Escherichia coli K-12 substr. MG1655 Enzyme: 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)

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]. When visualised at the single molecule level, the unfolding and translocation of substrate by ClpXP occurs in physical steps of varying size (1-4nm) which lack defined order [Cordova14]

ClpXP is required for limitation of lambda phage early DNA replication during slow growth [Wegrzyn00].

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, Russell14]|

Gene-Reaction Schematic

Expand/Contract the Schematic connections:

Gene-Reaction Schematic

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

Enzymatic reaction of: protease (ClpXP)

Inferred from experiment

EC Number:

a protein + H2O → a peptide + a peptide

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Component enzyme of ClpXP : ClpP serine protease

Synonyms: lopP, heat shock protein F21.5

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

Locations: cytosol, membrane

Subunit composition of ClpP serine protease = [ClpP]14

Map Position: [456,677 -> 457,300] (9.84 centisomes, 35°)
Length: 624 bp / 207 aa

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

GO Terms:
Biological Process:
Inferred from experimentGO:0006515 - misfolded or incompletely synthesized protein catabolic process [Andresen00]
Inferred from experimentGO:0009266 - response to temperature stimulus [Kroh90]
Inferred from experimentGO:0009408 - response to heat [Chuang93]
Inferred from experimentGO:0010498 - proteasomal protein catabolic process [Gottesman98]
Inferred by computational analysisGO:0006508 - proteolysis [UniProtGOA11a, GOA06, GOA01a]
Molecular Function:
Inferred from experimentGO:0004176 - ATP-dependent peptidase activity [Gottesman98]
Inferred from experimentGO:0005515 - protein binding [Lee10, Schmidt09, Maurizi91, Butland05]
Inferred from experimentInferred by computational analysisGO:0008236 - serine-type peptidase activity [UniProtGOA11a, Arribas93]
Inferred from experimentGO:0042802 - identical protein binding [Kessel95, Hauser14, Rajagopala14, Lasserre06]
Inferred by computational analysisGO:0004252 - serine-type endopeptidase activity [GOA06, GOA01a]
Inferred by computational analysisGO:0008233 - peptidase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016787 - hydrolase activity [UniProtGOA11a]
Cellular Component:
Inferred from experimentGO:0005829 - cytosol [Lasserre06]
Inferred from experimentGO:0016020 - membrane [Lasserre06]
Inferred by computational analysisGO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: cell processesadaptationstemperature extremes
information transferprotein relatedturnover, degradation
metabolismdegradation of macromoleculesproteins/peptides/glycopeptides
regulationtype of regulationposttranscriptionalproteases, cleavage of compounds

Unification Links: DIP:DIP-31838N, EcoliWiki:b0437, ModBase:P0A6G7, PR:PRO_000022298, Pride:P0A6G7, Protein Model Portal:P0A6G7, RefSeq:NP_414971, SMR:P0A6G7, UniProt:P0A6G7

Relationship Links: InterPro:IN-FAMILY:IPR001907, InterPro:IN-FAMILY:IPR018215, InterPro:IN-FAMILY:IPR023562, InterPro:IN-FAMILY:IPR029045, 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

a protein + H2O → a peptide + a peptide

ClpP is a serine protease with a chymotrypsin-like activity that is a part of the ClpAP, ClpAPX and ClpXP protease complexes [Arribas93, Wang97, Ortega04].

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, Wang98a]. This ring structure is required for proper protease function [Thompson98]. The active site 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].

Without the ClpA or ClpX ATPase chaperone components only short peptides can enter the ClpP cavity, thus ClpP alone cannot degrade folded proteins [Thompson94]. However, acyldepsipeptides [Kirstein09, Alexopoulos13] and other small molecule activators [Leung11] can activate ClpP to cleave folded proteins.

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].

Crystal structures of the ClpP tetradecamer have been solved at resolutions of 2.30 Å [Wang97], 1.90 Å [Bewley06], and an inactive V6A variant at 2.60 Å [Bewley06]. A structure with a peptide chloromethyl ketone covalently bound at each active site has been determined at 1.90 Å resolution [Szyk06]. A 3.20 Å structure of a ClpP mutant in which the two heptameric rings are crosslinked by disulfide bonds producing a compact state has been presented [Kimber10], and a structure with bound acyldepsipeptide ADEP1 has been solved at 1.90 Å resolution [Li10].

Analysis of a clpP::cat insertion mutant suggested that ATP-dependent ClpP proteolysis has a major in vivo role in processing aggregation-prone proteins and polypeptides released from inclusion bodies [Vera05].

Biophysical studies and analysis of deletion and point mutants in the N-terminus, channel loop, or helix A of ClpP suggest that the N-terminus acts as a gate controlling substrate access to the active sites. Binding of the ATPase subunits opens the gate and allows large polypeptides to enter the ClpP chamber [Lee10, Bewley09, Jennings08, Jennings08a, Effantin10, Religa11]. ClpP allosterically controls ClpA-catalyzed polypeptide translocation by reducing the cooperativity between the ClpA ATP binding sites [Miller13].

ClpP is a major regulator of transcript levels in nitric oxide-stressed E. coli and the ClpA and ClpX ATPase adapters are required for this function. A ΔclpP mutant resulted in a substantially increased nitric oxide-mediated stasis and a decreased nitric oxide clearance rate relative to wild-type. The mutation caused widespread perturbations in the expression of nitric oxide-responsive genes, suggesting the use of ClpP as a drug target [Robinson15].

Reviews: [Alexopoulos12, Yu07]

Gene Citations: [Gottesman93, Li00]

Essentiality data for clpP knockouts:

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

Subunit of ClpXP: ClpX ATP-dependent protease specificity component and chaperone

Synonyms: lopC

Gene: clpX Accession Numbers: EG10159 (EcoCyc), b0438, ECK0432

Locations: cytosol

Subunit composition of ClpX ATP-dependent protease specificity component and chaperone = [ClpX]6

Map Position: [457,426 -> 458,700] (9.85 centisomes, 35°)
Length: 1275 bp / 424 aa

Molecular Weight of Polypeptide: 46.356 kD (from nucleotide sequence)

GO Terms:
Biological Process:
Inferred from experimentGO:0006508 - proteolysis [Gottesman98, Wojtkowiak93]
Inferred from experimentGO:0043335 - protein unfolding [Maillard11]
Inferred from experimentGO:0051301 - cell division [Camberg11]
Inferred by computational analysisGO:0006457 - protein folding [GOA06, GOA01a]
Inferred by computational analysisGO:0016032 - viral process [UniProtGOA11a]
Molecular Function:
Inferred from experimentGO:0004176 - ATP-dependent peptidase activity [Gottesman98, Wojtkowiak93]
Inferred from experimentInferred by computational analysisGO:0005524 - ATP binding [UniProtGOA11a, GOA06, GOA01a, Grimaud98]
Inferred from experimentGO:0016887 - ATPase activity [Banecki01]
Inferred from experimentGO:0042802 - identical protein binding [Rajagopala14, Stinson13, Glynn09]
Inferred by computational analysisGO:0000166 - nucleotide binding [UniProtGOA11a]
Inferred by computational analysisGO:0008270 - zinc ion binding [GOA01a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0046983 - protein dimerization activity [GOA01a]
Inferred by computational analysisGO:0051082 - unfolded protein binding [GOA06, GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: information transferprotein relatedchaperoning, repair (refolding)
information transferprotein relatedturnover, degradation
metabolismdegradation of macromoleculesproteins/peptides/glycopeptides

Unification Links: DIP:DIP-35907N, EcoliWiki:b0438, ModBase:P0A6H1, PR:PRO_000022300, Pride:P0A6H1, Protein Model Portal:P0A6H1, RefSeq:NP_414972, SMR:P0A6H1, Swiss-Model:P0A6H1, UniProt:P0A6H1

Relationship Links: InterPro:IN-FAMILY:IPR003593, InterPro:IN-FAMILY:IPR003959, InterPro:IN-FAMILY:IPR004487, InterPro:IN-FAMILY:IPR010603, InterPro:IN-FAMILY:IPR019489, InterPro:IN-FAMILY:IPR027417, Panther:IN-FAMILY:PTHR11262:SF4, PDB:Structure:1OVX, PDB:Structure:2DS5, PDB:Structure:2DS6, PDB:Structure:2DS7, PDB:Structure:2DS8, PDB:Structure:3HTE, PDB:Structure:3HWS, PDB:Structure:4I4L, PDB:Structure:4I4L, PDB:Structure:4I5O, PDB:Structure:4I5O, PDB:Structure:4I9K, PDB:Structure:4I9K, PDB:Structure:4I34, PDB:Structure:4I34, PDB:Structure:4I63, PDB:Structure:4I63, PDB:Structure:4I81, PDB:Structure:4I81, Pfam:IN-FAMILY:PF06689, Pfam:IN-FAMILY:PF07724, Pfam:IN-FAMILY:PF10431, Smart:IN-FAMILY:SM00382, Smart:IN-FAMILY:SM00994, Smart:IN-FAMILY:SM01086

ClpX is an ATP-dependent molecular chaperone that serves as a substrate-specifying adaptor for the ClpP serine protease in the ClpXP and ClpAXP protease complexes. ClpX is a member of the AAA+ (ATPases associated with diverse cellular activities) family of ATPases [Neuwald99, Kimura01]

ClpX protects the lambda O protein from heat-induced aggregation, disassembles lambda aggregates and enhances lambda DNA binding. ATP binding is required for all these effects, and disaggregation requires ATP hydrolysis [Wawrzynow95]. ClpX also converts inactive, dimeric TrfA into its monomeric form (capable of initiating replication of plasmid RK2) in an ATP-dependent manner [Konieczny97].

ClpX is required for normal replication of Mu transposase [MhammediAlaoui94]. ClpX catalyzes the ATP-dependent release of MuA from its active transposase tetramer form, allowing recruitment of host factors necessary for post-recombination steps in Mu transposition [Levchenko95, Kruklitis96]. ClpX is also able to globally unfold MuA monomers. ClpX recognizes a ten amino acid peptide from the carboxy-terminus of MuA when it is revealed by MuB. ClpX will recognize other proteins with this tag artificially attached [Levchenko97].

Each ClpX monomer has two PDZ domains that bind to the carboxy-terminus of target proteins. These domains show up as disordered sequence in NMR and are unstable when expressed independently [Levchenko97a, Smith99]. ClpX also has an ATP-binding site motif and a zinc-binding domain, the latter being a member of the treble clef zinc finger family, involved in macromolecular interactions [Gottesman93, Donaldson03].

ClpX recognises C-terminal residues 9-11 of the ssrA peptide tag (AANDENYALAA) [Flynn01]. Mutations in the central pore of the ClpX hexamer disrupt recognition of ssrA-tag containing substrates; the ssrA-tag interacts with pore loop regions (RKH loop; pore 1 loop and pore 2 loop) located in the central core of the ClpX hexamer [Siddiqui04, Farrell07, Martin07, Martin08, Martin08a]. The RKH loop, located at the entry to the central pore plays a role in determining substrate specificity [Farrell07]. Pore loop 1 (also called the axial pore loop) contains a conserved aromatic-hydrocarbon (Y153-V154) dipeptide; ClpX variants containing a Y153A substitution are defective in gripping ssrA tagged substrates to drive translocation and unfolding [Martin08a]. Axial pore loops function in a synergistic manner; in vitro the number of wild-type loops required for efficient degradation is dependent on the resistance of the protein substrate to mechanical unfolding [Iosefson15].

ClpX is a hexamer of ClpX monomers, stabilized by ATP binding and capable of capping ClpP tetradecamers [Grimaud98]. While the ClpX ATP-binding site is necessary for oligomerization and binding to ClpP, both processes continue in the absence of ATP [Banecki01]. ATP-bound ClpX is protease resistant [Singh01]. The carboxy-terminus of ClpX is required for interaction with ClpP, as is the tripeptide IGF, though the latter is dispensible for ClpX chaperone activities [Kim01, Singh01]. Mutations in the interface between the carboxy-terminus of each subunit and the ATPase domain of its neighbor prevent disassembly of bound substrate [Joshi03]. Packing of the the small AAA domain (residues 3199-424) against a neigbouring large AAA domain (residues 65-314) forms the major interface between ClpX subunits [Glynn09, Glynn12].

Functional ClpX is an asymmetric hexamer - ClpX subunits bind nucleotide with differing affinity and at least two ClpX subunits do not bind nucleotide [Hersch05]. ClpX forms an asymmetric hexamer containing two types of subunits: nucleotide free (termed U for unloaded) or containing bound nucleotide (termed L for loaded). The subunits are arranged in an L/U/L/L/U/L pattern [Glynn09]. L and U subunits switch dynamically during the ClpX cycle; disulfide cross-links which block L → U switching uncouple ATP hydrolysis from substrate unfolding and translocation in vitro [Stinson13].

SspB binding stimulates ClpX ATPase activity [Wah02].

ClpX is required for adaptation to and extended viability in stationary phase, as well as growth in SDS [Weichart03, Rajagopal02].

ClpX can be expressed without ClpP [Yoo94].

Reviews: [Burton05, Zolkiewski06]
Comments: [Inobe08a]

Citations: [Thibault06a, Thibault12, Thibault06, Wojtyra03, Stinson15]

Gene Citations: [Li00, Rhodius05]

Essentiality data for clpX knockouts:

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


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Camberg11: Camberg JL, Hoskins JR, Wickner S (2011). "The interplay of ClpXP with the cell division machinery in Escherichia coli." J Bacteriol 193(8);1911-8. PMID: 21317324

Chuang93: Chuang SE, Blattner FR (1993). "Characterization of twenty-six new heat shock genes of Escherichia coli." J Bacteriol 175(16);5242-52. PMID: 8349564

Cordova14: Cordova JC, Olivares AO, Shin Y, Stinson BM, Calmat S, Schmitz KR, Aubin-Tam ME, Baker TA, Lang MJ, Sauer RT (2014). "Stochastic but highly coordinated protein unfolding and translocation by the ClpXP proteolytic machine." Cell 158(3);647-58. PMID: 25083874

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Flynn01: Flynn JM, Levchenko I, Seidel M, Wickner SH, Sauer RT, Baker TA (2001). "Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis." Proc Natl Acad Sci U S A 98(19);10584-9. PMID: 11535833

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