CpxP is a periplasmic auxiliary protein of the Cpx two-component envelope stress response system in E. coli. Its primary function is to inhibit the autophosphorylation activity of the sensor kinase CpxA, thereby negatively regulating the Cpx stress response in the absence of envelope stress signals (PMID:17259177, PMID:21239493). CpxP forms an elongated homodimer with a cap-shaped structure. Its concave polar surface interacts with the periplasmic sensor domain of CpxA, while an extended hydrophobic cleft on its convex surface recognizes misfolded periplasmic proteins such as P pilus subunits (PMID:21239493). Upon detection of misfolded proteins (e.g., PapE), CpxP is displaced from CpxA and degraded by the DegP protease together with its substrate, thus activating the Cpx response (PMID:16303867, PMID:25207645). CpxP therefore acts as a dual-function adaptor protein, serving both as a signaling inhibitor and as a periplasmic adaptor that delivers misfolded proteins to DegP for degradation. UniProt describes CpxP as having only "mild protein chaperone activity" (PMID:21239493, PMID:21317898), and its primary evolved function is clearly that of a signaling modulator and proteolysis adaptor, not a general chaperone.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0030288
outer membrane-bounded periplasmic space
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: IBA annotation for periplasmic localization, consistent with the IDA annotation for the same term (PMID:9473036). CpxP is a well-established periplasmic protein with a signal peptide (residues 1-21).
Reason: Periplasmic localization of CpxP is confirmed experimentally (PMID:9473036, PMID:25207645) and phylogenetically by IBA. This is a core localization annotation.
|
|
GO:0051082
unfolded protein binding
|
IBA
GO_REF:0000033 |
MARK AS OVER ANNOTATED |
Summary: IBA annotation for unfolded protein binding. CpxP does interact with misfolded periplasmic proteins via its hydrophobic cleft (PMID:21239493), but this interaction is primarily in the context of its adaptor function for DegP-mediated proteolysis, not general chaperone holdase activity. UniProt explicitly describes CpxP as having only "mild protein chaperone activity" (PMID:21317898).
Reason: While CpxP does bind misfolded proteins, this is not its primary function. CpxP functions as a signaling inhibitor and proteolysis adaptor, not as a general chaperone. The "unfolded protein binding" annotation overstates the chaperone aspect and obscures the true function. The misfolded protein binding is in service of its adaptor role for DegP proteolysis (PMID:16303867) and signal transduction modulation (PMID:21239493), not for preventing aggregation per se. UniProt explicitly states "mild protein chaperone activity" (PMID:21317898).
Supporting Evidence:
PMID:16303867
CpxP functions as a periplasmic adaptor protein that is required for the effective proteolysis of a subset of misfolded substrates by the DegP protease.
PMID:21239493
an extended hydrophobic cleft on the convex surface suggests a potent substrate recognition site for misfolded pilus subunits
|
|
GO:0042597
periplasmic space
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: IEA annotation for periplasmic space localization. This is a broader parent of GO:0030288 (outer membrane-bounded periplasmic space) which is annotated with IDA and IBA evidence.
Reason: Periplasmic localization is well established. This broader IEA is acceptable alongside the more specific IDA annotation.
|
|
GO:0042802
identical protein binding
|
IPI
PMID:21317318 Structure of the periplasmic stress response protein CpxP. |
ACCEPT |
Summary: IPI annotation for identical protein binding. CpxP forms a homodimer, as demonstrated by crystal structure (PMID:21317318, PMID:21239493). The homodimer has an intertwined antiparallel alpha-helical structure.
Reason: CpxP homodimerization is well-established structurally and functionally. The crystal structures (PMID:21317318 at 2.85A, PMID:21239493 at 1.45A) confirm the dimer is the functional form. This is a meaningful interaction relevant to its biological function, not a generic "protein binding" annotation.
Supporting Evidence:
PMID:21317318
The structure revealed an antiparallel dimer of intertwined alpha-helices with a highly basic concave surface.
|
|
GO:0005515
protein binding
|
IDA
PMID:17259177 Purification, reconstitution, and characterization of the Cp... |
MODIFY |
Summary: IDA annotation for protein binding from Fleischer et al. (2007), which demonstrated direct protein-protein interaction between CpxP and CpxA in reconstituted proteoliposomes. CpxP inhibited CpxA autophosphorylation by 50%.
Reason: The "protein binding" term is too generic. CpxP binds CpxA specifically to inhibit its sensor kinase activity. A more informative term would be GO:0030547 "signaling receptor inhibitor activity" which captures the functional consequence of the binding -- inhibition of CpxA signaling.
Proposed replacements:
signaling receptor inhibitor activity
Supporting Evidence:
PMID:17259177
Purified tagless CpxP protein reduced the phosphorylation status of CpxA to 50% but had no effect on CpxA phosphotransfer or phosphatase activities.
|
|
GO:0030162
regulation of proteolysis
|
EXP
PMID:16303867 The extracytoplasmic adaptor protein CpxP is degraded with s... |
ACCEPT |
Summary: EXP annotation for regulation of proteolysis. Isaac et al. (2005) demonstrated that CpxP acts as a periplasmic adaptor protein required for the effective DegP-mediated degradation of misfolded P pilus subunits. The presence of misfolded substrate enhances CpxP proteolysis by DegP.
Reason: This is a well-supported core function. CpxP serves as an adaptor for DegP protease, facilitating the degradation of misfolded periplasmic proteins (PMID:16303867). This adaptor function for proteolysis is one of CpxP's two primary biological roles.
Supporting Evidence:
PMID:16303867
CpxP functions as a periplasmic adaptor protein that is required for the effective proteolysis of a subset of misfolded substrates by the DegP protease.
|
|
GO:0030288
outer membrane-bounded periplasmic space
|
IDA
PMID:9473036 CpxP, a stress-combative member of the Cpx regulon. |
ACCEPT |
Summary: IDA annotation for periplasmic localization based on Danese and Silhavy (1998). CpxP is a periplasmic protein induced by the Cpx system.
Reason: Direct experimental evidence confirms CpxP periplasmic localization (PMID:9473036). The protein has a signal peptide and is found in the periplasm.
Supporting Evidence:
PMID:9473036
cpxP specifies a periplasmic protein that can combat the lethal phenotype associated with the synthesis of a toxic envelope protein.
|
|
GO:0051082
unfolded protein binding
|
ISM
PMID:21239493 Structural basis for two-component system inhibition and pil... |
MARK AS OVER ANNOTATED |
Summary: ISM (sequence model) annotation for unfolded protein binding based on Zhou et al. (2011). The crystal structure revealed a hydrophobic cleft on the convex surface that may serve as a substrate recognition site for misfolded proteins.
Reason: Same reasoning as for the IBA annotation of this term. The hydrophobic cleft identified by structural analysis (PMID:21239493) is primarily involved in recognition of misfolded substrates for delivery to DegP protease, not for general chaperone holdase activity. CpxP has only "mild protein chaperone activity" per UniProt.
Supporting Evidence:
PMID:21239493
an extended hydrophobic cleft on the convex surface suggests a potent substrate recognition site for misfolded pilus subunits
|
|
GO:0051082
unfolded protein binding
|
IDA
PMID:21239493 Structural basis for two-component system inhibition and pil... |
MARK AS OVER ANNOTATED |
Summary: IDA annotation for unfolded protein binding from Zhou et al. (2011). This study showed CpxP binds misfolded PapE pilus subunits and promotes their degradation by DegP. The study also confirmed mild chaperone activity for CpxP.
Reason: CpxP does bind misfolded proteins, but this binding is primarily in the context of its adaptor function for DegP-mediated proteolysis and its role in sensing misfolded proteins for Cpx signaling, not general chaperone activity. Overexpression of CpxP leads to DegP-mediated degradation of misfolded pilus subunits (PMID:21239493). The primary function is signal transduction modulation and proteolysis adaptor activity, with chaperone activity being only mild and secondary.
Supporting Evidence:
PMID:21239493
CpxP both inhibits activation of CpxA and is indispensable for the quality control system of P pili
|
|
GO:0005515
protein binding
|
IDA
PMID:25207645 Dynamic interaction between the CpxA sensor kinase and the p... |
MODIFY |
Summary: IDA annotation for protein binding from Tschauner et al. (2014), which demonstrated direct physical interaction between CpxP and CpxA using bacterial two-hybrid and membrane-Strep-tagged protein interaction experiments. The interaction is dynamic and modulated by stress signals.
Reason: Same as the other protein binding annotation -- "protein binding" is too vague. This study specifically demonstrates CpxP-CpxA interaction that inhibits Cpx signaling. GO:0030547 "signaling receptor inhibitor activity" is more appropriate.
Proposed replacements:
signaling receptor inhibitor activity
Supporting Evidence:
PMID:25207645
CpxP modulates the activity of the Cpx system by dynamic interaction with CpxA in response to specific stresses.
|
|
GO:0006950
response to stress
|
IDA
PMID:9473036 CpxP, a stress-combative member of the Cpx regulon. |
ACCEPT |
Summary: IDA annotation for response to stress based on Danese and Silhavy (1998). CpxP combats extracytoplasmic protein-mediated toxicity and cpxP mutants are hypersensitive to alkaline pH.
Reason: CpxP is a core component of the envelope stress response, combating toxicity from misfolded periplasmic proteins (PMID:9473036, PMID:16303867). While this is a broad term, it accurately reflects CpxP's role. A more specific term could be considered, but this annotation is not incorrect.
Supporting Evidence:
PMID:9473036
cpxP specifies a periplasmic protein that can combat the lethal phenotype associated with the synthesis of a toxic envelope protein... cpxP and cpx mutant strains display hypersensitivity to growth in alkaline conditions.
|
Exported on March 22, 2026 at 02:17 AM
Organism: Escherichia coli
Sequence:
MRIVTAAVMASTLAVSSLSHAAEVGSGDNWHPGEELTQRSTQSHMFDGISLTEHQRQQMRDLMQQARHEQPPVNVSELETMHRLVTAENFDENAVRAQAEKMANEQIARQVEMAKVRNQMYRLLTPEQQAVLNEKHQQRMEQLRDVTQWQKSSSLKLLSSSNSRSQ
The architecture begins with IPR052211 (Cpx two-component system auxiliary protein family) spanning residues 1–155 and is overlapped internally by IPR012899 (LTXXQ motif family protein) from residues 6–144. The full-length coverage of the auxiliary Cpx-SpvX family signature at the N-terminus and across the core of the protein establishes a dedicated adaptor/scaffold rather than an enzyme. The embedded LTXXQ motif family signature points to a conserved structural module often used to stabilize oligomeric assemblies and mediate protein–protein interfaces. The absence of catalytic domain hallmarks and the dominance of interaction-centric families together indicate a non-enzymatic regulator that binds partners to modulate signal flow.
From this domain logic, the molecular function resolves to multivalent protein binding (GO:0005515). An auxiliary module that couples to a membrane sensor/transducer system achieves function by physically organizing the signaling complex rather than performing chemistry. Such an adaptor can bias the assembly and lifetime of the Cpx two-component pathway by tuning the association of the periplasmic sensor with cytosolic response regulators and associated RNA-binding effectors.
This binding-driven modulation situates the protein squarely within signal transduction (GO:0007165). By stabilizing or accelerating exchange within the Cpx pathway, the auxiliary factor can influence envelope-stress signaling cascades that govern transcriptional and post-transcriptional responses. The LTXXQ motif’s scaffold-like behavior supports a mechanism where transient oligomers and surface-exposed patches choreograph partner recruitment and turnover, thereby shaping downstream signaling dynamics.
Cellular localization follows from both the soluble interaction architecture and the functional coupling to envelope-stress signaling. The lack of transmembrane domains and the soluble nature implied by the family signatures point to the cytoplasm (GO:0005737), where the adaptor can access cytosolic faces of membrane-associated complexes and cytoplasmic response regulators. Cytoplasmic residence also allows rapid exchange with RNA-associated assemblies that interpret Cpx outputs.
Mechanistically, the protein likely nucleates a periplasm-to-cytosol signaling node by binding cytosolic components of the Cpx system and allied RNA-binding assemblies. By favoring specific oligomeric states and partner availabilities, it can increase the fidelity and speed of Cpx-mediated signal propagation. Expected partners include the membrane-associated sensor/transducer, periplasm-proximal folding modules that feed into Cpx, and cytosolic response regulators and RNA-binding proteins that execute the transcriptional/post-transcriptional arms of the pathway. Together, these interactions produce a tunable cytoplasmic hub that conditions envelope-stress signaling fidelity.
A soluble cytoplasmic auxiliary factor that assembles and stabilizes the envelope-stress signaling hub governed by the Cpx two-component pathway in Escherichia coli. By using a conserved interaction module to form transient oligomers, it binds pathway partners and conditions the assembly and lifetime of the signaling complex, thereby tuning downstream transcriptional and post-transcriptional responses without catalysis.
Auxiliary component of the Cpx stress protein system.
IPR052211, family) — residues 1-155IPR012899, family) — residues 6-144Molecular Function: molecular_function (GO:0003674), binding (GO:0005488), ion binding (GO:0043167), protein binding (GO:0005515), identical protein binding (GO:0042802), cation binding (GO:0043169), metal ion binding (GO:0046872), transition metal ion binding (GO:0046914), zinc ion binding (GO:0008270)
Biological Process: biological_process (GO:0008150), cellular process (GO:0009987), protein folding (GO:0006457), chaperone-mediated protein folding (GO:0061077)
Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), intracellular anatomical structure (GO:0005622), organelle (GO:0043226), envelope (GO:0031975), membrane (GO:0016020), cytoplasm (GO:0005737), organelle membrane (GO:0031090), organelle envelope (GO:0031967), photosynthetic membrane (GO:0034357), intracellular organelle (GO:0043229), outer membrane (GO:0019867), membrane-bounded organelle (GO:0043227), mitochondrial envelope (GO:0005740), organelle outer membrane (GO:0031968), intracellular membrane-bounded organelle (GO:0043231), bounding membrane of organelle (GO:0098588), mitochondrial membrane (GO:0031966), mitochondrial outer membrane (GO:0005741)
Generated by BioReason
Exported on March 22, 2026 at 02:17 AM
Organism: Escherichia coli
Sequence:
MRIVTAAVMASTLAVSSLSHAAEVGSGDNWHPGEELTQRSTQSHMFDGISLTEHQRQQMRDLMQQARHEQPPVNVSELETMHRLVTAENFDENAVRAQAEKMANEQIARQVEMAKVRNQMYRLLTPEQQAVLNEKHQQRMEQLRDVTQWQKSSSLKLLSSSNSRSQ
The architecture begins with IPR052211 (Cpx two-component system auxiliary protein family) spanning residues 1–155 and is overlapped internally by IPR012899 (LTXXQ motif family protein) from residues 6–144. The full-length coverage of the auxiliary Cpx-SpvX family signature at the N-terminus and across the core of the protein establishes a dedicated adaptor/scaffold rather than an enzyme. The embedded LTXXQ motif family signature points to a conserved structural module often used to stabilize oligomeric assemblies and mediate protein–protein interfaces. The absence of catalytic domain hallmarks and the dominance of interaction-centric families together indicate a non-enzymatic regulator that binds partners to modulate signal flow.
From this domain logic, the molecular function resolves to multivalent protein binding (GO:0005515). An auxiliary module that couples to a membrane sensor/transducer system achieves function by physically organizing the signaling complex rather than performing chemistry. Such an adaptor can bias the assembly and lifetime of the Cpx two-component pathway by tuning the association of the periplasmic sensor with cytosolic response regulators and associated RNA-binding effectors.
This binding-driven modulation situates the protein squarely within signal transduction (GO:0007165). By stabilizing or accelerating exchange within the Cpx pathway, the auxiliary factor can influence envelope-stress signaling cascades that govern transcriptional and post-transcriptional responses. The LTXXQ motif’s scaffold-like behavior supports a mechanism where transient oligomers and surface-exposed patches choreograph partner recruitment and turnover, thereby shaping downstream signaling dynamics.
Cellular localization follows from both the soluble interaction architecture and the functional coupling to envelope-stress signaling. The lack of transmembrane domains and the soluble nature implied by the family signatures point to the cytoplasm (GO:0005737), where the adaptor can access cytosolic faces of membrane-associated complexes and cytoplasmic response regulators. Cytoplasmic residence also allows rapid exchange with RNA-associated assemblies that interpret Cpx outputs.
Mechanistically, the protein likely nucleates a periplasm-to-cytosol signaling node by binding cytosolic components of the Cpx system and allied RNA-binding assemblies. By favoring specific oligomeric states and partner availabilities, it can increase the fidelity and speed of Cpx-mediated signal propagation. Expected partners include the membrane-associated sensor/transducer, periplasm-proximal folding modules that feed into Cpx, and cytosolic response regulators and RNA-binding proteins that execute the transcriptional/post-transcriptional arms of the pathway. Together, these interactions produce a tunable cytoplasmic hub that conditions envelope-stress signaling fidelity.
A soluble cytoplasmic auxiliary factor that assembles and stabilizes the envelope-stress signaling hub governed by the Cpx two-component pathway in Escherichia coli. By using a conserved interaction module to form transient oligomers, it binds pathway partners and conditions the assembly and lifetime of the signaling complex, thereby tuning downstream transcriptional and post-transcriptional responses without catalysis.
Auxiliary component of the Cpx stress protein system.
IPR052211, family) — residues 1-155IPR012899, family) — residues 6-144Molecular Function: molecular_function (GO:0003674), binding (GO:0005488), ion binding (GO:0043167), protein binding (GO:0005515), identical protein binding (GO:0042802), cation binding (GO:0043169), metal ion binding (GO:0046872), transition metal ion binding (GO:0046914), zinc ion binding (GO:0008270)
Biological Process: biological_process (GO:0008150), cellular process (GO:0009987), protein folding (GO:0006457), chaperone-mediated protein folding (GO:0061077)
Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), intracellular anatomical structure (GO:0005622), organelle (GO:0043226), envelope (GO:0031975), membrane (GO:0016020), cytoplasm (GO:0005737), organelle membrane (GO:0031090), organelle envelope (GO:0031967), photosynthetic membrane (GO:0034357), intracellular organelle (GO:0043229), outer membrane (GO:0019867), membrane-bounded organelle (GO:0043227), mitochondrial envelope (GO:0005740), organelle outer membrane (GO:0031968), intracellular membrane-bounded organelle (GO:0043231), bounding membrane of organelle (GO:0098588), mitochondrial membrane (GO:0031966), mitochondrial outer membrane (GO:0005741)
Generated by BioReason
Source: CpxP-deep-research-bioreason-rl.md
The BioReason functional summary describes CpxP as:
A soluble cytoplasmic auxiliary factor that assembles and stabilizes the envelope-stress signaling hub governed by the Cpx two-component pathway in Escherichia coli. By using a conserved interaction module to form transient oligomers, it binds pathway partners and conditions the assembly and lifetime of the signaling complex, thereby tuning downstream transcriptional and post-transcriptional responses without catalysis.
This summary contains two major errors:
Wrong localization: CpxP is described as "cytoplasmic," but it is a well-established periplasmic protein with a signal peptide (residues 1-21). The curated review and multiple crystal structures (PMID:21239493, PMID:21317318) confirm periplasmic localization. This is a critical error since CpxP's function depends on its periplasmic location, where it directly interacts with the periplasmic sensor domain of CpxA.
Vague functional description: The summary describes CpxP generically as "tuning downstream transcriptional and post-transcriptional responses." In reality, CpxP has two well-defined functions: (a) it inhibits CpxA autophosphorylation by binding its periplasmic sensor domain, acting as a negative regulator of the Cpx pathway (PMID:17259177), and (b) it functions as a periplasmic adaptor protein that delivers misfolded proteins (e.g., PapE pilus subunits) to the DegP protease for degradation (PMID:16303867).
The summary correctly identifies CpxP as non-catalytic and associated with the Cpx pathway, but misses the dual-function adaptor/inhibitor mechanism and gets the cellular compartment wrong.
Notably, the GO term predictions include mitochondrial terms (GO:0005741 mitochondrial outer membrane, GO:0005740 mitochondrial envelope) which are nonsensical for a bacterial protein.
Comparison with interpro2go:
CpxP has no GO_REF:0000002 annotations in the curated review. The BioReason model correctly identifies the Cpx system association from IPR052211, but then misinterprets the localization and function. The model's CC predictions include periplasmic space (GO:0042597) and outer membrane-bounded periplasmic space (GO:0030288) in its GO terms, contradicting its own functional summary that says "cytoplasmic." This internal inconsistency suggests the narrative generation and GO prediction pipelines may not be well integrated.
The trace correctly identifies the IPR052211 (Cpx auxiliary protein) and IPR012899 (LTXXQ motif) domains. However, it then infers cytoplasmic localization "from the absence of transmembrane segments," ignoring that the protein has a signal peptide for periplasmic export. The trace also mentions "RNA-binding assemblies" as interaction partners, which has no experimental support for CpxP.
id: P0AE85
gene_symbol: CpxP
product_type: PROTEIN
status: IN_PROGRESS
taxon:
id: NCBITaxon:83333
label: Escherichia coli (strain K12)
description: CpxP is a periplasmic auxiliary protein of the Cpx two-component envelope
stress response system in E. coli. Its primary function is to inhibit the autophosphorylation
activity of the sensor kinase CpxA, thereby negatively regulating the Cpx stress
response in the absence of envelope stress signals (PMID:17259177, PMID:21239493).
CpxP forms an elongated homodimer with a cap-shaped structure. Its concave polar
surface interacts with the periplasmic sensor domain of CpxA, while an extended
hydrophobic cleft on its convex surface recognizes misfolded periplasmic proteins
such as P pilus subunits (PMID:21239493). Upon detection of misfolded proteins (e.g.,
PapE), CpxP is displaced from CpxA and degraded by the DegP protease together with
its substrate, thus activating the Cpx response (PMID:16303867, PMID:25207645).
CpxP therefore acts as a dual-function adaptor protein, serving both as a signaling
inhibitor and as a periplasmic adaptor that delivers misfolded proteins to DegP
for degradation. UniProt describes CpxP as having only "mild protein chaperone activity"
(PMID:21239493, PMID:21317898), and its primary evolved function is clearly that
of a signaling modulator and proteolysis adaptor, not a general chaperone.
existing_annotations:
- term:
id: GO:0030288
label: outer membrane-bounded periplasmic space
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: IBA annotation for periplasmic localization, consistent with the IDA
annotation for the same term (PMID:9473036). CpxP is a well-established periplasmic
protein with a signal peptide (residues 1-21).
action: ACCEPT
reason: Periplasmic localization of CpxP is confirmed experimentally (PMID:9473036,
PMID:25207645) and phylogenetically by IBA. This is a core localization annotation.
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: IBA annotation for unfolded protein binding. CpxP does interact with
misfolded periplasmic proteins via its hydrophobic cleft (PMID:21239493), but
this interaction is primarily in the context of its adaptor function for DegP-mediated
proteolysis, not general chaperone holdase activity. UniProt explicitly describes
CpxP as having only "mild protein chaperone activity" (PMID:21317898).
action: MARK_AS_OVER_ANNOTATED
reason: While CpxP does bind misfolded proteins, this is not its primary function.
CpxP functions as a signaling inhibitor and proteolysis adaptor, not as a general
chaperone. The "unfolded protein binding" annotation overstates the chaperone
aspect and obscures the true function. The misfolded protein binding is in service
of its adaptor role for DegP proteolysis (PMID:16303867) and signal transduction
modulation (PMID:21239493), not for preventing aggregation per se. UniProt explicitly
states "mild protein chaperone activity" (PMID:21317898).
supported_by:
- reference_id: PMID:16303867
supporting_text: CpxP functions as a periplasmic adaptor protein that is required
for the effective proteolysis of a subset of misfolded substrates by the DegP
protease.
- reference_id: PMID:21239493
supporting_text: an extended hydrophobic cleft on the convex surface suggests
a potent substrate recognition site for misfolded pilus subunits
- term:
id: GO:0042597
label: periplasmic space
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: IEA annotation for periplasmic space localization. This is a broader
parent of GO:0030288 (outer membrane-bounded periplasmic space) which is annotated
with IDA and IBA evidence.
action: ACCEPT
reason: Periplasmic localization is well established. This broader IEA is acceptable
alongside the more specific IDA annotation.
- term:
id: GO:0042802
label: identical protein binding
evidence_type: IPI
original_reference_id: PMID:21317318
review:
summary: IPI annotation for identical protein binding. CpxP forms a homodimer,
as demonstrated by crystal structure (PMID:21317318, PMID:21239493). The homodimer
has an intertwined antiparallel alpha-helical structure.
action: ACCEPT
reason: CpxP homodimerization is well-established structurally and functionally.
The crystal structures (PMID:21317318 at 2.85A, PMID:21239493 at 1.45A) confirm
the dimer is the functional form. This is a meaningful interaction relevant
to its biological function, not a generic "protein binding" annotation.
supported_by:
- reference_id: PMID:21317318
supporting_text: The structure revealed an antiparallel dimer of intertwined
alpha-helices with a highly basic concave surface.
- term:
id: GO:0005515
label: protein binding
evidence_type: IDA
original_reference_id: PMID:17259177
review:
summary: IDA annotation for protein binding from Fleischer et al. (2007), which
demonstrated direct protein-protein interaction between CpxP and CpxA in reconstituted
proteoliposomes. CpxP inhibited CpxA autophosphorylation by 50%.
action: MODIFY
reason: The "protein binding" term is too generic. CpxP binds CpxA specifically
to inhibit its sensor kinase activity. A more informative term would be GO:0030547
"signaling receptor inhibitor activity" which captures the functional consequence
of the binding -- inhibition of CpxA signaling.
proposed_replacement_terms:
- id: GO:0030547
label: signaling receptor inhibitor activity
supported_by:
- reference_id: PMID:17259177
supporting_text: Purified tagless CpxP protein reduced the phosphorylation status
of CpxA to 50% but had no effect on CpxA phosphotransfer or phosphatase activities.
- term:
id: GO:0030162
label: regulation of proteolysis
evidence_type: EXP
original_reference_id: PMID:16303867
review:
summary: EXP annotation for regulation of proteolysis. Isaac et al. (2005) demonstrated
that CpxP acts as a periplasmic adaptor protein required for the effective DegP-mediated
degradation of misfolded P pilus subunits. The presence of misfolded substrate
enhances CpxP proteolysis by DegP.
action: ACCEPT
reason: This is a well-supported core function. CpxP serves as an adaptor for
DegP protease, facilitating the degradation of misfolded periplasmic proteins
(PMID:16303867). This adaptor function for proteolysis is one of CpxP's two
primary biological roles.
supported_by:
- reference_id: PMID:16303867
supporting_text: CpxP functions as a periplasmic adaptor protein that is required
for the effective proteolysis of a subset of misfolded substrates by the DegP
protease.
- term:
id: GO:0030288
label: outer membrane-bounded periplasmic space
evidence_type: IDA
original_reference_id: PMID:9473036
review:
summary: IDA annotation for periplasmic localization based on Danese and Silhavy
(1998). CpxP is a periplasmic protein induced by the Cpx system.
action: ACCEPT
reason: Direct experimental evidence confirms CpxP periplasmic localization (PMID:9473036).
The protein has a signal peptide and is found in the periplasm.
supported_by:
- reference_id: PMID:9473036
supporting_text: cpxP specifies a periplasmic protein that can combat the lethal
phenotype associated with the synthesis of a toxic envelope protein.
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: ISM
original_reference_id: PMID:21239493
review:
summary: ISM (sequence model) annotation for unfolded protein binding based on
Zhou et al. (2011). The crystal structure revealed a hydrophobic cleft on the
convex surface that may serve as a substrate recognition site for misfolded
proteins.
action: MARK_AS_OVER_ANNOTATED
reason: Same reasoning as for the IBA annotation of this term. The hydrophobic
cleft identified by structural analysis (PMID:21239493) is primarily involved
in recognition of misfolded substrates for delivery to DegP protease, not for
general chaperone holdase activity. CpxP has only "mild protein chaperone activity"
per UniProt.
supported_by:
- reference_id: PMID:21239493
supporting_text: an extended hydrophobic cleft on the convex surface suggests
a potent substrate recognition site for misfolded pilus subunits
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IDA
original_reference_id: PMID:21239493
review:
summary: IDA annotation for unfolded protein binding from Zhou et al. (2011).
This study showed CpxP binds misfolded PapE pilus subunits and promotes their
degradation by DegP. The study also confirmed mild chaperone activity for CpxP.
action: MARK_AS_OVER_ANNOTATED
reason: CpxP does bind misfolded proteins, but this binding is primarily in the
context of its adaptor function for DegP-mediated proteolysis and its role in
sensing misfolded proteins for Cpx signaling, not general chaperone activity.
Overexpression of CpxP leads to DegP-mediated degradation of misfolded pilus
subunits (PMID:21239493). The primary function is signal transduction modulation
and proteolysis adaptor activity, with chaperone activity being only mild and
secondary.
supported_by:
- reference_id: PMID:21239493
supporting_text: CpxP both inhibits activation of CpxA and is indispensable
for the quality control system of P pili
- term:
id: GO:0005515
label: protein binding
evidence_type: IDA
original_reference_id: PMID:25207645
review:
summary: IDA annotation for protein binding from Tschauner et al. (2014), which
demonstrated direct physical interaction between CpxP and CpxA using bacterial
two-hybrid and membrane-Strep-tagged protein interaction experiments. The interaction
is dynamic and modulated by stress signals.
action: MODIFY
reason: Same as the other protein binding annotation -- "protein binding" is too
vague. This study specifically demonstrates CpxP-CpxA interaction that inhibits
Cpx signaling. GO:0030547 "signaling receptor inhibitor activity" is more appropriate.
proposed_replacement_terms:
- id: GO:0030547
label: signaling receptor inhibitor activity
supported_by:
- reference_id: PMID:25207645
supporting_text: CpxP modulates the activity of the Cpx system by dynamic interaction
with CpxA in response to specific stresses.
- term:
id: GO:0006950
label: response to stress
evidence_type: IDA
original_reference_id: PMID:9473036
review:
summary: IDA annotation for response to stress based on Danese and Silhavy (1998).
CpxP combats extracytoplasmic protein-mediated toxicity and cpxP mutants are
hypersensitive to alkaline pH.
action: ACCEPT
reason: CpxP is a core component of the envelope stress response, combating toxicity
from misfolded periplasmic proteins (PMID:9473036, PMID:16303867). While this
is a broad term, it accurately reflects CpxP's role. A more specific term could
be considered, but this annotation is not incorrect.
supported_by:
- reference_id: PMID:9473036
supporting_text: cpxP specifies a periplasmic protein that can combat the lethal
phenotype associated with the synthesis of a toxic envelope protein... cpxP
and cpx mutant strains display hypersensitivity to growth in alkaline conditions.
references:
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:9473036
title: CpxP, a stress-combative member of the Cpx regulon.
findings:
- statement: CpxP is a periplasmic protein induced by the Cpx system
- statement: CpxP combats extracytoplasmic protein-mediated toxicity
- statement: CpxP mutants are hypersensitive to alkaline pH
- id: PMID:16303867
title: The extracytoplasmic adaptor protein CpxP is degraded with substrate by DegP.
findings:
- statement: CpxP functions as a periplasmic adaptor for DegP-mediated proteolysis
of misfolded substrates
- statement: Misfolded protein substrate enhances CpxP proteolysis by DegP
- id: PMID:17259177
title: Purification, reconstitution, and characterization of the CpxRAP envelope
stress system of Escherichia coli.
findings:
- statement: CpxP directly inhibits CpxA autophosphorylation by 50% in reconstituted
proteoliposomes
- statement: CpxP has no effect on CpxA phosphotransfer or phosphatase activities
- id: PMID:21239493
title: Structural basis for two-component system inhibition and pilus sensing by
the auxiliary CpxP protein.
findings:
- statement: CpxP crystal structure at 1.45A shows cap-shaped dimer with polar concave
and hydrophobic convex surfaces
- statement: Concave polar surface interacts with CpxA sensor domain
- statement: Hydrophobic cleft on convex surface recognizes misfolded pilus subunits
- id: PMID:21317318
title: Structure of the periplasmic stress response protein CpxP.
findings:
- statement: CpxP crystal structure at 2.85A reveals antiparallel dimer of intertwined
alpha-helices
- statement: CpxP maintains dimeric state but may undergo structural adjustment
at alkaline pH
- id: PMID:21317898
title: Genetic selection designed to stabilize proteins uncovers a chaperone called
Spy.
findings:
- statement: CpxP has mild protein chaperone activity
- id: PMID:25207645
title: Dynamic interaction between the CpxA sensor kinase and the periplasmic accessory
protein CpxP mediates signal recognition in E. coli.
findings:
- statement: CpxP physically interacts with CpxA in unstressed cells
- statement: High salt and misfolded PapE displace CpxP from CpxA in vivo
core_functions:
- molecular_function:
id: GO:0030547
label: signaling receptor inhibitor activity
directly_involved_in:
- id: GO:0070298
label: negative regulation of phosphorelay signal transduction system
locations:
- id: GO:0030288
label: outer membrane-bounded periplasmic space
description: CpxP inhibits autophosphorylation of the CpxA sensor kinase by directly
binding its periplasmic domain via its concave polar surface. This is the primary
evolved function of CpxP -- maintaining the Cpx envelope stress response in an
off state in the absence of inducing signals.
supported_by:
- reference_id: PMID:17259177
supporting_text: Purified tagless CpxP protein reduced the phosphorylation status
of CpxA to 50%
- reference_id: PMID:25207645
supporting_text: CpxP modulates the activity of the Cpx system by dynamic interaction
with CpxA