clpX

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0002020 protease binding	IPI PMID:14536075 Flexible linkers leash the substrate binding domain of SspB ...	KEEP AS NON CORE	Summary: ClpX binds the ClpP peptidase (protease) to form the ClpXP protease; the cited paper studies SspB-mediated substrate delivery to ClpXP complexes. Reason: ClpX docking onto ClpP is firmly established (ClpX hexamers bind the ClpP tetradecamer in an ATP-dependent way, PMID:9575205; Zn-free ClpX cannot bind ClpP, PMID:11278349), and the CAFA IPI with ClpP from the SspB/ClpXP delivery-complex paper is consistent with this. Protease binding is a true, informative statement about how ClpX acts, but the activity it serves is captured more directly by membership of the endopeptidase Clp complex and the peptidase activator / ATP-dependent unfolding functions, so it is kept as non-core. Supporting Evidence: PMID:9575205 ClpP, which is composed of two seven-membered rings stacked face-to-face, interacts with the nucleotide-stabilized hexamer of ClpX to form a complex that could be isolated by gel filtration. PMID:11278349 ClpX, free of Zn(II), cannot oligomerize, bind to ClpP, or participate in ClpXP-dependent proteolysis.
GO:0004176 ATP-dependent peptidase activity	IDA PMID:14536075 Flexible linkers leash the substrate binding domain of SspB ...	ACCEPT	Summary: ClpXP degrades SspB-delivered GFP-ssrA in an ATP-dependent manner; the SspB C-terminal peptide stimulates ClpX ATPase and blocks delivery. Reason: The paper (abstract only cached; CAFA annotation) measures ATP-dependent degradation of GFP-ssrA by purified ClpXP, with and without the SspB adaptor. The peptide-bond hydrolysis itself is catalysed by ClpP; ClpX contributes the ATP dependence, substrate recognition and unfolding of the ClpXP holoenzyme. The annotation therefore describes the activity of the ClpXP complex in which ClpX is the indispensable ATPase subunit, which is how GO and the human CLPX review represent it; it is accepted as a core, complex-level activity. Supporting Evidence: PMID:14536075 A synthetic peptide containing the 10 C-terminal residues of SspB binds ClpX, stimulates its ATPase activity, and prevents SspB-mediated delivery of GFP-ssrA for ClpXP degradation.
GO:0004176 ATP-dependent peptidase activity	IDA PMID:8226769 Isolation and characterization of ClpX, a new ATP-dependent ...	ACCEPT	Summary: CACAO IDA. Wojtkowiak et al. purified, from E. coli extracts, an ATP-dependent lambda O-degrading protease composed of ClpP and ClpX, and showed it is substrate-specific. Reason: CACAO row. What the paper shows for clpX: using 14C-labelled lambda O as substrate, an ATP-dependent protease activity was purified to homogeneity and shown to consist of ClpP and a 46 kDa subunit identified by N-terminal sequencing as ClpX; the ClpXP protease degrades lambda O but not casein, lambda P or DnaK (only the abstract is cached; GONUTS was offline). The term matches the assay (ATP-dependent proteolysis by the purified enzyme) at the right granularity, so the student annotation is sound. The peptide-bond hydrolysis itself is catalysed by ClpP; ClpX contributes the ATP dependence, substrate recognition and unfolding of the ClpXP holoenzyme. The annotation therefore describes the activity of the ClpXP complex in which ClpX is the indispensable ATPase subunit, which is how GO and the human CLPX review represent it; it is accepted as a core, complex-level activity. Supporting Evidence: PMID:8226769 identified capable of degrading lambda O protein to acid-soluble fragments in an ATP-dependent fashion. One of these activities was purified to homogeneity and shown to be composed of two different polypeptides. PMID:8226769 These results suggest that ClpX protein directs ClpP protease to specific substrates.
GO:0004176 ATP-dependent peptidase activity	IDA PMID:9573050 The ClpXP and ClpAP proteases degrade proteins with carboxy-...	ACCEPT	Summary: CACAO IDA. Gottesman et al. reconstituted ATP-dependent degradation of SsrA-tagged lambda repressor N-domain with purified ClpX, ClpP and ATP. Reason: CACAO row. What the paper shows for clpX: in vitro degradation of SsrA-tagged substrates with purified components required the wild-type SsrA tail, ClpP plus either ClpA or ClpX, and ATP; in vivo degradation also depended on ClpXP/ClpAP (abstract cached; full text is in PMC but not cached here). The term matches the reconstituted ATP-dependent proteolysis assay; it is not a downstream phenotype. The peptide-bond hydrolysis itself is catalysed by ClpP; ClpX contributes the ATP dependence, substrate recognition and unfolding of the ClpXP holoenzyme. The annotation therefore describes the activity of the ClpXP complex in which ClpX is the indispensable ATPase subunit, which is how GO and the human CLPX review represent it; it is accepted as a core, complex-level activity. Supporting Evidence: PMID:9573050 Degradation in vitro of SsrA-tagged substrates was reproduced with purified components and required a substrate with a wild-type SsrA tail, the presence of both ClpP and either ClpA or ClpX, and ATP.
GO:0005515 protein binding	IPI PMID:16606699 Large-scale identification of protein-protein interaction of...	MODIFY	Summary: High-throughput His-tag pull-down (Arifuzzaman et al.) recovered the ClpX-ClpP interaction. Reason: The partner is ClpP (P0A6G7), the peptidase whose binding by ClpX is the basis of the ClpXP protease (PMID:9575205). Bare protein binding is uninformative under the protein-binding policy. The interaction supports the more informative GO:0002020 protease binding, which this gene already carries from PMID:14536075. Proposed replacements: protease binding Supporting Evidence: PMID:16606699 A large-scale comprehensive pull-down assay was performed using a His-tagged Escherichia coli ORF clone library. PMID:9575205 ClpP, which is composed of two seven-membered rings stacked face-to-face, interacts with the nucleotide-stabilized hexamer of ClpX to form a complex that could be isolated by gel filtration.
GO:0005515 protein binding	IPI PMID:19183285 Controlled degradation by ClpXP protease tunes the levels of...	MODIFY	Summary: IntAct curated a ClpX-ClpP interaction from the UvrA degradation paper (Pruteanu & Baker), which shows UvrA turnover after UV is ClpXP-dependent. Reason: The partner is ClpP. Bare protein binding is uninformative under the protein-binding policy. The ClpX-ClpP interaction is the formation of the ClpXP protease and is better captured as GO:0002020 protease binding (already on this gene); the UvrA work itself shows ClpXP-dependent degradation of UvrA. Proposed replacements: protease binding Supporting Evidence: PMID:19183285 During post-UV recovery, UvrA levels decrease principally as a result of ClpXP-dependent protein degradation. PMID:9575205 ClpP, which is composed of two seven-membered rings stacked face-to-face, interacts with the nucleotide-stabilized hexamer of ClpX to form a complex that could be isolated by gel filtration.
GO:0005515 protein binding	IPI PMID:19368884 Optimal efficiency of ClpAP and ClpXP chaperone-proteases is...	MODIFY	Summary: Maglica et al. analysed 1:1 and 2:1 ClpXP assemblies, showing single-ended complexes degrade substrates efficiently. Reason: The partner is ClpP. Bare protein binding is uninformative under the protein-binding policy. The paper characterises ClpX-ClpP complexes of defined stoichiometry, which supports GO:0002020 protease binding (already on this gene) and membership of the endopeptidase Clp complex (accepted from the same paper). Proposed replacements: protease binding Supporting Evidence: PMID:19368884 Rapid-kinetic fluorescence measurements and steady-state experiments indicate that single 2:1 ClpAP or ClpXP complexes are as efficient in substrate degradation as two 1:1 ClpAP or ClpXP assemblies.
GO:0005515 protein binding	IPI PMID:19541655 ClpXP protease degrades the cytoskeletal protein, FtsZ, and ...	REMOVE	Summary: Camberg et al. showed ClpXP degrades FtsZ protomers and polymers; ClpX N-domain recognises FtsZ polymers via an FtsZ C-terminal signal. Reason: The partner is FtsZ, a ClpXP substrate. Bare protein binding is uninformative under the protein-binding policy. No GO molecular-function term describes binding a protease substrate for degradation more informatively without over-interpreting a substrate interaction, so the generic row is removed; the FtsZ interaction itself is real and is reflected in the review through ClpX's role in regulating cell division. Supporting Evidence: PMID:19541655 We found that FtsZ is degraded by E. coli ClpXP, an ATP-dependent protease.
GO:0005515 protein binding	IPI PMID:25866879 Subunit asymmetry and roles of conformational switching in t...	MODIFY	Summary: Stinson et al. used covalently linked ClpX hexamers with ClpP to dissect subunit switching; IntAct recorded the ClpX-ClpP interaction. Reason: The partner is ClpP. Bare protein binding is uninformative under the protein-binding policy. ClpX rings function with ClpP to degrade substrates; the interaction is captured as GO:0002020 protease binding (already on this gene). Proposed replacements: protease binding Supporting Evidence: PMID:25866879 The hexameric AAA+ ring of Escherichia coli ClpX, an ATP-dependent machine for protein unfolding and translocation, functions with the ClpP peptidase to degrade target substrates.
GO:0005524 ATP binding	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic inference of ATP binding across the ClpX/Clp ATPase family (PTN008295243). Reason: The node covers AAA+ Clp unfoldases; E. coli ClpX is a well-characterised member with its own experimental ATP binding evidence, so the inheritance is sound. ClpX has a single Walker-type ATP site per subunit (UniProt ATP binding 120..127; HAMAP MF_00175) and ATP binding drives hexamer stabilisation, ClpP binding and the mechanical cycle. Supporting Evidence: PMID:11278349 We show that the single ATP-binding site of ClpX is required for a variety of tasks, namely, the stabilization of the ClpXZn(II) oligomeric structure, binding to ClpP, and the ClpXP-dependent proteolysis of the lambdaO replication protein. PMID:23622246 ClpX, a AAA+ ring homohexamer, uses the energy of ATP binding and hydrolysis to power conformational changes that unfold and translocate target proteins into the ClpP peptidase for degradation.
GO:0005524 ATP binding	IDA PMID:14536075 Flexible linkers leash the substrate binding domain of SspB ...	ACCEPT	Summary: CAFA IDA from the SspB delivery paper, which measures stimulation of ClpX ATPase by the SspB C-terminal peptide. Reason: ATPase stimulation implies ATP binding; the claim is independently established (PMID:11278349, PMID:9575205). ClpX has a single Walker-type ATP site per subunit (UniProt ATP binding 120..127; HAMAP MF_00175) and ATP binding drives hexamer stabilisation, ClpP binding and the mechanical cycle. Supporting Evidence: PMID:14536075 A synthetic peptide containing the 10 C-terminal residues of SspB binds ClpX, stimulates its ATPase activity, and prevents SspB-mediated delivery of GFP-ssrA for ClpXP degradation. PMID:11278349 We show that the single ATP-binding site of ClpX is required for a variety of tasks, namely, the stabilization of the ClpXZn(II) oligomeric structure, binding to ClpP, and the ClpXP-dependent proteolysis of the lambdaO replication protein.
GO:0005524 ATP binding	IDA PMID:9575205 Enzymatic and structural similarities between the Escherichi...	ACCEPT	Summary: EcoCyc IDA. Grimaud et al. showed the ClpX hexamer is stabilised by ATP or non-hydrolysable ATP analogs. Reason: ClpX has a single Walker-type ATP site per subunit (UniProt ATP binding 120..127; HAMAP MF_00175) and ATP binding drives hexamer stabilisation, ClpP binding and the mechanical cycle. Supporting Evidence: PMID:9575205 ClpX subunits (Mr 46, 000) associate to form a six-membered ring (Mr approximately 280, 000) that is stabilized by binding of ATP or nonhydrolyzable analogs of ATP.
GO:0005524 ATP binding	IEA GO_REF:0000120	ACCEPT	Summary: Combined automated annotation from InterPro AAA+ ATPase and ClpX signatures and UniRule. Reason: Consistent with direct evidence. ClpX has a single Walker-type ATP site per subunit (UniProt ATP binding 120..127; HAMAP MF_00175) and ATP binding drives hexamer stabilisation, ClpP binding and the mechanical cycle. Supporting Evidence: file:ECOLI/clpX/clpX-uniprot.txt Belongs to the ClpX chaperone family. PMID:11278349 We show that the single ATP-binding site of ClpX is required for a variety of tasks, namely, the stabilization of the ClpXZn(II) oligomeric structure, binding to ClpP, and the ClpXP-dependent proteolysis of the lambdaO replication protein.
GO:0005829 cytosol	IDA PMID:15911532 Localization, annotation, and comparison of the Escherichia ...	ACCEPT	Summary: EcoCyc IDA from a fractionation/2D-gel proteome assigning E. coli proteins to cytosol, periplasm and membranes. Reason: ClpXP is a cytoplasmic protease (substrates include SsrA-tagged nascent chains, FtsZ, UvrA and the cytoplasmic RseA fragment) and ClpX has no signal peptide or transmembrane segment. A whole-proteome fractionation is a single assay but agrees with all functional data. Supporting Evidence: PMID:15911532 2,160 were annotated and assigned to the cytosol, periplasm, inner membrane, and outer membrane by biochemical fractionation followed by two-dimensional gel electrophoresis and tandem mass spectrometry. PMID:15371343 ClpXP functions in concert with SspB to efficiently recognize and degrade RseA(1-108), and thereby releases sigma(E).
GO:0005829 cytosol	IDA PMID:18304323 Protein abundance profiling of the Escherichia coli cytosol.	ACCEPT	Summary: EcoCyc IDA from LC-MS/MS profiling of the E. coli MC4100 cytosolic fraction. Reason: ClpXP is a cytoplasmic protease (substrates include SsrA-tagged nascent chains, FtsZ, UvrA and the cytoplasmic RseA fragment) and ClpX has no signal peptide or transmembrane segment. ClpX is not named in the cached text (likely in the supplementary list), but EcoCyc's annotation is consistent with the biology. Supporting Evidence: PMID:18304323 we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100.
GO:0006457 protein folding	IEA GO_REF:0000120	MARK AS OVER ANNOTATED	Summary: Automated protein folding annotation from the ClpX family signature (IPR004487) and UniRule. Reason: ClpX's chaperone activity in the absence of ClpP is remodelling and disassembly (e.g. MuA transpososome, lambda O replication complexes) by ATP-driven unfolding, not assisting proteins to reach a native fold. Protein folding as a process is not what ClpX does; protein unfolding (GO:0043335, accepted) describes it. Supporting Evidence: file:ECOLI/clpX/clpX-uniprot.txt Can perform chaperone functions in the absence of ClpP. file:ECOLI/clpX/clpX-uniprot.txt Interacts with Mu phage DDE-recombinase A; this interaction remodels the viral transpososome for replication. PMID:12941278 The ability to denature more stable proteins simply by using more ATP endows ClpX with a robust unfolding activity required for its biological roles in degradation and complex disassembly.
GO:0008270 zinc ion binding	IEA GO_REF:0000002	ACCEPT	Summary: InterPro (IPR010603, ClpX zinc-binding domain) mapping to zinc ion binding. Reason: Banecki et al. showed purified ClpX is a Zn(II) metalloprotein and Zn(II) is needed for oligomerisation, ClpP binding and proteolysis; UniProt records four Cys Zn ligands in the ClpX-type ZB domain. Supporting Evidence: PMID:11278349 Using an improved purification procedure we show that the ClpX protein is a metalloprotein complexed with Zn(II) cations. PMID:11278349 ClpX, free of Zn(II), cannot oligomerize, bind to ClpP, or participate in ClpXP-dependent proteolysis. file:ECOLI/clpX/clpX-uniprot.txt Binds 1 Zn(2+) ion per subunit.
GO:0009368 endopeptidase Clp complex	IPI PMID:19368884 Optimal efficiency of ClpAP and ClpXP chaperone-proteases is...	ACCEPT	Summary: ComplexPortal: ClpX is the ATPase subunit of the ClpXP endopeptidase Clp complex. Reason: ClpX hexamers cap one or both ends of the ClpP tetradecamer (PMID:9575205); this is the complex in which ClpX acts. Supporting Evidence: PMID:19368884 Rapid-kinetic fluorescence measurements and steady-state experiments indicate that single 2:1 ClpAP or ClpXP complexes are as efficient in substrate degradation as two 1:1 ClpAP or ClpXP assemblies. PMID:9575205 ClpP, which is composed of two seven-membered rings stacked face-to-face, interacts with the nucleotide-stabilized hexamer of ClpX to form a complex that could be isolated by gel filtration. file:ECOLI/clpX/clpX-uniprot.txt Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits
GO:0009376 HslUV protease complex	IBA GO_REF:0000033	MODIFY	Summary: IBA to HslUV protease complex from PTN000137358, whose only listed experimental donor is E. coli ClpX itself. Reason: HslUV is the HslU ATPase with the HslV peptidase; ClpX is not a component. The only WITH/FROM donor is P0A6H1, whose own experimental HslUV row (CAFA, PMID:14536075) is itself a wrong-complex assignment for the ClpXP protease. The essence (subunit of an ATP-dependent two-component protease) holds, but the correct complex is GO:0009368 endopeptidase Clp complex, which ClpX already carries. Propagation Review Root cause: SOURCE BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000137358 · PTN000137358 SOURCE BAD Only listed descendant evidence is P0A6H1 itself, whose CAFA IDA (PMID:14536075) assigns the HslUV complex to ClpX although the paper concerns ClpXP; ClpX belongs to the endopeptidase Clp complex. Proposed replacements: endopeptidase Clp complex Supporting Evidence: PMID:9575205 ClpP, which is composed of two seven-membered rings stacked face-to-face, interacts with the nucleotide-stabilized hexamer of ClpX to form a complex that could be isolated by gel filtration. file:ECOLI/clpX/clpX-uniprot.txt Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits
GO:0009376 HslUV protease complex	IDA PMID:14536075 Flexible linkers leash the substrate binding domain of SspB ...	MODIFY	Summary: CAFA IDA to HslUV protease complex from a paper about SspB-mediated delivery to ClpXP. Reason: The paper studies SspB delivery complexes with ClpXP (ClpX plus ClpP); nothing in it concerns HslU or HslV, and ClpX is not an HslUV subunit. The complex is mis-chosen: the essence (ClpX is part of an ATP-dependent protease complex) is correct and maps to GO:0009368 endopeptidase Clp complex. Recorded as a source defect. Proposed replacements: endopeptidase Clp complex Supporting Evidence: PMID:14536075 A synthetic peptide containing the 10 C-terminal residues of SspB binds ClpX, stimulates its ATPase activity, and prevents SspB-mediated delivery of GFP-ssrA for ClpXP degradation. PMID:9575205 ClpP, which is composed of two seven-membered rings stacked face-to-face, interacts with the nucleotide-stabilized hexamer of ClpX to form a complex that could be isolated by gel filtration.
GO:0016887 ATP hydrolysis activity	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic inference of ATP hydrolysis activity for the ClpX/Clp ATPase family. Reason: Sound IBA; P0A6H1 is among the experimentally grounded descendants. ClpX is the ATPase engine of ClpXP: ATP hydrolysis powers unfolding and translocation; E185Q and R370K mutants abolish hydrolysis (UniProt MUTAGEN, PMID:23622246). Supporting Evidence: PMID:25866879 a covalent ClpX ring with one subunit locked in the U conformation catalyzes robust ATP hydrolysis, with each unlocked subunit able to bind and hydrolyze ATP PMID:21529717 ClpX hydrolyzes ATP to generate mechanical force and translocate polypeptides through its central pore.
GO:0016887 ATP hydrolysis activity	IDA PMID:11278349 Structure-function analysis of the zinc-binding region of th...	ACCEPT	Summary: CACAO IDA. Banecki et al. characterised the Zn-binding region of ClpX, describing ClpX as an ATPase whose single ATP site is needed for oligomer stability, ClpP binding and lambda O proteolysis. Reason: CACAO row. What the paper shows for clpX: purified ClpX is a Zn(II) metalloprotein; its single ATP-binding site is required for oligomer stabilisation, ClpP binding and ClpXP degradation of lambda O, and Zn release impairs ATP binding. The abstract (all that is cached; GONUTS was offline) states ClpX is an ATPase but foregrounds ATP binding rather than a hydrolysis measurement, so the specific ATPase figure cannot be checked here. The activity is firmly established for ClpX elsewhere (PMID:25866879, PMID:21529717), so the term is correct and the curator's reading of the full text is deferred to. Supporting Evidence: PMID:11278349 The ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. PMID:11278349 We show that the single ATP-binding site of ClpX is required for a variety of tasks, namely, the stabilization of the ClpXZn(II) oligomeric structure, binding to ClpP, and the ClpXP-dependent proteolysis of the lambdaO replication protein. PMID:25866879 a covalent ClpX ring with one subunit locked in the U conformation catalyzes robust ATP hydrolysis, with each unlocked subunit able to bind and hydrolyze ATP
GO:0016887 ATP hydrolysis activity	IEA GO_REF:0000002	ACCEPT	Summary: InterPro AAA+ ATPase core (IPR003959) mapping to ATP hydrolysis activity. Reason: ClpX is the ATPase engine of ClpXP: ATP hydrolysis powers unfolding and translocation; E185Q and R370K mutants abolish hydrolysis (UniProt MUTAGEN, PMID:23622246). Supporting Evidence: PMID:25866879 a covalent ClpX ring with one subunit locked in the U conformation catalyzes robust ATP hydrolysis, with each unlocked subunit able to bind and hydrolyze ATP
GO:0030163 protein catabolic process	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic inference that Clp ATPases participate in protein catabolism. Reason: ClpX recognises, unfolds and translocates substrates into ClpP for degradation, so it does part of the work of protein catabolism (SsrA-tagged proteins, RseA, FtsZ, UvrA, lambda O). Supporting Evidence: PMID:19914167 ClpX is a AAA+ machine that uses the energy of ATP binding and hydrolysis to unfold native proteins and translocate unfolded polypeptides into the ClpP peptidase. PMID:9573050 Degradation in vitro of SsrA-tagged substrates was reproduced with purified components and required a substrate with a wild-type SsrA tail, the presence of both ClpP and either ClpA or ClpX, and ATP. PMID:15371343 ClpXP functions in concert with SspB to efficiently recognize and degrade RseA(1-108), and thereby releases sigma(E).
GO:0042802 identical protein binding	IPI PMID:19914167 Structures of asymmetric ClpX hexamers reveal nucleotide-dep...	KEEP AS NON CORE	Summary: Crystal structures of asymmetric ClpX hexamers (Glynn et al.). Reason: ClpX functions as a homohexameric ring; self-association is required for activity. Identical protein binding is true but describes assembly rather than the unfoldase activity, so it is non-core. Supporting Evidence: PMID:19914167 The crystal structures presented here reveal striking asymmetry in ring hexamers of nucleotide-free and nucleotide-bound ClpX.
GO:0042802 identical protein binding	IPI PMID:23622246 Nucleotide binding and conformational switching in the hexam...	KEEP AS NON CORE	Summary: Structures and tethered hexamers showing nucleotide-dependent subunit switching (Stinson et al. 2013). Reason: ClpX functions as a homohexameric ring; self-association is required for activity. Kept as non-core. Supporting Evidence: PMID:23622246 ClpX, a AAA+ ring homohexamer, uses the energy of ATP binding and hydrolysis to power conformational changes that unfold and translocate target proteins into the ClpP peptidase for degradation.
GO:0042802 identical protein binding	IPI PMID:24561554 The binary protein-protein interaction landscape of Escheric...	KEEP AS NON CORE	Summary: Genome-wide yeast two-hybrid screen detected ClpX self-interaction. Reason: ClpX functions as a homohexameric ring; self-association is required for activity. The Y2H self-interaction is consistent with the hexamer; kept as non-core. Supporting Evidence: PMID:24561554 we performed yeast two-hybrid screens of 3,305 baits against 3,606 preys PMID:9575205 ClpX subunits (Mr 46, 000) associate to form a six-membered ring (Mr approximately 280, 000) that is stabilized by binding of ATP or nonhydrolyzable analogs of ATP.
GO:0042802 identical protein binding	IPI PMID:25866879 Subunit asymmetry and roles of conformational switching in t...	KEEP AS NON CORE	Summary: Covalently tethered ClpX hexamers (Stinson et al. 2015). Reason: ClpX functions as a homohexameric ring; self-association is required for activity. Kept as non-core. Supporting Evidence: PMID:25866879 The hexameric AAA+ ring of Escherichia coli ClpX, an ATP-dependent machine for protein unfolding and translocation, functions with the ClpP peptidase to degrade target substrates.
GO:0043335 protein unfolding	IDA PMID:21529717 ClpX(P) generates mechanical force to unfold and translocate...	ACCEPT	Summary: CACAO IDA. Aubin-Tam et al. directly observed force-induced unfolding of substrate domains by ClpX alone and by ClpXP in optical-trap single-molecule experiments. Reason: CACAO row. What the paper shows for clpX (full text cached): dual-trap optical tweezers record ClpX hydrolysing ATP to translocate a tethered polypeptide, unfolding folded domains in steps of 1-3 nm, slipping and retrying at stable domains, with ClpP binding reducing slips and GFP unravelling cooperatively under ClpXP. This is a direct assay of ClpX disrupting non-covalent structure in substrate proteins, exactly the GO:0043335 definition, at the right granularity. Core process. Supporting Evidence: PMID:21529717 We report direct observations of mechanical, force-induced protein unfolding by the ClpX unfoldase from E. coli, alone, and in complex with the ClpP peptidase. PMID:21529717 ClpX hydrolyzes ATP to generate mechanical force and translocate polypeptides through its central pore. PMID:12941278 The ability to denature more stable proteins simply by using more ATP endows ClpX with a robust unfolding activity required for its biological roles in degradation and complex disassembly.
GO:0044183 protein folding chaperone	IEA GO_REF:0000104	MODIFY	Summary: UniRule-based transfer of protein folding chaperone. Reason: The term is correct but less specific than the ATP-dependent chaperone term this gene already carries (GO:0140662, from InterPro). ClpX can act as an ATP-dependent chaperone without ClpP (UniProt), but its chaperone activity is remodelling/disassembly by unfolding (e.g. MuA transpososome) rather than promoting folding. GO has no ATP-dependent protein unfoldase MF; GO:0140662 is the closest existing term and is kept as non-core, while the core activity is recorded as ATP hydrolysis activity coupled to protein unfolding. Proposed replacements: ATP-dependent protein folding chaperone Supporting Evidence: file:ECOLI/clpX/clpX-uniprot.txt Can perform chaperone functions in the absence of ClpP. PMID:11278349 The ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone.
GO:0046983 protein dimerization activity	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: InterPro ClpX zinc-binding domain (IPR010603) mapping to protein dimerization activity. Reason: The N-terminal ClpX-type zinc-binding domain is reported to form dimers and Zn(II) is needed for oligomerisation (PMID:11278349). The claim is plausible but peripheral to the unfoldase function and is kept as non-core. Supporting Evidence: PMID:11278349 ClpX, free of Zn(II), cannot oligomerize, bind to ClpP, or participate in ClpXP-dependent proteolysis.
GO:0051301 cell division	IBA GO_REF:0000033	MODIFY	Summary: IBA to cell division from PTN000137358, donors E. coli ClpX and M. tuberculosis ClpX (P9WPB9). Reason: The donors' evidence is that ClpX modulates FtsZ (degradation in E. coli; Mtb ClpX inhibits FtsZ assembly), i.e. regulation of division rather than execution of it. ClpXP degrades FtsZ and so tunes FtsZ levels and polymer dynamics (PMID:19541655); ClpX does not itself perform a step of cytokinesis. The process the evidence supports is regulation of cell division (GO:0051302), the paper's own framing ('modulates'). Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000137358 · PTN000137358 SUPPORTS TRANSFER The node placement is plausible (E. coli and M. tuberculosis ClpX both act on FtsZ), but donor evidence shows modulation of FtsZ and division, so the inherited term should be regulation of cell division. Proposed replacements: regulation of cell division Supporting Evidence: PMID:19541655 These results suggest that ClpXP may participate in cell division by modulating the equilibrium between free and polymeric FtsZ via degradation of FtsZ filaments and protomers. PMID:21317324 Our results demonstrate that ClpXP modulates division in cells lacking MinC by a mechanism that requires ATP-dependent degradation.
GO:0051301 cell division	IGI PMID:21317324 The interplay of ClpXP with the cell division machinery in E...	MODIFY	Summary: CACAO IGI with ftsZ. Camberg et al. 2011: clpX deletion suppresses ftsZ84 filamentation and reduces FtsZ84 degradation, and exacerbates filamentation of a delta-minC strain. Reason: CACAO row. What the paper shows for clpX (abstract cached; PMC full text not retrievable; GONUTS offline): genetic interactions of delta-clpX with ftsZ84 (suppression of filamentation, slower FtsZ84 turnover) and with delta-minC (delayed division), interpreted by the authors as ClpXP modulating division through ATP-dependent degradation of FtsZ and possibly other division proteins. The IGI is real, but cell division is a phenotype-level reading: ClpX acts upstream by degrading a division protein. The correct granularity is regulation of cell division. ClpXP degrades FtsZ and so tunes FtsZ levels and polymer dynamics (PMID:19541655); ClpX does not itself perform a step of cytokinesis. The process the evidence supports is regulation of cell division (GO:0051302), the paper's own framing ('modulates'). Proposed replacements: regulation of cell division Supporting Evidence: PMID:21317324 In the ftsZ84 strain, which is temperature sensitive for filamentation due to a mutation in ftsZ, we observed that deletion of clpX or clpP suppresses filamentation and reduces FtsZ84 degradation. PMID:21317324 Our results demonstrate that ClpXP modulates division in cells lacking MinC by a mechanism that requires ATP-dependent degradation. PMID:19541655 These results suggest that ClpXP may participate in cell division by modulating the equilibrium between free and polymeric FtsZ via degradation of FtsZ filaments and protomers.
GO:0097718 disordered domain specific binding	IPI PMID:14536075 Flexible linkers leash the substrate binding domain of SspB ...	ACCEPT	Summary: CAFA IPI with SspB: the unstructured C-terminal tail of the SspB adaptor docks onto ClpX. Reason: The abstract shows SspB's C-terminal 40-50 residues are unstructured and that a 10-residue C-terminal SspB peptide binds ClpX and stimulates its ATPase. Binding the disordered ClpX-binding (XB) tail of the adaptor is how ClpX recruits adaptor-delivered substrates; the term matches the evidence. Supporting Evidence: PMID:14536075 The C-terminal 40-50 residues of SspB are unstructured but are required for SspB to form substrate-delivery complexes with ClpXP. PMID:14536075 A synthetic peptide containing the 10 C-terminal residues of SspB binds ClpX, stimulates its ATPase activity, and prevents SspB-mediated delivery of GFP-ssrA for ClpXP degradation.
GO:0140662 ATP-dependent protein folding chaperone	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: InterPro ClpX family (IPR004487) mapping to ATP-dependent protein folding chaperone. Reason: ClpX can act as an ATP-dependent chaperone without ClpP (UniProt), but its chaperone activity is remodelling/disassembly by unfolding (e.g. MuA transpososome) rather than promoting folding. GO has no ATP-dependent protein unfoldase MF; GO:0140662 is the closest existing term and is kept as non-core, while the core activity is recorded as ATP hydrolysis activity coupled to protein unfolding. Supporting Evidence: file:ECOLI/clpX/clpX-uniprot.txt Can perform chaperone functions in the absence of ClpP. file:ECOLI/clpX/clpX-uniprot.txt Interacts with Mu phage DDE-recombinase A; this interaction remodels the viral transpososome for replication. PMID:11278349 The ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone.
GO:0016504 peptidase activator activity	IDA PMID:9575205 Enzymatic and structural similarities between the Escherichi...	NEW	Summary: ClpX binding to ClpP induces conformational changes that increase ClpP catalytic efficiency and access, giving ClpXP high activity on oligopeptides. Reason: ClpX directly binds ClpP and increases its peptidase activity (PMID:9575205), matching the GO:0016504 definition. ClpX here does the work itself (binding and activating the peptidase). The comparator check holds: human CLPX carries GO:0016504 by IDA in this repository's review. Not in current E. coli GOA. Supporting Evidence: PMID:9575205 ClpX and ClpA interactions with ClpP result in structurally analogous complexes and induce similar conformational changes that affect the accessibility and the catalytic efficiency of ClpP active sites. PMID:9575205 ClpP, which is composed of two seven-membered rings stacked face-to-face, interacts with the nucleotide-stabilized hexamer of ClpX to form a complex that could be isolated by gel filtration.

Gene Description

Existing Annotations Review

Core Functions

ATP-dependent unfoldase of the ClpXP protease: the ClpX hexamer binds degron-tagged or adaptor-delivered substrates, hydrolyses ATP to unfold them mechanically, and translocates the polypeptide into the ClpP chamber for degradation.

Activation of the ClpP peptidase: ClpX docks on ClpP and induces conformational changes that open access to, and increase the catalytic efficiency of, the ClpP active sites, making the ClpXP holoenzyme an ATP-dependent peptidase.

Substrate selection via adaptor docking: ClpX binds the disordered C-terminal ClpX-binding peptide of the SspB adaptor, which tethers ssrA-tagged proteins and RseA(1-108) to ClpXP, and so regulates substrate choice (for example releasing sigma-E).

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