Escherichia coli K-12 substr. MG1655 Enzyme: 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 (extended summary available)

ClpAP is a serine protease complex responsible for the ATP-dependent degradation of a number of proteins [Katayama88]. ClpA functions as an ATP-dependent chaperone component and ClpP as the serine protease component. Substrates for ClpAP include the plasmid P1 replication initiator RepA, HemA and a number of carbon starvation proteins [Wickner94, Wang99c, 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, Farrell05]. However, ClpXP and SspB together are responsible for the in vivo degradation of the majority of SsrA-tagged proteins [Lies08]. 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]. Although ClpAP alone can recognize N-end rule motifs, binding of the adaptor protein ClpS specifically enhances their turnover. The ClpS-ClpAP complex recognizes an N-end motif using both a free alpha-amino group and the identity of the N-terminal residue. The identity of adjacent residues can also affect recognition, and the distance between the N-end residue and the folded portion of a protein is critical [Wang08b].

ClpAP consists of a ClpP tetradecamer capped at one or both ends by ClpA hexamers [Kessel95, Ishikawa04]. 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].

ClpAP activity is enhanced by the formation of nucleoprotein complexes with the DNA-bound replication initiation protein TrfA [Kubik12].

Real time physical measurements of the ClpAP complex assembly pathway provided evidence for a tetrameric ClpA intermediate during hexamer formation and cooperativity in the association of ClpA hexamers with the ClpP core cylinder [Kress07]. The influence of the architectural symmetry of the ClpAP complex on its activity has been studied using kinetic methods [Maglica09].

Cryoelectron microscopy has been used to visualize the ClpAP translocation pathway for the model substrate RepA from bacteriophage P1 [Ishikawa01]. The ClpAP mechanism involves alternation between substrate translocation and proteolysis, which allows processive cleavage of peptides that have similar lengths [Choi05b, Katayama88]. Data using homodimeric RepA and a heterodimeric RepA N-terminal deletion mutant suggest that ClpAP can unfold and degrade dimeric substrates even if only one subunit contains the ClpA recognition signal [Sharma05a]. ClpP allosterically influences ClpA catalyzed polypeptide translocation by reducing the cooperativity between ATP binding sites on ClpA [Miller13b]. Mechanochemical studies using single-molecule optical trapping have been performed to directly measure how ClpAP unfolds and translocates multidomain protein substrates [Olivares14].

Reviews: [Gur13, Dougan12, Schmidt09, Yu07, Baker06]

Gene-Reaction Schematic

Gene-Reaction Schematic

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

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.

ClpAP hydrolyzes proteins to small peptides in the presence of ATP and Mg2+. α-Casein can serve as an assay substrate [Choi05b].

Component enzyme of ClpAP : 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: [455,901 -> 456,524] (9.83 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 [Andresen00a]
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 [Lee10a, Schmidt09a, 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, Wang97g, Ortega04].

The ClpP protease is a tetradecamer, consisting of two heptamers of ClpP subunits stacked head-to-head [Kessel95, Shin96a]. 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, Wang98e]. 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 [Reid01a].

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 [Wang97g], 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 [Lee10a, Bewley09, Jennings08, Jennings08a, Effantin10, Religa11]. ClpP allosterically controls ClpA-catalyzed polypeptide translocation by reducing the cooperativity between the ClpA ATP binding sites [Miller13b].

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, Li00b]

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 ClpAP: ClpA ATP-dependent protease specificity component and chaperone

Synonyms: cipA, lopD, ATP-binding component of serine protease

Gene: clpA Accession Numbers: EG10156 (EcoCyc), b0882, ECK0873

Locations: cytosol

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

Map Position: [922,487 -> 924,763] (19.88 centisomes, 72°)
Length: 2277 bp / 758 aa

Molecular Weight of Polypeptide: 84.207 kD (from nucleotide sequence), 81.0 kD (experimental) [Katayama88]

GO Terms:
Biological Process:
Inferred from experimentGO:0006508 - proteolysis [Gottesman98]
Inferred from experimentGO:0006979 - response to oxidative stress [Krisko14]
Inferred from experimentGO:0043335 - protein unfolding [Kress09]
Inferred by computational analysisGO:0019538 - protein metabolic process [GOA01a]
Molecular Function:
Inferred from experimentInferred by computational analysisGO:0004176 - ATP-dependent peptidase activity [GOA01a, Gottesman98]
Inferred from experimentGO:0005515 - protein binding [Maurizi91, Hauser14, Rajagopala14, Schmidt09a, Butland05, Xia04, Zeth02, Guo02]
Inferred from experimentInferred by computational analysisGO:0005524 - ATP binding [UniProtGOA11a, GOA01a, Singh94, Miller14]
Inferred from experimentGO:0016887 - ATPase activity [Katayama88]
Inferred by computational analysisGO:0000166 - nucleotide binding [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08]

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

Unification Links: DIP:DIP-35409N, EcoliWiki:b0882, ModBase:P0ABH9, PR:PRO_000022296, Pride:P0ABH9, Protein Model Portal:P0ABH9, RefSeq:NP_415403, SMR:P0ABH9, UniProt:P0ABH9

Relationship Links: InterPro:IN-FAMILY:IPR001270, InterPro:IN-FAMILY:IPR003593, InterPro:IN-FAMILY:IPR003959, InterPro:IN-FAMILY:IPR004176, InterPro:IN-FAMILY:IPR013461, InterPro:IN-FAMILY:IPR018368, InterPro:IN-FAMILY:IPR019489, InterPro:IN-FAMILY:IPR023150, InterPro:IN-FAMILY:IPR027417, InterPro:IN-FAMILY:IPR028299, Panther:IN-FAMILY:PTHR11638:SF14, PDB:Structure:1K6K, PDB:Structure:1KSF, PDB:Structure:1LZW, PDB:Structure:1MBU, PDB:Structure:1MBV, PDB:Structure:1MBX, PDB:Structure:1MG9, PDB:Structure:1R6B, PDB:Structure:1R6C, PDB:Structure:1R6O, PDB:Structure:1R6Q, Pfam:IN-FAMILY:PF00004, Pfam:IN-FAMILY:PF02861, Pfam:IN-FAMILY:PF07724, Pfam:IN-FAMILY:PF10431, Prints:IN-FAMILY:PR00300, Prosite:IN-FAMILY:PS00870, Prosite:IN-FAMILY:PS00871, Smart:IN-FAMILY:SM00382, Smart:IN-FAMILY:SM01086


ClpA is an ATP-dependent molecular chaperone that serves as a substrate-specifying adapter for the ClpP serine protease in the ClpAP and ClpAXP protease complexes. ClpA is a member of the AAA+ (ATPases associated with diverse cellular activities) superfamily of ATPases [Neuwald99].

In its capacity as a chaperone, ClpA activates the RepA replication initiator protein of plasmid F1 in an ATP-dependent manner, converting it from a dimer to a monomer [Wickner94]. This activity requires interaction between ClpA and the amino-terminus of RepA [Hoskins00]. Should the RepA amino-terminus be blocked, ClpA can still interact with it as long as there is an accessible amino acid tract at the RepA carboxy-terminus [Hoskins06].

ClpA lacking its own amino-terminal domain is still able to function as both chaperone and protease adaptor, though it is less effective in both roles than the wild-type protein [Lo01].

Each ClpA monomer has two domains, leading to a double-stacked ring structure in the complete ClpA hexamer [Beuron98]. The putative substrate-recognition domain of ClpA is stable and folds independently, unlike the matching domains in ClpB and ClpX [Smith99a]. Each ClpA monomer has two AAA+ modules (consensus ATP-binding sites), the first of which interacts with the amino-terminal domain of the protein [Gottesman90, Guo02a]. A lysine mutation in either ATP-binding site prevents the ATP-dependent formation of the ClpA hexamer, as well as disrupting ATPase activity and removing the ability to activate ClpP. Mutants in the second ATP-binding site were still able to stimulate degradation of some shorter peptide substrates requiring nucleotide binding, but not hydrolysis [Singh94, Seol95a].

The ClpA hexamer forms in an ATP-dependent manner [Kessel95]. Successful formation of the hexamer and subsequent interaction with ClpP requires the carboxy-terminus of ClpA. In its ATP-bound state, ClpA is protease resistant [Singh01].

ClpA is required for the ATP-dependent degradation of certain substrates by ClpP, including some abnormal proteins and the in vitro test substrate casein [Katayama88, Hinnerwisch05]. ClpA binds to the SsrA degradation peptide tag, with one tag binding per ClpA hexamer. This interaction does not depend on either ATP-binding domain in ClpA [Piszczek05]. The amino-terminal domain of ClpA is required for binding nonspecific protein substrates that have not been tagged with SsrA [Xia04].

NEM inhibits ClpA function by introducing a bulky alkyl group but not by directly binding to a catalytic residue [Seol97a].

ClpA is required for maximal growth in SDS, normal adaptation to and extended viability in stationary phase and for activity of bacteriophage Mu [Rajagopal02, Weichart03, Shapiro93].

The clpA gene contains a sequence for an internal translational initiation and therefore encode two polypeptides with different sizes (ClpA65 and ClpA84) [Seol94]. The 65 kDa form prevents degradation of ClpA by ClpAP [Seol95b].

ClpS binds to the ClpA amino-terminus and affects the specificity of protein degradation by the ClpAP chaperone-protease complex, possibly by interfering with interactions between substrate and ClpA [Dougan02]. ClpS stimulates ClpAP recognition and degradation of aggregated protein substrates while it inhibits degradation of non-aggregated substrates including ClpA [Dougan02].

A crystal structure of the ClpA N terminus shows a zinc binding site [Guo02]. Crystal structures of ClpS bound to the N-terminal region of ClpA are presented at 2.3 Å [Guo02], 2.5 Å [Zeth02], and 3.3 Å [Guo02] resolution. Crystal structures have also been solved for full-length ClpA, the isolated N-terminal domain of ClpA, the ClpS-N complex, and the Zn2+-bound ClpS-N complex at 2.25 Å 2.15 Å 2.35 Å and 2.25 Å resolution, respectively [Xia04].

Free ClpAP that is not in complex with ClpS can degrade both SsrA-tagged proteins, and ClpA itself via an autodegradation tag at the ClpA C-terminus. ClpS inhibits this autodegradation [Maglica08].

Methods have been published for the evaluation of ClpA subunit association and allosteric regulation [Lucius12], the unfolding activity of ClpA [Ohgita11], and the mechanism and time course of enzyme catalyzed polypeptide translocation [Lucius11]. At thermodynamic equilibrium ClpA is a mixture of monomers and tetramers in the absence of nucleoside triphosphates [Veronese09] and further analysis showed a temperature-dependent monomer-dimer-tetramer equilibrium [Veronese10].

Site-directed mutagenesis has revealed structural elements in both the N-domain and central pore of the ClpA hexamer that are important for substrate recognition and unfolding [Erbse08], as well as the role of the flexible linker region connecting the N-domains and central pore [CranzMileva08]. Substrate translocation by ClpA occurs via ATP-dependent movements of the D2 domain loop [Bohon08]. In the absence of ClpP, ClpA translocates polypeptides directionally, processively and in discrete steps [Rajendar10]. The relative binding affinity of ClpA for several different polypeptide substrates has been quantitated [Li13d]. Mechanochemical data demonstrate that ClpA is a faster polypeptide unfoldase than ClpX, but ClpA is a slower translocase which moves in smaller, more regular steps than ClpX [Olivares14].

Mutagenesis studies also revealed that the two ATPase domains of ClpA operate independently, but ATP hydrolysis in both domains is required for efficient processing of highly stable protein substrates [Kress09]. Evaluation of the effect of various nucleotides and their analogs on ClpA oligomer assembly suggested a role for the γ phosphate group of ATP in a conformational switch to high peptide binding activity [Veronese11]. ClpP allosterically affects ClpA-catalyzed polypeptide translocation by reducing the cooperativity between the ATP binding sites on ClpA [Miller13b]. The ATP analog ATPγS competes with ATP for binding to the ClpA D1 domain ATP binding site, but does not effectively compete with ATP for binding to the D2 domain site [Miller14].

An assay method based on Forster resonance energy transfer (FRET) was developed to monitor the steady-state kinetics of enzymatic unfolding and processing by AAA+ proteases using an engineered dimeric fusion protein substrate. ClpX was shown to be a more efficient unfoldase than ClpA, although ClpA unfolding activity was enhanced by ClpP. ClpAP degraded the dimeric substrate faster than ClpXP. Both complexes unfolded and degraded one subunit of the dimer, the other subunit being passively unfolded by release from the dimer [Baytshtok15].

clpA shows differential codon adaptation, resulting in differential translation efficiency signatures, in aerotolerant compared to obligate anaerobic microbes. It was therefore predicted to play a role in the oxidative stress response. A clpA deletion mutant was shown to be more sensitive than wild-type specifically to hydrogen peroxide exposure, but not other stresses [Krisko14].

Review: [Zolkiewski06]

Essentiality data for clpA 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]


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

Alexopoulos13: Alexopoulos J, Ahsan B, Homchaudhuri L, Husain N, Cheng YQ, Ortega J (2013). "Structural determinants stabilizing the axial channel of ClpP for substrate translocation." Mol Microbiol 90(1);167-80. PMID: 23927726

Andresen00a: 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

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

Baker06: Baker TA, Sauer RT (2006). "ATP-dependent proteases of bacteria: recognition logic and operating principles." Trends Biochem Sci 31(12);647-53. PMID: 17074491

Baytshtok15: Baytshtok V, Baker TA, Sauer RT (2015). "Assaying the kinetics of protein denaturation catalyzed by AAA+ unfolding machines and proteases." Proc Natl Acad Sci U S A 112(17);5377-82. PMID: 25870262

Beuron98: Beuron F, Maurizi MR, Belnap DM, Kocsis E, Booy FP, Kessel M, Steven AC (1998). "At sixes and sevens: characterization of the symmetry mismatch of the ClpAP chaperone-assisted protease." J Struct Biol 123(3);248-59. PMID: 9878579

Bewley06: Bewley MC, Graziano V, Griffin K, Flanagan JM (2006). "The asymmetry in the mature amino-terminus of ClpP facilitates a local symmetry match in ClpAP and ClpXP complexes." J Struct Biol 153(2);113-28. PMID: 16406682

Bewley09: Bewley MC, Graziano V, Griffin K, Flanagan JM (2009). "Turned on for degradation: ATPase-independent degradation by ClpP." J Struct Biol 165(2);118-25. PMID: 19038348

Bohon08: Bohon J, Jennings LD, Phillips CM, Licht S, Chance MR (2008). "Synchrotron protein footprinting supports substrate translocation by ClpA via ATP-induced movements of the D2 loop." Structure 16(8);1157-65. PMID: 18682217

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Choi05b: Choi KH, Licht S (2005). "Control of peptide product sizes by the energy-dependent protease ClpAP." Biochemistry 44(42);13921-31. PMID: 16229481

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

CranzMileva08: Cranz-Mileva S, Imkamp F, Kolygo K, Maglica Z, Kress W, Weber-Ban E (2008). "The flexible attachment of the N-domains to the ClpA ring body allows their use on demand." J Mol Biol 378(2);412-24. PMID: 18358489

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

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

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

Dougan12: Dougan DA, Micevski D, Truscott KN (2012). "The N-end rule pathway: from recognition by N-recognins, to destruction by AAA+proteases." Biochim Biophys Acta 1823(1);83-91. PMID: 21781991

Effantin10: Effantin G, Maurizi MR, Steven AC (2010). "Binding of the ClpA unfoldase opens the axial gate of ClpP peptidase." J Biol Chem 285(19);14834-40. PMID: 20236930

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

Erbse08: Erbse AH, Wagner JN, Truscott KN, Spall SK, Kirstein J, Zeth K, Turgay K, Mogk A, Bukau B, Dougan DA (2008). "Conserved residues in the N-domain of the AAA+ chaperone ClpA regulate substrate recognition and unfolding." FEBS J 275(7);1400-10. PMID: 18279386

Farrell05: Farrell CM, Grossman AD, Sauer RT (2005). "Cytoplasmic degradation of ssrA-tagged proteins." Mol Microbiol 57(6);1750-61. PMID: 16135238

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

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

GOA01a: 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."

Gottesman90: Gottesman S, Clark WP, Maurizi MR (1990). "The ATP-dependent Clp protease of Escherichia coli. Sequence of clpA and identification of a Clp-specific substrate." J Biol Chem 1990;265(14);7886-93. PMID: 2186030

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