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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

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, Wang99a, 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, Seol95b, 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].

Gene-Reaction Schematic: ?


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.


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)
Length: 624 bp / 207 aa

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

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 [Chuang93]
GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0006950 - response to stress Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0008236 - serine-type peptidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, 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 [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, 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

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

Catalyzes:
a protein + H2O → a peptide + a peptide

Summary:
ClpP is a serine protease with a chymotrypsin-like activity that is a part of the ClpAP, ClpAPX and ClpXP protease complexes [Arribas93, Wang97h].

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, Wang98m]. This ring structure is required for proper protease function [Thompson98a]. 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 [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].

Review: [Alexopoulos12]

Gene Citations: [Gottesman93, Li00c]

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]

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)
Length: 2277 bp / 758 aa

Molecular Weight of Polypeptide: 84.207 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006508 - proteolysis Inferred from experiment [Katayama88]
GO:0006979 - response to oxidative stress Inferred from experiment [Krisko14]
GO:0006200 - ATP catabolic process Inferred by computational analysis [GOA01]
GO:0019538 - protein metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Hauser14, Rajagopala14, Schmidt09, Butland05, Xia04, Zeth02, Guo02c]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0004176 - ATP-dependent peptidase activity Inferred by computational analysis [GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: information transfer protein related chaperoning, repair (refolding)
information transfer protein related turnover, degradation
metabolism degradation of macromolecules proteins/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 , String:511145.b0882 , UniProt:P0ABH9

Relationship Links: InterPro:IN-FAMILY:IPR001270 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR003959 , InterPro:IN-FAMILY:IPR004176 , InterPro:IN-FAMILY:IPR013093 , 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

Summary:
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.

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 [Smith99]. 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, Guo02b]. 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, Seol95].

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 [Seol95a].

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 [Guo02c]. Crystal structures of ClpS bound to the N-terminal region of ClpA are presented at 2.3 Å [Guo02c], 2.5 Å [Zeth02], and 3.3 Å [Guo02c] resolution.

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].

Essentiality data for clpA 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]

References

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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

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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

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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

Piszczek05: Piszczek G, Rozycki J, Singh SK, Ginsburg A, Maurizi MR (2005). "The molecular chaperone, ClpA has a single high affinity peptide binding site per hexamer." J Biol Chem 280(13):12221-30. PMID: 15657062

Rajagopal02: Rajagopal S, Sudarsan N, Nickerson KW (2002). "Sodium dodecyl sulfate hypersensitivity of clpP and clpB mutants of Escherichia coli." Appl Environ Microbiol 68(8);4117-21. PMID: 12147516

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Reid01a: Reid BG, Fenton WA, Horwich AL, Weber-Ban EU (2001). "ClpA mediates directional translocation of substrate proteins into the ClpP protease." Proc Natl Acad Sci U S A 98(7);3768-72. PMID: 11259663

Schmidt09: Schmidt R, Zahn R, Bukau B, Mogk A (2009). "ClpS is the recognition component for Escherichia coli substrates of the N-end rule degradation pathway." Mol Microbiol 72(2);506-17. PMID: 19317833

Seol94: Seol JH, Yoo SJ, Kim KI, Kang MS, Ha DB, Chung CH (1994). "The 65-kDa protein derived from the internal translational initiation site of the clpA gene inhibits the ATP-dependent protease Ti in Escherichia coli." J Biol Chem 269(47);29468-73. PMID: 7961929

Seol95: Seol JH, Baek SH, Kang MS, Ha DB, Chung CH (1995). "Distinctive roles of the two ATP-binding sites in ClpA, the ATPase component of protease Ti in Escherichia coli." J Biol Chem 270(14);8087-92. PMID: 7713911

Seol95a: Seol JH, Yoo SJ, Kang MS, Ha DB, Chung CH (1995). "The 65-kDa protein derived from the internal translational start site of the clpA gene blocks autodegradation of ClpA by the ATP-dependent protease Ti in Escherichia coli." FEBS Lett 377(1);41-3. PMID: 8543014

Seol95b: Seol JH, Woo KM, Kang MS, Ha DB, Chung CH (1995). "Requirement of ATP hydrolysis for assembly of ClpA/ClpP complex, the ATP-dependent protease Ti in Escherichia coli." Biochem Biophys Res Commun 217(1);41-51. PMID: 8526938

Seol97a: Seol JH, Kwon JA, Yoo SJ, Kim HS, Kang MS, Chung CH (1997). "Site-directed mutagenesis of the Cys residues in ClpA, the ATPase component of protease Ti (ClpAP) in Escherichia coli." Biol Chem 378(10);1205-9. PMID: 9372193

Shapiro93: Shapiro JA (1993). "A role for the Clp protease in activating Mu-mediated DNA rearrangements." J Bacteriol 175(9);2625-31. PMID: 8386721

Shin96a: Shin DH, Lee CS, Chung CH, Suh SW (1996). "Molecular symmetry of the ClpP component of the ATP-dependent Clp protease, an Escherichia coli homolog of 20 S proteasome." J Mol Biol 262(2);71-6. PMID: 8831780

Singh01: Singh SK, Rozycki J, Ortega J, Ishikawa T, Lo J, Steven AC, Maurizi MR (2001). "Functional domains of the ClpA and ClpX molecular chaperones identified by limited proteolysis and deletion analysis." J Biol Chem 276(31);29420-9. PMID: 11346657

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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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