." Mol Cell 13(3);443-9. PMID: 14967151

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Chuang93a: Chuang SE, Blattner FR (1993). "Characterization of twenty-six new heat shock genes of Escherichia coli." J Bacteriol 175(16);5242-52. PMID: 8349564

Czyz01: Czyz A, Zielke R, Wegrzyn G (2001). "Rapid degradation of bacteriophage lambda O protein by ClpP/ClpX protease influences the lysis-versus-lysogenization decision of the phage under certain growth conditions of the host cells." Arch Virol 146(8);1487-98. PMID: 11676412

Damerau93: Damerau K, St John AC (1993). "Role of Clp protease subunits in degradation of carbon starvation proteins in Escherichia coli." J Bacteriol 175(1);53-63. PMID: 8416909

Dougan02: Dougan DA, Reid BG, Horwich AL, Bukau B (2002). "ClpS, a substrate modulator of the ClpAP machine." Mol Cell 2002;9(3);673-83. PMID: 11931773

EngelbergKulka98: Engelberg-Kulka H, Reches M, Narasimhan S, Schoulaker-Schwarz R, Klemes Y, Aizenman E, Glaser G (1998). "rexB of bacteriophage lambda is an anti-cell death gene." Proc Natl Acad Sci U S A 1998;95(26);15481-6. PMID: 9860994

Flanagan95: Flanagan JM, Wall JS, Capel MS, Schneider DK, Shanklin J (1995). "Scanning transmission electron microscopy and small-angle scattering provide evidence that native Escherichia coli ClpP is a tetradecamer with an axial pore." Biochemistry 34(34);10910-7. PMID: 7662672

Flynn03: Flynn JM, Neher SB, Kim YI, Sauer RT, Baker TA (2003). "Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals." Mol Cell 11(3);671-83. PMID: 12667450

Flynn04: Flynn JM, Levchenko I, Sauer RT, Baker TA (2004). "Modulating substrate choice: the SspB adaptor delivers a regulator of the extracytoplasmic-stress response to the AAA+ protease ClpXP for degradation." Genes Dev 18(18);2292-301. PMID: 15371343

Frank96: Frank EG, Ennis DG, Gonzalez M, Levine AS, Woodgate R (1996). "Regulation of SOS mutagenesis by proteolysis." Proc Natl Acad Sci U S A 93(19);10291-6. PMID: 8816793

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Gottesman93: Gottesman S, Clark WP, de Crecy-Lagard V, Maurizi MR (1993). "ClpX, an alternative subunit for the ATP-dependent Clp protease of Escherichia coli. Sequence and in vivo activities." J Biol Chem 1993;268(30);22618-26. PMID: 8226770

Gottesman98: Gottesman S, Roche E, Zhou Y, Sauer RT (1998). "The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system." Genes Dev 12(9);1338-47. PMID: 9573050

Grimaud98: Grimaud R, Kessel M, Beuron F, Steven AC, Maurizi MR (1998). "Enzymatic and structural similarities between the Escherichia coli ATP-dependent proteases, ClpXP and ClpAP." J Biol Chem 273(20);12476-81. PMID: 9575205

Hauser14: Hauser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P (2014). "A Second-generation Protein-Protein Interaction Network of Helicobacter pylori." Mol Cell Proteomics 13(5);1318-29. PMID: 24627523

Hersch04: Hersch GL, Baker TA, Sauer RT (2004). "SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags." Proc Natl Acad Sci U S A 101(33);12136-41. PMID: 15297609

Ishikawa: Ishikawa T, Maurizi MR, Steven AC "The N-terminal substrate-binding domain of ClpA unfoldase is highly mobile and extends axially from the distal surface of ClpAP protease." J Struct Biol 146(1-2);180-8. PMID: 15037249

Jones98: Jones JM, Welty DJ, Nakai H (1998). "Versatile action of Escherichia coli ClpXP as protease or molecular chaperone for bacteriophage Mu transposition." J Biol Chem 273(1);459-65. PMID: 9417104

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Katayama88: Katayama Y, Gottesman S, Pumphrey J, Rudikoff S, Clark WP, Maurizi MR (1988). "The two-component, ATP-dependent Clp protease of Escherichia coli. Purification, cloning, and mutational analysis of the ATP-binding component." J Biol Chem 263(29);15226-36. PMID: 3049606

Katayama90: Katayama Y, Kasahara A, Kuraishi H, Amano F (1990). "Regulation of activity of an ATP-dependent protease, Clp, by the amount of a subunit, ClpA, in the growth of Escherichia coli cells." J Biochem (Tokyo) 108(1);37-41. PMID: 2121722

Kenniston04: Kenniston JA, Burton RE, Siddiqui SM, Baker TA, Sauer RT "Effects of local protein stability and the geometric position of the substrate degradation tag on the efficiency of ClpXP denaturation and degradation." J Struct Biol 146(1-2) 2004;130-40. PMID: 15037244

Kessel95: Kessel M, Maurizi MR, Kim B, Kocsis E, Trus BL, Singh SK, Steven AC (1995). "Homology in structural organization between E. coli ClpAP protease and the eukaryotic 26 S proteasome." J Mol Biol 250(5);587-94. PMID: 7623377

Kim00a: Kim YI, Burton RE, Burton BM, Sauer RT, Baker TA (2000). "Dynamics of substrate denaturation and translocation by the ClpXP degradation machine." Mol Cell 5(4);639-48. PMID: 10882100

Kroh90: Kroh HE, Simon LD (1990). "The ClpP component of Clp protease is the sigma 32-dependent heat shock protein F21.5." J Bacteriol 172(10);6026-34. PMID: 2211522

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Lehnherr95: Lehnherr H, Yarmolinsky MB (1995). "Addiction protein Phd of plasmid prophage P1 is a substrate of the ClpXP serine protease of Escherichia coli." Proc Natl Acad Sci U S A 92(8);3274-7. PMID: 7724551

Levchenko00: Levchenko I, Seidel M, Sauer RT, Baker TA (2000). "A specificity-enhancing factor for the ClpXP degradation machine." Science 289(5488);2354-6. PMID: 11009422

Li00a: Li C, Tao YP, Simon LD (2000). "Expression of different-size transcripts from the clpP-clpX operon of Escherichia coli during carbon deprivation." J Bacteriol 182(23);6630-7. PMID: 11073905

Maillard11: Maillard RA, Chistol G, Sen M, Righini M, Tan J, Kaiser CM, Hodges C, Martin A, Bustamante C (2011). "ClpX(P) generates mechanical force to unfold and translocate its protein substrates." Cell 145(3);459-69. PMID: 21529717

Makovets98: Makovets S, Titheradge AJ, Murray NE (1998). "ClpX and ClpP are essential for the efficient acquisition of genes specifying type IA and IB restriction systems." Mol Microbiol 28(1);25-35. PMID: 9593294

Martin07: Martin A, Baker TA, Sauer RT (2007). "Distinct static and dynamic interactions control ATPase-peptidase communication in a AAA+ protease." Mol Cell 27(1);41-52. PMID: 17612489

Maurizi13: Maurizi MR, Stan G (2013). "ClpX Shifts into High Gear to Unfold Stable Proteins." Cell 155(3);502-4. PMID: 24243009

Maurizi90: Maurizi MR, Clark WP, Kim SH, Gottesman S (1990). "Clp P represents a unique family of serine proteases." J Biol Chem 265(21);12546-52. PMID: 2197276

Maurizi90a: Maurizi MR, Clark WP, Katayama Y, Rudikoff S, Pumphrey J, Bowers B, Gottesman S (1990). "Sequence and structure of Clp P, the proteolytic component of the ATP-dependent Clp protease of Escherichia coli." J Biol Chem 265(21);12536-45. PMID: 2197275

Maurizi94: Maurizi MR, Thompson MW, Singh SK, Kim SH (1994). "Endopeptidase Clp: ATP-dependent Clp protease from Escherichia coli." Methods Enzymol 244;314-31. PMID: 7845217

Maurizi98: Maurizi MR, Singh SK, Thompson MW, Kessel M, Ginsburg A (1998). "Molecular properties of ClpAP protease of Escherichia coli: ATP-dependent association of ClpA and clpP." Biochemistry 37(21);7778-86. PMID: 9601038

Maxwell00: Maxwell KL, Davidson AR, Murialdo H, Gold M (2000). "Thermodynamic and functional characterization of protein W from bacteriophage lambda. The three C-terminal residues are critical for activity." J Biol Chem 275(25);18879-86. PMID: 10770927

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Other References Related to Gene Regulation

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

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Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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