Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0006457 protein folding	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for protein folding. Skp is involved in the biogenesis pathway of outer membrane proteins, but its primary role is as a holdase/carrier rather than a classical foldase. Skp maintains OMP substrates in an unfolded state during periplasmic transit (PMID:19181847). The OmpA beta-barrel domain remains unfolded while bound to Skp (PMID:19181847). Folding and insertion into the outer membrane only occurs after release from Skp at the BAM complex, often requiring LPS (PMID:12509434). While Skp participates in the broader folding pathway, a more accurate description would be that Skp prevents premature folding/aggregation and escorts OMPs to the site of folding. The IBA annotation is reasonable at a high level given its role in the OMP biogenesis pathway. Reason: Although Skp acts more as a holdase/carrier than a classical foldase, it participates in the broader protein folding pathway for OMPs. The IBA annotation is phylogenetically sound and represents a legitimate, if broad, annotation of Skp's biological role. Supporting Evidence: PMID:19181847 while bound to Skp, the beta-barrel domain of OmpA is maintained in an unfolded state, whereas the periplasmic domain is folded in its native conformation PMID:12509434 Skp alone was not sufficient to facilitate membrane insertion and folding of OmpA. In addition, lipopolysaccharide (LPS) was required. OmpA remained unfolded when bound to Skp and LPS in solution.
GO:0050821 protein stabilization	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for protein stabilization. This is well-supported by multiple experimental studies. Skp prevents aggregation of unfolded OMP intermediates in the periplasm (PMID:10455120, PMID:15304217, PMID:23796519). In skp null mutants combined with degP deletion, protein aggregates accumulate in the periplasm (PMID:10455120). Skp protects substrates from aggregation in a cavity-dependent manner (PMID:19181847). Reason: Core function of Skp as a holdase chaperone. IBA annotation is strongly supported by experimental evidence from multiple laboratories. Supporting Evidence: PMID:10455120 in the absence of an active DegP, a lack of Skp leads to the accumulation of protein aggregates in the periplasm PMID:15304217 The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP
GO:0042597 periplasmic space	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation based on UniProt subcellular location mapping. Consistent with extensive experimental evidence for periplasmic localization (PMID:1838129, PMID:8730870, PMID:10455120). The more specific term GO:0030288 (outer membrane-bounded periplasmic space) is also annotated with IDA evidence. This broader IEA annotation is acceptable as it does not conflict with the more specific experimental evidence. Reason: Correct but less specific than the IDA-supported GO:0030288 annotation. Acceptable as a general IEA annotation. Supporting Evidence: PMID:1838129 Skp partitions with beta-lactamase into the fraction of soluble, periplasmic proteins
GO:0051082 unfolded protein binding	IEA GO_REF:0000002	MODIFY	Summary: IEA annotation from InterPro (IPR005632, Chaperone_Skp). While Skp does bind unfolded proteins, GO:0051082 is being considered for obsoletion as it is overly broad and fails to distinguish between different modes of chaperone action. Skp is a true carrier chaperone that escorts unfolded OMPs from the Sec translocon/inner membrane to the BAM complex in the outer membrane (PMID:10455120, PMID:19181847). The term GO:0140309 (unfolded protein carrier activity) precisely captures this escort/carrier function. Reason: GO:0051082 is being reviewed for obsoletion. Skp functions as an unfolded protein carrier -- it binds unfolded OMPs at the inner membrane and escorts them across the periplasm to the BAM complex for outer membrane insertion. This is a carrier/escort function, not merely binding. Proposed replacements: unfolded protein carrier activity Supporting Evidence: PMID:10455120 Skp is a molecular chaperone involved in generating and maintaining the solubility of early folding intermediates of outer membrane proteins in the periplasmic space of Gram-negative bacteria PMID:19181847 This domain-based chaperoning mechanism allows the transport of beta-barrels across the periplasm in an unfolded state, which may be important for efficient insertion into the outer membrane
GO:0005515 protein binding	IPI PMID:19181847 The cavity-chaperone Skp protects its substrate from aggrega...	MODIFY	Summary: IPI annotation for protein binding based on Skp interaction with OmpA (with/from UniProtKB:P0A910). This study demonstrated by NMR and crosslinking that the OmpA beta-barrel is bound within the Skp cavity while the periplasmic domain protrudes outside (PMID:19181847). However, GO:0005515 (protein binding) is uninformative. The interaction is better captured by the more specific GO:0140309 (unfolded protein carrier activity) or GO:0042802 (identical protein binding) for the homotrimerization. Reason: Protein binding is too vague and uninformative for curation purposes. The specific interaction with unfolded OMPs is the functional essence, which is better represented by GO:0140309 (unfolded protein carrier activity). Proposed replacements: unfolded protein carrier activity Supporting Evidence: PMID:19181847 the OmpA beta-barrel is bound deep within the Skp cavity, whereas the folded periplasmic domain protrudes outside of the cavity where it tumbles independently from the rest of the complex
GO:0005515 protein binding	IPI PMID:24077225 Conformation and dynamics of the periplasmic membrane-protei...	MODIFY	Summary: IPI annotation for protein binding based on Skp interaction with OmpA (with/from UniProtKB:P0A910) and OmpX (UniProtKB:P0A917). This study used high-resolution NMR to characterize Skp complexes with OmpX and tOmpA, showing that OMP substrates populate a dynamic conformational ensemble while bound to Skp (PMID:24077225). As with the other protein binding annotations, GO:0005515 is uninformative. Note: the GOA file shows two rows for this PMID with different with/from values (P0A910 and P0A917). Reason: Protein binding is too vague. The specific interaction with unfolded OMPs is better represented by GO:0140309 (unfolded protein carrier activity). Proposed replacements: unfolded protein carrier activity Supporting Evidence: PMID:24077225 The Skp trimer constitutes a flexible architectural scaffold that becomes more rigid upon substrate binding. The OMP substrates populate a dynamic conformational ensemble
GO:0042802 identical protein binding	IPI PMID:16858726 A complexomic study of Escherichia coli using two-dimensiona...	ACCEPT	Summary: IPI annotation for identical protein binding (homotrimerization) from a complexomic study using 2D blue native/SDS-PAGE. Skp was identified as a homomultimeric complex (PMID:16858726). Skp is a well-established homotrimer (PMID:15304217, PMID:15101556). The trimerization is essential for its chaperone function as the three subunits form the cavity that captures OMPs. Reason: Homotrimerization is a core structural feature of Skp required for its chaperone function. The identical protein binding annotation accurately captures the self-association into the functional trimer. Supporting Evidence: PMID:16858726 50 heteromultimeric and 256 homomultimeric protein complexes were found PMID:15304217 The structure of the Skp trimer resembles a jellyfish with alpha-helical tentacles protruding from a beta barrel body defining a central cavity
GO:0042802 identical protein binding	IPI PMID:19181847 The cavity-chaperone Skp protects its substrate from aggrega...	ACCEPT	Summary: IPI annotation for identical protein binding from Walton et al. 2009, which used NMR and crosslinking to study the Skp trimer-OmpA complex. The Skp trimer is integral to the cavity chaperone mechanism (PMID:19181847). Duplicate of the GO:0042802 annotation from PMID:16858726 in terms of GO term, but valid with different evidence. Reason: Valid additional evidence for homotrimerization from a different study. Supporting Evidence: PMID:19181847 The 17-kDa protein (Skp) is a periplasmic chaperone that assists the folding and insertion of many OMPs
GO:0042802 identical protein binding	IPI PMID:24077225 Conformation and dynamics of the periplasmic membrane-protei...	ACCEPT	Summary: IPI annotation for identical protein binding from Burmann et al. 2013 NMR study of Skp-OMP complexes. Confirms the trimeric nature of Skp (PMID:24077225). Reason: Valid additional evidence for homotrimerization from a different study. Supporting Evidence: PMID:24077225 The Skp trimer constitutes a flexible architectural scaffold that becomes more rigid upon substrate binding
GO:0006457 protein folding	IDA PMID:12509434 Folding and insertion of the outer membrane protein OmpA is ...	ACCEPT	Summary: IDA annotation for protein folding from Bulieris et al. 2003. This study demonstrated that Skp, together with LPS, assists the folding and insertion of OmpA into phospholipid bilayers in vitro (PMID:12509434). Importantly, Skp alone was not sufficient -- LPS was also required. OmpA remained unfolded when bound to Skp. Thus Skp acts as a carrier/holdase in the folding pathway rather than directly catalyzing folding. The protein folding annotation is acceptable in the broader sense that Skp participates in the pathway leading to OMP folding. Reason: Skp participates in the OMP folding pathway, even though its direct role is as a holdase/carrier rather than a foldase. The annotation is acceptable at the biological process level. Supporting Evidence: PMID:12509434 Skp alone was not sufficient to facilitate membrane insertion and folding of OmpA. In addition, lipopolysaccharide (LPS) was required PMID:12509434 unfolded OmpA in complex with Skp and LPS folded faster into phospholipid bilayers than urea-unfolded OmpA
GO:0043165 Gram-negative-bacterium-type cell outer membrane assembly	IDA PMID:8730870 A periplasmic protein (Skp) of Escherichia coli selectively ...	ACCEPT	Summary: IDA annotation from Chen and Henning 1996, the foundational paper identifying Skp as a periplasmic chaperone for OMPs. They showed Skp selectively binds OMPs (OmpA, OmpC, OmpF, LamB) and that skp deletion mutants have much-reduced concentrations of outer membrane proteins (PMID:8730870). This is a core biological process annotation for Skp. Reason: Core function. Skp is directly involved in outer membrane assembly by escorting OMPs across the periplasm to the outer membrane. Supporting Evidence: PMID:8730870 The mutant was viable but possessed much-reduced concentrations of outer membrane proteins. This defect was fully restored by a plasmid-borne skp gene
GO:0050821 protein stabilization	EXP PMID:10455120 Skp, a molecular chaperone of gram-negative bacteria, is req...	ACCEPT	Summary: EXP annotation from Schaefer et al. 1999 demonstrating Skp's role in maintaining solubility of OMP folding intermediates. In skp/degP double mutants, protein aggregates accumulate in the periplasm (PMID:10455120). Skp is required for the release of newly translocated OMPs from the plasma membrane and maintenance of their solubility. Reason: Core function of Skp. Preventing aggregation and maintaining solubility of unfolded OMPs is the essence of its holdase/carrier activity. Supporting Evidence: PMID:10455120 in the absence of an active DegP, a lack of Skp leads to the accumulation of protein aggregates in the periplasm PMID:10455120 Skp is a molecular chaperone involved in generating and maintaining the solubility of early folding intermediates of outer membrane proteins
GO:0050821 protein stabilization	IDA PMID:12509434 Folding and insertion of the outer membrane protein OmpA is ...	ACCEPT	Summary: IDA annotation from Bulieris et al. 2003. Demonstrated that Skp prevents aggregation of unfolded OmpA and maintains it in a soluble complex (PMID:12509434). OmpA remained unfolded but soluble when bound to Skp. Reason: Consistent with Skp's core holdase function of preventing aggregation. Supporting Evidence: PMID:12509434 OmpA remained unfolded when bound to Skp and LPS in solution. From this complex, OmpA folded spontaneously into lipid bilayers
GO:0050821 protein stabilization	IDA PMID:15304217 Crystal structure of Skp, a prefoldin-like chaperone that pr...	ACCEPT	Summary: IDA annotation from the Skp crystal structure paper (Walton and Sousa 2004). Demonstrated that Skp prevents aggregation of model substrates in vitro in an ATP-independent manner (PMID:15304217). The structure reveals the cavity where substrates are protected from aggregation. Reason: Structural and biochemical evidence for Skp's anti-aggregation function. Supporting Evidence: PMID:15304217 The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP
GO:0050821 protein stabilization	IDA PMID:23796519 Dissecting the effects of periplasmic chaperones on the in v...	ACCEPT	Summary: IDA annotation from McMorran et al. 2013. Demonstrated that Skp can rescue the OMP PagP from aggregation and promote its subsequent folding and membrane insertion (PMID:23796519). Skp-mediated delivery of PagP to liposomes is influenced by electrostatic interactions between the chaperone and lipid. Reason: Additional evidence from a different OMP substrate (PagP) confirming Skp's role in preventing OMP aggregation. Supporting Evidence: PMID:23796519 folding and membrane insertion of PagP can be restored, in part, by Skp in conditions that strongly favour PagP aggregation PMID:23796519 the key role of Skp in holding aggregation-prone OMPs prior to their direct or indirect delivery to the membrane
GO:0051082 unfolded protein binding	IDA PMID:19181847 The cavity-chaperone Skp protects its substrate from aggrega...	MODIFY	Summary: IDA annotation from Walton et al. 2009. NMR experiments provided direct evidence that the OmpA beta-barrel domain is maintained in an unfolded state while bound deep within the Skp cavity (PMID:19181847). This confirms Skp binds unfolded proteins, but GO:0051082 fails to capture the carrier/escort function. GO:0140309 (unfolded protein carrier activity) is more appropriate as Skp transports unfolded OMPs from the inner membrane to the BAM complex. Reason: GO:0051082 is being reviewed for obsoletion and does not distinguish Skp's carrier function from simple binding. Skp is a cavity chaperone that physically escorts unfolded OMPs across the periplasm. Proposed replacements: unfolded protein carrier activity Supporting Evidence: PMID:19181847 while bound to Skp, the beta-barrel domain of OmpA is maintained in an unfolded state PMID:19181847 This domain-based chaperoning mechanism allows the transport of beta-barrels across the periplasm in an unfolded state
GO:0051082 unfolded protein binding	IDA PMID:24077225 Conformation and dynamics of the periplasmic membrane-protei...	MODIFY	Summary: IDA annotation from Burmann et al. 2013. High-resolution NMR showed that OMP substrates bound to Skp populate a dynamic conformational ensemble with structural interconversion rates on the submillisecond timescale (PMID:24077225). The dynamic state enables energy-independent substrate release. As with other GO:0051082 annotations, GO:0140309 is more appropriate. Reason: GO:0051082 being reviewed for obsoletion. Skp's function is better described as unfolded protein carrier activity given the escort function across the periplasm. Proposed replacements: unfolded protein carrier activity Supporting Evidence: PMID:24077225 The dynamic state allows for energy-independent substrate release and provides a general paradigm for the conformation of OMP polypeptides bound to energy-independent chaperones
GO:0001530 lipopolysaccharide binding	RCA PMID:15304217 Crystal structure of Skp, a prefoldin-like chaperone that pr...	ACCEPT	Summary: RCA annotation for LPS binding from the crystal structure paper. Walton and Sousa 2004 identified a putative LPS binding site on the outer surface of Skp (residues 97-108) and showed that Skp can interact directly with LPS (PMID:15304217). LPS binding is functionally important because LPS is required together with Skp for efficient OMP folding and membrane insertion (PMID:12509434). The annotation is supported by the structural identification of the binding site and functional studies. Reason: LPS binding is a functionally relevant interaction for Skp's chaperone activity. Structural and functional evidence support this annotation, even though the evidence code is RCA. Supporting Evidence: PMID:15304217 Skp can interact directly with membrane lipids and lipopolysaccharide (LPS). These interactions are needed for efficient Skp-assisted folding of membrane proteins. We have identified a putative LPS binding site on the outer surface of Skp
GO:0030288 outer membrane-bounded periplasmic space	IDA PMID:8730870 A periplasmic protein (Skp) of Escherichia coli selectively ...	ACCEPT	Summary: IDA annotation from Chen and Henning 1996. Skp was identified as a periplasmic protein by subcellular fractionation and affinity chromatography with OmpF-bound sepharose (PMID:8730870). The periplasmic localization is consistent with Skp's role in escorting OMPs across the periplasm. Reason: Core localization annotation. Periplasmic space is where Skp functions as an OMP carrier. Supporting Evidence: PMID:8730870 Proteins of the periplasmic space were fractionated on an affinity column with sepharose-bound outer membrane porin OmpF. A 17 kDa polypeptide was the predominant protein retained by this column
GO:0030288 outer membrane-bounded periplasmic space	IDA PMID:1838129 Skp is a periplasmic Escherichia coli protein requiring SecA...	ACCEPT	Summary: IDA annotation from Thome and Mueller 1991, one of the earliest papers establishing Skp's periplasmic localization. Using subcellular fractionation with precautions to avoid non-specific electrostatic interactions, Skp partitioned with beta-lactamase into the soluble periplasmic fraction (PMID:1838129). Reason: Early definitive evidence for periplasmic localization using careful fractionation methods. Supporting Evidence: PMID:1838129 Upon cellular subfractionation (avoiding non-specific electrostatic interactions) Skp partitions with beta-lactamase into the fraction of soluble, periplasmic proteins
GO:0043165 Gram-negative-bacterium-type cell outer membrane assembly	EXP PMID:11698367 Genetic evidence for parallel pathways of chaperone activity...	ACCEPT	Summary: EXP annotation from Rizzitello et al. 2001. This genetic study demonstrated synthetic lethality between skp and surA mutations, establishing that Skp and SurA function in parallel chaperone pathways for OMP biogenesis (PMID:11698367). Loss of both pathways results in severely reduced envelope protein levels and bacteriostatic/bactericidal effects. Reason: Key genetic evidence establishing Skp's role in outer membrane assembly through a parallel chaperone pathway with SurA. Supporting Evidence: PMID:11698367 null mutations in skp and surA, as well as in degP and surA, result in synthetic phenotypes, suggesting that Skp, SurA, and DegP are functionally redundant PMID:11698367 we propose that Skp and DegP are components of the same pathway and that SurA is a component of a separate pathway
GO:0051082 unfolded protein binding	IPI PMID:10455120 Skp, a molecular chaperone of gram-negative bacteria, is req...	MODIFY	Summary: IPI annotation from Schaefer et al. 1999 (with/from UniProtKB:P0A910 = OmpA). Using crosslinking, they showed Skp interacts with OmpA near the plasma membrane and binds specifically to pOmpA nascent chains after release from ribosomes (PMID:10455120). This demonstrates binding to early unfolded intermediates. However, GO:0140309 better captures the carrier function. Reason: GO:0051082 being reviewed for obsoletion. The interaction represents Skp's carrier function, capturing unfolded OMPs for periplasmic transit. Proposed replacements: unfolded protein carrier activity Supporting Evidence: PMID:10455120 Following its transmembrane translocation, OmpA interacts with Skp in close vicinity to the plasma membrane PMID:10455120 Skp was also found to bind strongly and specifically to pOmpA nascent chains after their release from the ribosome suggesting the ability of Skp to recognize early folding intermediates of outer membrane proteins
GO:0051082 unfolded protein binding	IPI PMID:12509434 Folding and insertion of the outer membrane protein OmpA is ...	MODIFY	Summary: IPI annotation from Bulieris et al. 2003 (with/from UniProtKB:P0A910 = OmpA). Demonstrated direct binding of Skp to unfolded OmpA, forming a soluble complex from which OmpA can fold into lipid bilayers when LPS is present (PMID:12509434). GO:0140309 is more appropriate. Reason: GO:0051082 being reviewed for obsoletion. The Skp-OmpA interaction is part of Skp's carrier function. Proposed replacements: unfolded protein carrier activity Supporting Evidence: PMID:12509434 OmpA remained unfolded when bound to Skp and LPS in solution. From this complex, OmpA folded spontaneously into lipid bilayers
GO:0051604 protein maturation	IDA PMID:9914480 Affinity of the periplasmic chaperone Skp of Escherichia col...	MARK AS OVER ANNOTATED	Summary: IDA annotation from de Cock et al. 1999 (annotated by CACAO). This study showed Skp interacts specifically with non-native outer membrane proteins and proposed that Skp is required for efficient targeting of unfolded OMPs to the membrane (PMID:9914480). While Skp contributes to the maturation pathway of OMPs, the term protein maturation (GO:0051604) is overly generic. The more specific process annotation GO:0043165 (Gram-negative-bacterium-type cell outer membrane assembly) captures the same biology more precisely. Reason: Protein maturation is too generic. Skp's role in OMP maturation is better captured by GO:0043165 (Gram-negative-bacterium-type cell outer membrane assembly) which is already annotated with strong experimental evidence. Supporting Evidence: PMID:9914480 We propose that Skp is required in vivo for the efficient targeting of unfolded outer membrane proteins to the membrane
GO:0006457 protein folding	IMP PMID:10455120 Skp, a molecular chaperone of gram-negative bacteria, is req...	ACCEPT	Summary: IMP annotation from Schaefer et al. 1999. In skp null mutants, there is a specific defect in the release of newly translocated OMPs from the plasma membrane (PMID:10455120). The skp/degP double mutant shows protein aggregate accumulation. This mutant phenotype evidence supports Skp's role in the OMP folding pathway, though Skp itself acts as a holdase/carrier rather than a foldase. Reason: Mutant phenotype evidence supporting Skp's involvement in the broader OMP folding pathway. Consistent with other protein folding annotations. Supporting Evidence: PMID:10455120 Pulse labeling of OmpA in spheroplasts prepared from an skp null mutant revealed a specific requirement of Skp for the release of newly translocated outer membrane proteins from the plasma membrane
GO:0030288 outer membrane-bounded periplasmic space	IDA PMID:10455120 Skp, a molecular chaperone of gram-negative bacteria, is req...	ACCEPT	Summary: IDA annotation for periplasmic localization from Schaefer et al. 1999. Crosslinking experiments showed Skp interacts with OmpA near the plasma membrane in the periplasm (PMID:10455120). Additional evidence for the well-established periplasmic localization. Reason: Additional experimental evidence for periplasmic localization, consistent with other IDA annotations. Supporting Evidence: PMID:10455120 OmpA interacts with Skp in close vicinity to the plasma membrane
GO:0051082 unfolded protein binding	IPI PMID:9914480 Affinity of the periplasmic chaperone Skp of Escherichia col...	MODIFY	Summary: IPI annotation from de Cock et al. 1999 (with/from UniProtKB:P02932 = PhoE and UniProtKB:P0A910 = OmpA). Demonstrated specific interaction of Skp with outer membrane proteins in their non-native state (PMID:9914480). Two entries exist for this PMID with different with/from values. GO:0140309 is more appropriate. Reason: GO:0051082 being reviewed for obsoletion. Skp's interaction with non-native OMPs is part of its carrier/escort function. Proposed replacements: unfolded protein carrier activity Supporting Evidence: PMID:9914480 it interacts specifically with outer membrane proteins that are in their non-native state
GO:0001530 lipopolysaccharide binding	IPI PMID:17928002 The trimeric periplasmic chaperone Skp of Escherichia coli f...	ACCEPT	Summary: IPI annotation from Qu et al. 2007 (with/from UniProtKB:P0A910 = OmpA). This study showed that LPS binds to OmpA-Skp complexes at low stoichiometries, and that in the ternary complex, tryptophan residues of OmpA are located closer to the surface than in binary complexes (PMID:17928002). This structural change may explain how LPS facilitates membrane insertion. The IPI evidence here reflects LPS interaction with the Skp-OMP complex, supporting Skp's LPS binding. Reason: LPS binding to Skp-OMP complexes is functionally important for the OMP biogenesis pathway. Well-supported by biophysical evidence. Supporting Evidence: PMID:17928002 Lipopolysaccharide (LPS), a major component of the outer membrane of Gram-negative bacteria, bound to OmpA.Skp(3) complexes at low stoichiometries PMID:17928002 in this ternary complex, the tryptophan residues of the transmembrane domain of OmpA were located closer to the surface than in binary OmpA.Skp(3) complexes
GO:0043165 Gram-negative-bacterium-type cell outer membrane assembly	IDA PMID:12509434 Folding and insertion of the outer membrane protein OmpA is ...	ACCEPT	Summary: IDA annotation from Bulieris et al. 2003. Demonstrated that Skp together with LPS assists the folding and insertion of OmpA into phospholipid bilayers in vitro (PMID:12509434). This reconstitution of the Skp-assisted OMP folding pathway directly supports its role in outer membrane assembly. Reason: In vitro reconstitution of Skp-assisted OMP membrane insertion provides direct evidence for its role in outer membrane assembly. Supporting Evidence: PMID:12509434 unfolded OmpA in complex with Skp and LPS folded faster into phospholipid bilayers than urea-unfolded OmpA
GO:0043165 Gram-negative-bacterium-type cell outer membrane assembly	IGI PMID:17908933 Defining the roles of the periplasmic chaperones SurA, Skp, ...	ACCEPT	Summary: IGI annotation from Sklar et al. 2007 (with/from UniProtKB:P0ABZ6 = SurA). Genetic interaction evidence showing that Skp functions in a parallel pathway with DegP to rescue OMPs that fall off the primary SurA pathway (PMID:17908933). Loss of both the SurA and Skp/DegP pathways is synthetic lethal. Reason: Genetic interaction evidence placing Skp in the OMP biogenesis pathway, parallel to SurA. Supporting Evidence: PMID:17908933 DegP/Skp function to rescue OMPs that fall off the SurA pathway PMID:17908933 SurA is the primary chaperone responsible for the periplasmic transit of the bulk mass of OMPs to the YaeT complex. The role of Skp and DegP is amplified in the absence of SurA
GO:0043165 Gram-negative-bacterium-type cell outer membrane assembly	IPI PMID:17908933 Defining the roles of the periplasmic chaperones SurA, Skp, ...	ACCEPT	Summary: IPI annotation from Sklar et al. 2007 (with/from UniProtKB:P0A940 = BamA/YaeT). This study established the relationship between Skp and the BAM complex (YaeT), showing that SurA and YaeT interact directly in vivo and that Skp functions in a parallel delivery pathway (PMID:17908933). Reason: Physical interaction evidence placing Skp in the context of the BAM complex OMP assembly machinery. Supporting Evidence: PMID:17908933 we demonstrate that SurA and YaeT interact directly in vivo PMID:17908933 Evidence presented suggests that DegP/Skp function to rescue OMPs that fall off the SurA pathway
GO:0051082 unfolded protein binding	IPI PMID:11278858 The early interaction of the outer membrane protein phoe wit...	MODIFY	Summary: IPI annotation from Harms et al. 2001 (with/from UniProtKB:P02932 = PhoE). Crosslinking experiments demonstrated that Skp interacts with newly translocated PhoE at the periplasmic side of the inner membrane, even when PhoE is still in a transmembrane orientation in the translocase (PMID:11278858). This demonstrates Skp captures OMPs very early in their biogenesis. GO:0140309 is more appropriate. Reason: GO:0051082 being reviewed for obsoletion. Early capture of OMPs at the translocon is part of Skp's carrier function. Proposed replacements: unfolded protein carrier activity Supporting Evidence: PMID:11278858 Newly translocated PhoE protein could be cross-linked to the periplasmic chaperone Skp at the periplasmic side of the inner membrane PMID:11278858 PhoE closely interacts with the chaperone when the protein is still in a transmembrane orientation in the translocase
GO:0051082 unfolded protein binding	IPI PMID:17928002 The trimeric periplasmic chaperone Skp of Escherichia coli f...	MODIFY	Summary: IPI annotation from Qu et al. 2007 (with/from UniProtKB:P0A910, P0A940, P76045). Comprehensive biophysical study showing Skp trimer forms 1:1 stable complexes with multiple bacterial OMPs (OmpA, OmpG, YaeT, NalP, FomA) with nanomolar dissociation constants (PMID:17928002). Binding is pH-dependent and requires electrostatic interactions. Skp efficiently shielded OmpA tryptophan residues from quenching. GO:0140309 is more appropriate. Reason: GO:0051082 being reviewed for obsoletion. The stable 1:1 complex formation and shielding of OMP transmembrane domains is characteristic of carrier chaperone activity. Proposed replacements: unfolded protein carrier activity Supporting Evidence: PMID:17928002 The Skp trimer formed 1:1 complexes, OMP.Skp(3), with bacterial OMPs, independent of their size or origin. The dissociation constants of these OMP.Skp(3) complexes were all in the nanomolar range, indicating that they are stable PMID:17928002 Skp efficiently shielded tryptophan residues of the transmembrane strands of OmpA against fluorescence quenching by aqueous acrylamide
GO:0005829 cytosol	HDA PMID:16858726 A complexomic study of Escherichia coli using two-dimensiona...	REMOVE	Summary: HDA annotation for cytosolic localization from a complexomic study using 2D blue native/SDS-PAGE (PMID:16858726). Skp is a secreted periplasmic protein with a signal peptide (aa 1-20) that is exported via the Sec pathway (PMID:1838129). Its primary localization is the periplasm, not the cytosol. The cytosolic detection may represent pre-export Skp or a fractionation artifact. This annotation is inconsistent with the well-established periplasmic localization. Reason: Skp is exported to the periplasm via the Sec pathway and its functional localization is the periplasmic space, not the cytosol. The HDA detection likely reflects pre-export protein or a fractionation artifact. Multiple IDA-supported annotations confirm periplasmic localization. Supporting Evidence: PMID:1838129 Skp is synthesized as a larger precursor that is processed upon translocation across the plasma membrane. Translocation is dependent on the H(+)-gradient, ATP, SecA, and SecY

Core Functions

Unfolded protein carrier activity -- escorts unfolded outer membrane proteins (OMPs) from the Sec translocon at the inner membrane across the periplasm to the BAM complex for insertion into the outer membrane

Molecular Function:

unfolded protein carrier activity

Directly Involved In:

Gram-negative-bacterium-type cell outer membrane assembly

Cellular Locations:

outer membrane-bounded periplasmic space

Supporting Evidence:

PMID:10455120
Skp is a molecular chaperone involved in generating and maintaining the solubility of early folding intermediates of outer membrane proteins in the periplasmic space of Gram-negative bacteria
PMID:19181847
This domain-based chaperoning mechanism allows the transport of beta-barrels across the periplasm in an unfolded state, which may be important for efficient insertion into the outer membrane

Homotrimerization -- Skp forms a functional homotrimer with a jellyfish-like architecture that creates the central cavity required for substrate binding

Molecular Function:

identical protein binding

Cellular Locations:

outer membrane-bounded periplasmic space

Supporting Evidence:

PMID:15304217
The structure of the Skp trimer resembles a jellyfish with alpha-helical tentacles protruding from a beta barrel body defining a central cavity

Lipopolysaccharide binding -- Skp binds LPS which is required for efficient Skp-assisted folding and insertion of OMPs into membranes

Molecular Function:

lipopolysaccharide binding

Directly Involved In:

Gram-negative-bacterium-type cell outer membrane assembly

Supporting Evidence:

PMID:15304217
Skp can interact directly with membrane lipids and lipopolysaccharide (LPS). These interactions are needed for efficient Skp-assisted folding of membrane proteins
PMID:12509434
Skp alone was not sufficient to facilitate membrane insertion and folding of OmpA. In addition, lipopolysaccharide (LPS) was required

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

PMID:1838129

Skp is a periplasmic Escherichia coli protein requiring SecA and SecY for export.

Skp is synthesized as a precursor with a signal peptide and exported to the periplasm via the Sec pathway

"Skp is synthesized as a larger precursor that is processed upon translocation across the plasma membrane. Translocation is dependent on the H(+)-gradient, ATP, SecA, and SecY"

PMID:8730870

A periplasmic protein (Skp) of Escherichia coli selectively binds a class of outer membrane proteins.

Skp selectively binds OMPs (OmpA, OmpC, OmpF, LamB) and skp deletion reduces OMP levels

"it could be demonstrated that it bound outer membrane proteins, following SDS-PAGE, with high selectivity. Among these were OmpA, OmpC, OmpF and the maltoporin LamB"

PMID:9914480

Affinity of the periplasmic chaperone Skp of Escherichia coli for phospholipids, lipopolysaccharides and non-native outer membrane proteins. Role of Skp in the biogenesis of outer membrane protein.

Skp interacts specifically with non-native OMPs and associates with phospholipid membranes and LPS

"it interacts specifically with outer membrane proteins that are in their non-native state"

PMID:10455120

Skp, a molecular chaperone of gram-negative bacteria, is required for the formation of soluble periplasmic intermediates of outer membrane proteins.

Skp is required for release of newly translocated OMPs from the inner membrane and maintenance of their solubility in the periplasm

"Skp is a molecular chaperone involved in generating and maintaining the solubility of early folding intermediates of outer membrane proteins in the periplasmic space of Gram-negative bacteria"

PMID:11278858

The early interaction of the outer membrane protein phoe with the periplasmic chaperone Skp occurs at the cytoplasmic membrane.

Skp captures PhoE at the inner membrane during translocation

"Newly translocated PhoE protein could be cross-linked to the periplasmic chaperone Skp at the periplasmic side of the inner membrane"

PMID:11698367

Genetic evidence for parallel pathways of chaperone activity in the periplasm of Escherichia coli.

Skp and DegP function in a parallel chaperone pathway to SurA for OMP biogenesis

"we propose that Skp and DegP are components of the same pathway and that SurA is a component of a separate pathway"

PMID:12509434

Folding and insertion of the outer membrane protein OmpA is assisted by the chaperone Skp and by lipopolysaccharide.

Skp and LPS together facilitate OmpA folding and insertion into lipid bilayers in vitro

"unfolded OmpA in complex with Skp and LPS folded faster into phospholipid bilayers than urea-unfolded OmpA"

PMID:15304217

Crystal structure of Skp, a prefoldin-like chaperone that protects soluble and membrane proteins from aggregation.

Skp forms a jellyfish-like trimer with a central cavity for substrate binding and has an LPS binding site

"The structure of the Skp trimer resembles a jellyfish with alpha-helical tentacles protruding from a beta barrel body defining a central cavity"

PMID:16858726

A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis.

PMID:17908933

Defining the roles of the periplasmic chaperones SurA, Skp, and DegP in Escherichia coli.

SurA is the primary OMP chaperone; Skp/DegP rescue OMPs that fall off the SurA pathway

"SurA is the primary chaperone responsible for the periplasmic transit of the bulk mass of OMPs to the YaeT complex. The role of Skp and DegP is amplified in the absence of SurA"

PMID:17928002

The trimeric periplasmic chaperone Skp of Escherichia coli forms 1:1 complexes with outer membrane proteins via hydrophobic and electrostatic interactions.

Skp trimer forms stable 1:1 complexes with multiple bacterial OMPs with nanomolar affinity

"The Skp trimer formed 1:1 complexes, OMP.Skp(3), with bacterial OMPs, independent of their size or origin. The dissociation constants of these OMP.Skp(3) complexes were all in the nanomolar range"

PMID:19181847

The cavity-chaperone Skp protects its substrate from aggregation but allows independent folding of substrate domains.

Skp holds OmpA beta-barrel unfolded in its cavity while allowing the periplasmic domain to fold independently

"while bound to Skp, the beta-barrel domain of OmpA is maintained in an unfolded state, whereas the periplasmic domain is folded in its native conformation"

PMID:23796519

Dissecting the effects of periplasmic chaperones on the in vitro folding of the outer membrane protein PagP.

Skp rescues aggregation-prone PagP and delivers it for membrane insertion via electrostatic interactions

"the key role of Skp in holding aggregation-prone OMPs prior to their direct or indirect delivery to the membrane"

PMID:24077225

Conformation and dynamics of the periplasmic membrane-protein-chaperone complexes OmpX-Skp and tOmpA-Skp.

OMP substrates bound to Skp populate a dynamic conformational ensemble enabling energy-independent release

"The dynamic state allows for energy-independent substrate release and provides a general paradigm for the conformation of OMP polypeptides bound to energy-independent chaperones"

📚 Additional Documentation

Deep Research Bioreason

(Skp-deep-research-bioreason.md)

BioReason Chat Export

Exported on March 22, 2026 at 02:19 AM

Organism: Escherichia coli

Sequence:

MKKWLLAAGLGLALATSAQAADKIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRMETDLQAKMKKLQSMKAGSDRTKLEKDVMAQRQTFAQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQVK

Thinking Trace

I begin with the InterPro architecture. The sequence is dominated by IPR005632 (Chaperone protein Skp family) spanning residues 1–161, with a nested IPR024930 (Skp domain superfamily) covering residues 19–161. This compact, single-module layout indicates a stand-alone small heat shock chaperone that lacks transmembrane segments or secretion signals and is therefore soluble. Skp-family signatures denote ATP-independent holdase/chaperone modules that bind non-native polypeptides through hydrophobic surfaces and oligomerize to stabilize unfolded substrates. The N-to-C continuity of the Skp core (1–161 and 19–161) suggests that oligomerization and client-binding determinants are distributed across the same structural unit rather than modularized elsewhere—an architecture that causes high avidity for misfolded proteins and efficient substrate triage.

From this domain logic, the molecular function follows as protein binding with a bias toward non-native substrates. The absence of catalytic motifs and the chaperone lineage of Skp argue for GO:0005515 as the conservative functional umbrella for binding-driven assistance rather than enzymatic refolding. The Skp scaffold binds and stabilizes unfolded clients, preventing irreversible aggregation until downstream pathways recover or degrade them.

This binding-driven chaperoning directly instantiates the biological process of managing proteostasis during thermal and general environmental insults. By buffering aggregation and channeling clients into refolding or clearance, the protein operates within stress adaptation pathways; this places it in the overarching process of GO:0006950 response to stress. In bacteria, such holdases are activated during heat shock and other proteotoxic conditions, buffering the unfolded proteome and coordinating handoff to ATP-dependent systems.

Cellular localization is inferred from the soluble, non-secretory architecture and the organismal context. A cytosolic chaperone in Escherichia coli would patrol the interior aqueous compartment where translation and folding occur, consistent with GO:0005737 cytoplasm. The soluble Skp fold and lack of membrane features reinforce this intracellular, cytoplasmic residency.

Mechanistically, the Skp module oligomerizes to create a client-binding cage that captures exposed hydrophobic patches on misfolded proteins. This holdase action stabilizes substrates and orchestrates their fate: transiently sequestering them and handing them off to ATP-dependent machineries such as the DnaK/DnaJ/GrpE system, the ClpB disaggregase, and protease hubs like ClpXP or the HslUV pathway. I therefore hypothesize that this chaperone collaborates with cytosolic folding and quality-control factors—DnaK, DnaJ, GrpE, and ClpB—to balance refolding versus degradation during environmental stress, particularly heat shock and oxidative challenges that elevate the unfolded protein load.

Functional Summary

A cytoplasmic small heat shock chaperone in Escherichia coli that binds and stabilizes non-native polypeptides without ATP hydrolysis, preventing their aggregation during environmental stress. By oligomerizing into a holdase scaffold, it sequesters unfolded clients and coordinates their refolding or turnover alongside cytosolic proteostasis pathways, thereby maintaining protein homeostasis under heat and related insults.

UniProt Summary

Seems to be involved in heat shock escape pathway.

InterPro Domains

Chaperone protein Skp (IPR005632, family) — residues 1-161
Skp domain superfamily (IPR024930, homologous_superfamily) — residues 19-161

GO Terms

Molecular Function: molecular_function (GO:0003674), binding (GO:0005488), protein binding (GO:0005515), identical protein binding (GO:0042802)

Biological Process: biological_process (GO:0008150), metabolic process (GO:0008152), biological regulation (GO:0065007), localization (GO:0051179), cellular process (GO:0009987), regulation of biological quality (GO:0065008), cellular localization (GO:0051641), nitrogen compound metabolic process (GO:0006807), protein folding (GO:0006457), establishment of localization (GO:0051234), cellular component organization or biogenesis (GO:0071840), organic substance metabolic process (GO:0071704), primary metabolic process (GO:0044238), macromolecule localization (GO:0033036), protein maturation by protein folding (GO:0022417), organonitrogen compound metabolic process (GO:1901564), cellular component biogenesis (GO:0044085), protein metabolic process (GO:0019538), cellular macromolecule localization (GO:0070727), cellular component organization (GO:0016043), chaperone-mediated protein folding (GO:0061077), regulation of protein stability (GO:0031647), localization within membrane (GO:0051668), macromolecule metabolic process (GO:0043170), establishment of protein localization (GO:0045184), protein maturation (GO:0051604), membrane biogenesis (GO:0044091), protein stabilization (GO:0050821), protein localization (GO:0008104), external encapsulating structure organization (GO:0045229), gene expression (GO:0010467), establishment of protein localization to membrane (GO:0090150), membrane organization (GO:0061024), protein localization to membrane (GO:0072657), cellular component assembly (GO:0022607), cell envelope organization (GO:0043163), membrane assembly (GO:0071709), protein insertion into membrane (GO:0051205)

Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), cytosol (GO:0005829), intracellular anatomical structure (GO:0005622), envelope (GO:0031975), cytoplasm (GO:0005737), periplasmic space (GO:0042597), cell envelope (GO:0030313), outer membrane-bounded periplasmic space (GO:0030288)

Generated by BioReason

Deep Research Bioreason Rl

(Skp-deep-research-bioreason-rl.md)

BioReason Chat Export

Exported on March 22, 2026 at 02:19 AM

Organism: Escherichia coli

Sequence:

MKKWLLAAGLGLALATSAQAADKIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRMETDLQAKMKKLQSMKAGSDRTKLEKDVMAQRQTFAQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQVK

Thinking Trace

Functional Summary

UniProt Summary

Seems to be involved in heat shock escape pathway.

InterPro Domains

Chaperone protein Skp (IPR005632, family) — residues 1-161
Skp domain superfamily (IPR024930, homologous_superfamily) — residues 19-161

GO Terms

Molecular Function: molecular_function (GO:0003674), binding (GO:0005488), protein binding (GO:0005515), identical protein binding (GO:0042802)

Generated by BioReason

Bioreason Rl Review

(Skp-bioreason-rl-review.md)

BioReason-Pro RL Review: Skp (E. coli)

Source: Skp-deep-research-bioreason-rl.md

Correctness: 2/5
Completeness: 2/5

Functional Summary Review

The BioReason functional summary describes Skp as:

A cytoplasmic small heat shock chaperone in Escherichia coli that binds and stabilizes non-native polypeptides without ATP hydrolysis, preventing their aggregation during environmental stress. By oligomerizing into a holdase scaffold, it sequesters unfolded clients and coordinates their refolding or turnover alongside cytosolic proteostasis pathways, thereby maintaining protein homeostasis under heat and related insults.

This summary contains a fundamental localization error and misidentifies the biological context:

Wrong localization: Skp is described as "cytoplasmic," but it is a well-established periplasmic chaperone. Skp has a signal peptide and is exported to the periplasm, where it functions as a carrier for unfolded outer membrane proteins (OMPs). The curated review confirms periplasmic localization (GO:0030288) with extensive experimental support (PMID:15304217, PMID:10455120).
Wrong substrate class: The summary describes Skp as binding generic "non-native polypeptides" during "heat and related insults." In reality, Skp specifically escorts unfolded outer membrane beta-barrel proteins (OmpA, OmpC, OmpF, LamB, PhoE, OmpX, OmpG) from the Sec translocon across the periplasm to the BAM complex for outer membrane insertion. It is not a general stress chaperone.
Wrong pathway: The summary describes Skp as working with "cytosolic proteostasis pathways" including "DnaK/DnaJ/GrpE system, the ClpB disaggregase, and protease hubs like ClpXP." These are all cytoplasmic systems. Skp actually works in a parallel periplasmic pathway with DegP, serving as a backup to the primary SurA pathway for OMP biogenesis.
Correctly identified as ATP-independent: This aspect is accurate.

The jellyfish-like homotrimeric architecture (alpha-helical tentacles from a beta-barrel body) is one of Skp's defining features but is not captured. The functional summary is essentially describing a generic cytoplasmic sHSP, not the specific periplasmic OMP carrier that Skp actually is.

Comparison with interpro2go:

The curated review's interpro2go annotations include unfolded protein binding (GO:0051082), which is noted as overly simplistic -- Skp is better described as having unfolded protein carrier activity (GO:0140309). BioReason recapitulates the same interpro2go-level "unfolded protein binding" interpretation but then adds incorrect cytoplasmic context. The model fails to extract the periplasmic localization despite the GO terms including periplasmic space (GO:0042597) and outer membrane-bounded periplasmic space (GO:0030288). Again, the narrative contradicts the model's own GO predictions.

Notes on thinking trace

The trace correctly identifies IPR005632 (Chaperone protein Skp family) and IPR024930 (Skp domain superfamily), but then reasons that "the absence of transmembrane segments or secretion signals" places it in the cytoplasm. This is incorrect -- the sequence does contain a signal peptide (residues 1-20, MKKWLLAAGLGLALATSAQA), which the model apparently failed to detect. The signal peptide was even present in the input sequence.

📄 View Raw YAML

id: P0AEU7
gene_symbol: Skp
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:83333
  label: Escherichia coli (strain K12)
description: Skp is a homotrimeric periplasmic chaperone in E. coli that functions
  as an ATP-independent carrier for unfolded outer membrane proteins (OMPs). Structurally,
  Skp adopts a jellyfish-like architecture with alpha-helical tentacles protruding
  from a beta-barrel body, defining a central cavity in which unfolded OMP substrates
  are bound (PMID:15304217). After OMPs emerge from the Sec translocon at the inner
  membrane, Skp captures them and maintains their solubility during transit through
  the periplasm to the BAM complex for insertion into the outer membrane (PMID:10455120,
  PMID:19181847). Skp functions in a parallel chaperone pathway with DegP, serving
  as a backup to the primary SurA pathway for OMP biogenesis (PMID:17908933). Skp
  binds specifically to bacterial OMPs including OmpA, OmpC, OmpF, LamB, PhoE, OmpX,
  and OmpG, forming stable 1:1 (OMP:Skp trimer) complexes with nanomolar dissociation
  constants via hydrophobic and electrostatic interactions (PMID:17928002). LPS binding
  to Skp-OMP complexes facilitates subsequent membrane insertion (PMID:12509434).
  Skp is architecturally similar to the archaeal/eukaryotic chaperone prefoldin/GimC
  (PMID:15304217).
existing_annotations:
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: IBA annotation for protein folding. Skp is involved in the biogenesis
      pathway of outer membrane proteins, but its primary role is as a holdase/carrier
      rather than a classical foldase. Skp maintains OMP substrates in an unfolded
      state during periplasmic transit (PMID:19181847). The OmpA beta-barrel domain
      remains unfolded while bound to Skp (PMID:19181847). Folding and insertion into
      the outer membrane only occurs after release from Skp at the BAM complex, often
      requiring LPS (PMID:12509434). While Skp participates in the broader folding
      pathway, a more accurate description would be that Skp prevents premature folding/aggregation
      and escorts OMPs to the site of folding. The IBA annotation is reasonable at
      a high level given its role in the OMP biogenesis pathway.
    action: ACCEPT
    reason: Although Skp acts more as a holdase/carrier than a classical foldase,
      it participates in the broader protein folding pathway for OMPs. The IBA annotation
      is phylogenetically sound and represents a legitimate, if broad, annotation
      of Skp's biological role.
    supported_by:
    - reference_id: PMID:19181847
      supporting_text: while bound to Skp, the beta-barrel domain of OmpA is maintained
        in an unfolded state, whereas the periplasmic domain is folded in its native
        conformation
    - reference_id: PMID:12509434
      supporting_text: Skp alone was not sufficient to facilitate membrane insertion
        and folding of OmpA. In addition, lipopolysaccharide (LPS) was required. OmpA
        remained unfolded when bound to Skp and LPS in solution.
- term:
    id: GO:0050821
    label: protein stabilization
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: IBA annotation for protein stabilization. This is well-supported by multiple
      experimental studies. Skp prevents aggregation of unfolded OMP intermediates
      in the periplasm (PMID:10455120, PMID:15304217, PMID:23796519). In skp null
      mutants combined with degP deletion, protein aggregates accumulate in the periplasm
      (PMID:10455120). Skp protects substrates from aggregation in a cavity-dependent
      manner (PMID:19181847).
    action: ACCEPT
    reason: Core function of Skp as a holdase chaperone. IBA annotation is strongly
      supported by experimental evidence from multiple laboratories.
    supported_by:
    - reference_id: PMID:10455120
      supporting_text: in the absence of an active DegP, a lack of Skp leads to the
        accumulation of protein aggregates in the periplasm
    - reference_id: PMID:15304217
      supporting_text: The ability of Skp to prevent the aggregation of model substrates
        in vitro is independent of ATP
- term:
    id: GO:0042597
    label: periplasmic space
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: IEA annotation based on UniProt subcellular location mapping. Consistent
      with extensive experimental evidence for periplasmic localization (PMID:1838129,
      PMID:8730870, PMID:10455120). The more specific term GO:0030288 (outer membrane-bounded
      periplasmic space) is also annotated with IDA evidence. This broader IEA annotation
      is acceptable as it does not conflict with the more specific experimental evidence.
    action: ACCEPT
    reason: Correct but less specific than the IDA-supported GO:0030288 annotation.
      Acceptable as a general IEA annotation.
    supported_by:
    - reference_id: PMID:1838129
      supporting_text: Skp partitions with beta-lactamase into the fraction of soluble,
        periplasmic proteins
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: IEA annotation from InterPro (IPR005632, Chaperone_Skp). While Skp does
      bind unfolded proteins, GO:0051082 is being considered for obsoletion as it
      is overly broad and fails to distinguish between different modes of chaperone
      action. Skp is a true carrier chaperone that escorts unfolded OMPs from the
      Sec translocon/inner membrane to the BAM complex in the outer membrane (PMID:10455120,
      PMID:19181847). The term GO:0140309 (unfolded protein carrier activity) precisely
      captures this escort/carrier function.
    action: MODIFY
    reason: GO:0051082 is being reviewed for obsoletion. Skp functions as an unfolded
      protein carrier -- it binds unfolded OMPs at the inner membrane and escorts
      them across the periplasm to the BAM complex for outer membrane insertion. This
      is a carrier/escort function, not merely binding.
    proposed_replacement_terms:
    - id: GO:0140309
      label: unfolded protein carrier activity
    supported_by:
    - reference_id: PMID:10455120
      supporting_text: Skp is a molecular chaperone involved in generating and maintaining
        the solubility of early folding intermediates of outer membrane proteins in
        the periplasmic space of Gram-negative bacteria
    - reference_id: PMID:19181847
      supporting_text: This domain-based chaperoning mechanism allows the transport
        of beta-barrels across the periplasm in an unfolded state, which may be important
        for efficient insertion into the outer membrane
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19181847
  review:
    summary: IPI annotation for protein binding based on Skp interaction with OmpA
      (with/from UniProtKB:P0A910). This study demonstrated by NMR and crosslinking
      that the OmpA beta-barrel is bound within the Skp cavity while the periplasmic
      domain protrudes outside (PMID:19181847). However, GO:0005515 (protein binding)
      is uninformative. The interaction is better captured by the more specific GO:0140309
      (unfolded protein carrier activity) or GO:0042802 (identical protein binding)
      for the homotrimerization.
    action: MODIFY
    reason: Protein binding is too vague and uninformative for curation purposes.
      The specific interaction with unfolded OMPs is the functional essence, which
      is better represented by GO:0140309 (unfolded protein carrier activity).
    proposed_replacement_terms:
    - id: GO:0140309
      label: unfolded protein carrier activity
    supported_by:
    - reference_id: PMID:19181847
      supporting_text: the OmpA beta-barrel is bound deep within the Skp cavity, whereas
        the folded periplasmic domain protrudes outside of the cavity where it tumbles
        independently from the rest of the complex
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24077225
  review:
    summary: 'IPI annotation for protein binding based on Skp interaction with OmpA
      (with/from UniProtKB:P0A910) and OmpX (UniProtKB:P0A917). This study used high-resolution
      NMR to characterize Skp complexes with OmpX and tOmpA, showing that OMP substrates
      populate a dynamic conformational ensemble while bound to Skp (PMID:24077225).
      As with the other protein binding annotations, GO:0005515 is uninformative.
      Note: the GOA file shows two rows for this PMID with different with/from values
      (P0A910 and P0A917).'
    action: MODIFY
    reason: Protein binding is too vague. The specific interaction with unfolded OMPs
      is better represented by GO:0140309 (unfolded protein carrier activity).
    proposed_replacement_terms:
    - id: GO:0140309
      label: unfolded protein carrier activity
    supported_by:
    - reference_id: PMID:24077225
      supporting_text: The Skp trimer constitutes a flexible architectural scaffold
        that becomes more rigid upon substrate binding. The OMP substrates populate
        a dynamic conformational ensemble
- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:16858726
  review:
    summary: IPI annotation for identical protein binding (homotrimerization) from
      a complexomic study using 2D blue native/SDS-PAGE. Skp was identified as a homomultimeric
      complex (PMID:16858726). Skp is a well-established homotrimer (PMID:15304217,
      PMID:15101556). The trimerization is essential for its chaperone function as
      the three subunits form the cavity that captures OMPs.
    action: ACCEPT
    reason: Homotrimerization is a core structural feature of Skp required for its
      chaperone function. The identical protein binding annotation accurately captures
      the self-association into the functional trimer.
    supported_by:
    - reference_id: PMID:16858726
      supporting_text: 50 heteromultimeric and 256 homomultimeric protein complexes
        were found
    - reference_id: PMID:15304217
      supporting_text: The structure of the Skp trimer resembles a jellyfish with
        alpha-helical tentacles protruding from a beta barrel body defining a central
        cavity
- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:19181847
  review:
    summary: IPI annotation for identical protein binding from Walton et al. 2009,
      which used NMR and crosslinking to study the Skp trimer-OmpA complex. The Skp
      trimer is integral to the cavity chaperone mechanism (PMID:19181847). Duplicate
      of the GO:0042802 annotation from PMID:16858726 in terms of GO term, but valid
      with different evidence.
    action: ACCEPT
    reason: Valid additional evidence for homotrimerization from a different study.
    supported_by:
    - reference_id: PMID:19181847
      supporting_text: The 17-kDa protein (Skp) is a periplasmic chaperone that assists
        the folding and insertion of many OMPs
- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:24077225
  review:
    summary: IPI annotation for identical protein binding from Burmann et al. 2013
      NMR study of Skp-OMP complexes. Confirms the trimeric nature of Skp (PMID:24077225).
    action: ACCEPT
    reason: Valid additional evidence for homotrimerization from a different study.
    supported_by:
    - reference_id: PMID:24077225
      supporting_text: The Skp trimer constitutes a flexible architectural scaffold
        that becomes more rigid upon substrate binding
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IDA
  original_reference_id: PMID:12509434
  review:
    summary: IDA annotation for protein folding from Bulieris et al. 2003. This study
      demonstrated that Skp, together with LPS, assists the folding and insertion
      of OmpA into phospholipid bilayers in vitro (PMID:12509434). Importantly, Skp
      alone was not sufficient -- LPS was also required. OmpA remained unfolded when
      bound to Skp. Thus Skp acts as a carrier/holdase in the folding pathway rather
      than directly catalyzing folding. The protein folding annotation is acceptable
      in the broader sense that Skp participates in the pathway leading to OMP folding.
    action: ACCEPT
    reason: Skp participates in the OMP folding pathway, even though its direct role
      is as a holdase/carrier rather than a foldase. The annotation is acceptable
      at the biological process level.
    supported_by:
    - reference_id: PMID:12509434
      supporting_text: Skp alone was not sufficient to facilitate membrane insertion
        and folding of OmpA. In addition, lipopolysaccharide (LPS) was required
    - reference_id: PMID:12509434
      supporting_text: unfolded OmpA in complex with Skp and LPS folded faster into
        phospholipid bilayers than urea-unfolded OmpA
- term:
    id: GO:0043165
    label: Gram-negative-bacterium-type cell outer membrane assembly
  evidence_type: IDA
  original_reference_id: PMID:8730870
  review:
    summary: IDA annotation from Chen and Henning 1996, the foundational paper identifying
      Skp as a periplasmic chaperone for OMPs. They showed Skp selectively binds OMPs
      (OmpA, OmpC, OmpF, LamB) and that skp deletion mutants have much-reduced concentrations
      of outer membrane proteins (PMID:8730870). This is a core biological process
      annotation for Skp.
    action: ACCEPT
    reason: Core function. Skp is directly involved in outer membrane assembly by
      escorting OMPs across the periplasm to the outer membrane.
    supported_by:
    - reference_id: PMID:8730870
      supporting_text: The mutant was viable but possessed much-reduced concentrations
        of outer membrane proteins. This defect was fully restored by a plasmid-borne
        skp gene
- term:
    id: GO:0050821
    label: protein stabilization
  evidence_type: EXP
  original_reference_id: PMID:10455120
  review:
    summary: EXP annotation from Schaefer et al. 1999 demonstrating Skp's role in
      maintaining solubility of OMP folding intermediates. In skp/degP double mutants,
      protein aggregates accumulate in the periplasm (PMID:10455120). Skp is required
      for the release of newly translocated OMPs from the plasma membrane and maintenance
      of their solubility.
    action: ACCEPT
    reason: Core function of Skp. Preventing aggregation and maintaining solubility
      of unfolded OMPs is the essence of its holdase/carrier activity.
    supported_by:
    - reference_id: PMID:10455120
      supporting_text: in the absence of an active DegP, a lack of Skp leads to the
        accumulation of protein aggregates in the periplasm
    - reference_id: PMID:10455120
      supporting_text: Skp is a molecular chaperone involved in generating and maintaining
        the solubility of early folding intermediates of outer membrane proteins
- term:
    id: GO:0050821
    label: protein stabilization
  evidence_type: IDA
  original_reference_id: PMID:12509434
  review:
    summary: IDA annotation from Bulieris et al. 2003. Demonstrated that Skp prevents
      aggregation of unfolded OmpA and maintains it in a soluble complex (PMID:12509434).
      OmpA remained unfolded but soluble when bound to Skp.
    action: ACCEPT
    reason: Consistent with Skp's core holdase function of preventing aggregation.
    supported_by:
    - reference_id: PMID:12509434
      supporting_text: OmpA remained unfolded when bound to Skp and LPS in solution.
        From this complex, OmpA folded spontaneously into lipid bilayers
- term:
    id: GO:0050821
    label: protein stabilization
  evidence_type: IDA
  original_reference_id: PMID:15304217
  review:
    summary: IDA annotation from the Skp crystal structure paper (Walton and Sousa
      2004). Demonstrated that Skp prevents aggregation of model substrates in vitro
      in an ATP-independent manner (PMID:15304217). The structure reveals the cavity
      where substrates are protected from aggregation.
    action: ACCEPT
    reason: Structural and biochemical evidence for Skp's anti-aggregation function.
    supported_by:
    - reference_id: PMID:15304217
      supporting_text: The ability of Skp to prevent the aggregation of model substrates
        in vitro is independent of ATP
- term:
    id: GO:0050821
    label: protein stabilization
  evidence_type: IDA
  original_reference_id: PMID:23796519
  review:
    summary: IDA annotation from McMorran et al. 2013. Demonstrated that Skp can rescue
      the OMP PagP from aggregation and promote its subsequent folding and membrane
      insertion (PMID:23796519). Skp-mediated delivery of PagP to liposomes is influenced
      by electrostatic interactions between the chaperone and lipid.
    action: ACCEPT
    reason: Additional evidence from a different OMP substrate (PagP) confirming Skp's
      role in preventing OMP aggregation.
    supported_by:
    - reference_id: PMID:23796519
      supporting_text: folding and membrane insertion of PagP can be restored, in
        part, by Skp in conditions that strongly favour PagP aggregation
    - reference_id: PMID:23796519
      supporting_text: the key role of Skp in holding aggregation-prone OMPs prior
        to their direct or indirect delivery to the membrane
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:19181847
  review:
    summary: IDA annotation from Walton et al. 2009. NMR experiments provided direct
      evidence that the OmpA beta-barrel domain is maintained in an unfolded state
      while bound deep within the Skp cavity (PMID:19181847). This confirms Skp binds
      unfolded proteins, but GO:0051082 fails to capture the carrier/escort function.
      GO:0140309 (unfolded protein carrier activity) is more appropriate as Skp transports
      unfolded OMPs from the inner membrane to the BAM complex.
    action: MODIFY
    reason: GO:0051082 is being reviewed for obsoletion and does not distinguish Skp's
      carrier function from simple binding. Skp is a cavity chaperone that physically
      escorts unfolded OMPs across the periplasm.
    proposed_replacement_terms:
    - id: GO:0140309
      label: unfolded protein carrier activity
    supported_by:
    - reference_id: PMID:19181847
      supporting_text: while bound to Skp, the beta-barrel domain of OmpA is maintained
        in an unfolded state
    - reference_id: PMID:19181847
      supporting_text: This domain-based chaperoning mechanism allows the transport
        of beta-barrels across the periplasm in an unfolded state
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:24077225
  review:
    summary: IDA annotation from Burmann et al. 2013. High-resolution NMR showed that
      OMP substrates bound to Skp populate a dynamic conformational ensemble with
      structural interconversion rates on the submillisecond timescale (PMID:24077225).
      The dynamic state enables energy-independent substrate release. As with other
      GO:0051082 annotations, GO:0140309 is more appropriate.
    action: MODIFY
    reason: GO:0051082 being reviewed for obsoletion. Skp's function is better described
      as unfolded protein carrier activity given the escort function across the periplasm.
    proposed_replacement_terms:
    - id: GO:0140309
      label: unfolded protein carrier activity
    supported_by:
    - reference_id: PMID:24077225
      supporting_text: The dynamic state allows for energy-independent substrate release
        and provides a general paradigm for the conformation of OMP polypeptides bound
        to energy-independent chaperones
- term:
    id: GO:0001530
    label: lipopolysaccharide binding
  evidence_type: RCA
  original_reference_id: PMID:15304217
  review:
    summary: RCA annotation for LPS binding from the crystal structure paper. Walton
      and Sousa 2004 identified a putative LPS binding site on the outer surface of
      Skp (residues 97-108) and showed that Skp can interact directly with LPS (PMID:15304217).
      LPS binding is functionally important because LPS is required together with
      Skp for efficient OMP folding and membrane insertion (PMID:12509434). The annotation
      is supported by the structural identification of the binding site and functional
      studies.
    action: ACCEPT
    reason: LPS binding is a functionally relevant interaction for Skp's chaperone
      activity. Structural and functional evidence support this annotation, even though
      the evidence code is RCA.
    supported_by:
    - reference_id: PMID:15304217
      supporting_text: Skp can interact directly with membrane lipids and lipopolysaccharide
        (LPS). These interactions are needed for efficient Skp-assisted folding of
        membrane proteins. We have identified a putative LPS binding site on the outer
        surface of Skp
- term:
    id: GO:0030288
    label: outer membrane-bounded periplasmic space
  evidence_type: IDA
  original_reference_id: PMID:8730870
  review:
    summary: IDA annotation from Chen and Henning 1996. Skp was identified as a periplasmic
      protein by subcellular fractionation and affinity chromatography with OmpF-bound
      sepharose (PMID:8730870). The periplasmic localization is consistent with Skp's
      role in escorting OMPs across the periplasm.
    action: ACCEPT
    reason: Core localization annotation. Periplasmic space is where Skp functions
      as an OMP carrier.
    supported_by:
    - reference_id: PMID:8730870
      supporting_text: Proteins of the periplasmic space were fractionated on an affinity
        column with sepharose-bound outer membrane porin OmpF. A 17 kDa polypeptide
        was the predominant protein retained by this column
- term:
    id: GO:0030288
    label: outer membrane-bounded periplasmic space
  evidence_type: IDA
  original_reference_id: PMID:1838129
  review:
    summary: IDA annotation from Thome and Mueller 1991, one of the earliest papers
      establishing Skp's periplasmic localization. Using subcellular fractionation
      with precautions to avoid non-specific electrostatic interactions, Skp partitioned
      with beta-lactamase into the soluble periplasmic fraction (PMID:1838129).
    action: ACCEPT
    reason: Early definitive evidence for periplasmic localization using careful fractionation
      methods.
    supported_by:
    - reference_id: PMID:1838129
      supporting_text: Upon cellular subfractionation (avoiding non-specific electrostatic
        interactions) Skp partitions with beta-lactamase into the fraction of soluble,
        periplasmic proteins
- term:
    id: GO:0043165
    label: Gram-negative-bacterium-type cell outer membrane assembly
  evidence_type: EXP
  original_reference_id: PMID:11698367
  review:
    summary: EXP annotation from Rizzitello et al. 2001. This genetic study demonstrated
      synthetic lethality between skp and surA mutations, establishing that Skp and
      SurA function in parallel chaperone pathways for OMP biogenesis (PMID:11698367).
      Loss of both pathways results in severely reduced envelope protein levels and
      bacteriostatic/bactericidal effects.
    action: ACCEPT
    reason: Key genetic evidence establishing Skp's role in outer membrane assembly
      through a parallel chaperone pathway with SurA.
    supported_by:
    - reference_id: PMID:11698367
      supporting_text: null mutations in skp and surA, as well as in degP and surA,
        result in synthetic phenotypes, suggesting that Skp, SurA, and DegP are functionally
        redundant
    - reference_id: PMID:11698367
      supporting_text: we propose that Skp and DegP are components of the same pathway
        and that SurA is a component of a separate pathway
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IPI
  original_reference_id: PMID:10455120
  review:
    summary: IPI annotation from Schaefer et al. 1999 (with/from UniProtKB:P0A910
      = OmpA). Using crosslinking, they showed Skp interacts with OmpA near the plasma
      membrane and binds specifically to pOmpA nascent chains after release from ribosomes
      (PMID:10455120). This demonstrates binding to early unfolded intermediates.
      However, GO:0140309 better captures the carrier function.
    action: MODIFY
    reason: GO:0051082 being reviewed for obsoletion. The interaction represents Skp's
      carrier function, capturing unfolded OMPs for periplasmic transit.
    proposed_replacement_terms:
    - id: GO:0140309
      label: unfolded protein carrier activity
    supported_by:
    - reference_id: PMID:10455120
      supporting_text: Following its transmembrane translocation, OmpA interacts with
        Skp in close vicinity to the plasma membrane
    - reference_id: PMID:10455120
      supporting_text: Skp was also found to bind strongly and specifically to pOmpA
        nascent chains after their release from the ribosome suggesting the ability
        of Skp to recognize early folding intermediates of outer membrane proteins
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IPI
  original_reference_id: PMID:12509434
  review:
    summary: IPI annotation from Bulieris et al. 2003 (with/from UniProtKB:P0A910
      = OmpA). Demonstrated direct binding of Skp to unfolded OmpA, forming a soluble
      complex from which OmpA can fold into lipid bilayers when LPS is present (PMID:12509434).
      GO:0140309 is more appropriate.
    action: MODIFY
    reason: GO:0051082 being reviewed for obsoletion. The Skp-OmpA interaction is
      part of Skp's carrier function.
    proposed_replacement_terms:
    - id: GO:0140309
      label: unfolded protein carrier activity
    supported_by:
    - reference_id: PMID:12509434
      supporting_text: OmpA remained unfolded when bound to Skp and LPS in solution.
        From this complex, OmpA folded spontaneously into lipid bilayers
- term:
    id: GO:0051604
    label: protein maturation
  evidence_type: IDA
  original_reference_id: PMID:9914480
  review:
    summary: IDA annotation from de Cock et al. 1999 (annotated by CACAO). This study
      showed Skp interacts specifically with non-native outer membrane proteins and
      proposed that Skp is required for efficient targeting of unfolded OMPs to the
      membrane (PMID:9914480). While Skp contributes to the maturation pathway of
      OMPs, the term protein maturation (GO:0051604) is overly generic. The more specific
      process annotation GO:0043165 (Gram-negative-bacterium-type cell outer membrane
      assembly) captures the same biology more precisely.
    action: MARK_AS_OVER_ANNOTATED
    reason: Protein maturation is too generic. Skp's role in OMP maturation is better
      captured by GO:0043165 (Gram-negative-bacterium-type cell outer membrane assembly)
      which is already annotated with strong experimental evidence.
    supported_by:
    - reference_id: PMID:9914480
      supporting_text: We propose that Skp is required in vivo for the efficient targeting
        of unfolded outer membrane proteins to the membrane
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IMP
  original_reference_id: PMID:10455120
  review:
    summary: IMP annotation from Schaefer et al. 1999. In skp null mutants, there
      is a specific defect in the release of newly translocated OMPs from the plasma
      membrane (PMID:10455120). The skp/degP double mutant shows protein aggregate
      accumulation. This mutant phenotype evidence supports Skp's role in the OMP
      folding pathway, though Skp itself acts as a holdase/carrier rather than a foldase.
    action: ACCEPT
    reason: Mutant phenotype evidence supporting Skp's involvement in the broader
      OMP folding pathway. Consistent with other protein folding annotations.
    supported_by:
    - reference_id: PMID:10455120
      supporting_text: Pulse labeling of OmpA in spheroplasts prepared from an skp
        null mutant revealed a specific requirement of Skp for the release of newly
        translocated outer membrane proteins from the plasma membrane
- term:
    id: GO:0030288
    label: outer membrane-bounded periplasmic space
  evidence_type: IDA
  original_reference_id: PMID:10455120
  review:
    summary: IDA annotation for periplasmic localization from Schaefer et al. 1999.
      Crosslinking experiments showed Skp interacts with OmpA near the plasma membrane
      in the periplasm (PMID:10455120). Additional evidence for the well-established
      periplasmic localization.
    action: ACCEPT
    reason: Additional experimental evidence for periplasmic localization, consistent
      with other IDA annotations.
    supported_by:
    - reference_id: PMID:10455120
      supporting_text: OmpA interacts with Skp in close vicinity to the plasma membrane
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IPI
  original_reference_id: PMID:9914480
  review:
    summary: IPI annotation from de Cock et al. 1999 (with/from UniProtKB:P02932 =
      PhoE and UniProtKB:P0A910 = OmpA). Demonstrated specific interaction of Skp
      with outer membrane proteins in their non-native state (PMID:9914480). Two entries
      exist for this PMID with different with/from values. GO:0140309 is more appropriate.
    action: MODIFY
    reason: GO:0051082 being reviewed for obsoletion. Skp's interaction with non-native
      OMPs is part of its carrier/escort function.
    proposed_replacement_terms:
    - id: GO:0140309
      label: unfolded protein carrier activity
    supported_by:
    - reference_id: PMID:9914480
      supporting_text: it interacts specifically with outer membrane proteins that
        are in their non-native state
- term:
    id: GO:0001530
    label: lipopolysaccharide binding
  evidence_type: IPI
  original_reference_id: PMID:17928002
  review:
    summary: IPI annotation from Qu et al. 2007 (with/from UniProtKB:P0A910 = OmpA).
      This study showed that LPS binds to OmpA-Skp complexes at low stoichiometries,
      and that in the ternary complex, tryptophan residues of OmpA are located closer
      to the surface than in binary complexes (PMID:17928002). This structural change
      may explain how LPS facilitates membrane insertion. The IPI evidence here reflects
      LPS interaction with the Skp-OMP complex, supporting Skp's LPS binding.
    action: ACCEPT
    reason: LPS binding to Skp-OMP complexes is functionally important for the OMP
      biogenesis pathway. Well-supported by biophysical evidence.
    supported_by:
    - reference_id: PMID:17928002
      supporting_text: Lipopolysaccharide (LPS), a major component of the outer membrane
        of Gram-negative bacteria, bound to OmpA.Skp(3) complexes at low stoichiometries
    - reference_id: PMID:17928002
      supporting_text: in this ternary complex, the tryptophan residues of the transmembrane
        domain of OmpA were located closer to the surface than in binary OmpA.Skp(3)
        complexes
- term:
    id: GO:0043165
    label: Gram-negative-bacterium-type cell outer membrane assembly
  evidence_type: IDA
  original_reference_id: PMID:12509434
  review:
    summary: IDA annotation from Bulieris et al. 2003. Demonstrated that Skp together
      with LPS assists the folding and insertion of OmpA into phospholipid bilayers
      in vitro (PMID:12509434). This reconstitution of the Skp-assisted OMP folding
      pathway directly supports its role in outer membrane assembly.
    action: ACCEPT
    reason: In vitro reconstitution of Skp-assisted OMP membrane insertion provides
      direct evidence for its role in outer membrane assembly.
    supported_by:
    - reference_id: PMID:12509434
      supporting_text: unfolded OmpA in complex with Skp and LPS folded faster into
        phospholipid bilayers than urea-unfolded OmpA
- term:
    id: GO:0043165
    label: Gram-negative-bacterium-type cell outer membrane assembly
  evidence_type: IGI
  original_reference_id: PMID:17908933
  review:
    summary: IGI annotation from Sklar et al. 2007 (with/from UniProtKB:P0ABZ6 = SurA).
      Genetic interaction evidence showing that Skp functions in a parallel pathway
      with DegP to rescue OMPs that fall off the primary SurA pathway (PMID:17908933).
      Loss of both the SurA and Skp/DegP pathways is synthetic lethal.
    action: ACCEPT
    reason: Genetic interaction evidence placing Skp in the OMP biogenesis pathway,
      parallel to SurA.
    supported_by:
    - reference_id: PMID:17908933
      supporting_text: DegP/Skp function to rescue OMPs that fall off the SurA pathway
    - reference_id: PMID:17908933
      supporting_text: SurA is the primary chaperone responsible for the periplasmic
        transit of the bulk mass of OMPs to the YaeT complex. The role of Skp and
        DegP is amplified in the absence of SurA
- term:
    id: GO:0043165
    label: Gram-negative-bacterium-type cell outer membrane assembly
  evidence_type: IPI
  original_reference_id: PMID:17908933
  review:
    summary: IPI annotation from Sklar et al. 2007 (with/from UniProtKB:P0A940 = BamA/YaeT).
      This study established the relationship between Skp and the BAM complex (YaeT),
      showing that SurA and YaeT interact directly in vivo and that Skp functions
      in a parallel delivery pathway (PMID:17908933).
    action: ACCEPT
    reason: Physical interaction evidence placing Skp in the context of the BAM complex
      OMP assembly machinery.
    supported_by:
    - reference_id: PMID:17908933
      supporting_text: we demonstrate that SurA and YaeT interact directly in vivo
    - reference_id: PMID:17908933
      supporting_text: Evidence presented suggests that DegP/Skp function to rescue
        OMPs that fall off the SurA pathway
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IPI
  original_reference_id: PMID:11278858
  review:
    summary: IPI annotation from Harms et al. 2001 (with/from UniProtKB:P02932 = PhoE).
      Crosslinking experiments demonstrated that Skp interacts with newly translocated
      PhoE at the periplasmic side of the inner membrane, even when PhoE is still
      in a transmembrane orientation in the translocase (PMID:11278858). This demonstrates
      Skp captures OMPs very early in their biogenesis. GO:0140309 is more appropriate.
    action: MODIFY
    reason: GO:0051082 being reviewed for obsoletion. Early capture of OMPs at the
      translocon is part of Skp's carrier function.
    proposed_replacement_terms:
    - id: GO:0140309
      label: unfolded protein carrier activity
    supported_by:
    - reference_id: PMID:11278858
      supporting_text: Newly translocated PhoE protein could be cross-linked to the
        periplasmic chaperone Skp at the periplasmic side of the inner membrane
    - reference_id: PMID:11278858
      supporting_text: PhoE closely interacts with the chaperone when the protein
        is still in a transmembrane orientation in the translocase
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IPI
  original_reference_id: PMID:17928002
  review:
    summary: IPI annotation from Qu et al. 2007 (with/from UniProtKB:P0A910, P0A940,
      P76045). Comprehensive biophysical study showing Skp trimer forms 1:1 stable
      complexes with multiple bacterial OMPs (OmpA, OmpG, YaeT, NalP, FomA) with nanomolar
      dissociation constants (PMID:17928002). Binding is pH-dependent and requires
      electrostatic interactions. Skp efficiently shielded OmpA tryptophan residues
      from quenching. GO:0140309 is more appropriate.
    action: MODIFY
    reason: GO:0051082 being reviewed for obsoletion. The stable 1:1 complex formation
      and shielding of OMP transmembrane domains is characteristic of carrier chaperone
      activity.
    proposed_replacement_terms:
    - id: GO:0140309
      label: unfolded protein carrier activity
    supported_by:
    - reference_id: PMID:17928002
      supporting_text: The Skp trimer formed 1:1 complexes, OMP.Skp(3), with bacterial
        OMPs, independent of their size or origin. The dissociation constants of these
        OMP.Skp(3) complexes were all in the nanomolar range, indicating that they
        are stable
    - reference_id: PMID:17928002
      supporting_text: Skp efficiently shielded tryptophan residues of the transmembrane
        strands of OmpA against fluorescence quenching by aqueous acrylamide
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: HDA
  original_reference_id: PMID:16858726
  review:
    summary: HDA annotation for cytosolic localization from a complexomic study using
      2D blue native/SDS-PAGE (PMID:16858726). Skp is a secreted periplasmic protein
      with a signal peptide (aa 1-20) that is exported via the Sec pathway (PMID:1838129).
      Its primary localization is the periplasm, not the cytosol. The cytosolic detection
      may represent pre-export Skp or a fractionation artifact. This annotation is
      inconsistent with the well-established periplasmic localization.
    action: REMOVE
    reason: Skp is exported to the periplasm via the Sec pathway and its functional
      localization is the periplasmic space, not the cytosol. The HDA detection likely
      reflects pre-export protein or a fractionation artifact. Multiple IDA-supported
      annotations confirm periplasmic localization.
    supported_by:
    - reference_id: PMID:1838129
      supporting_text: Skp is synthesized as a larger precursor that is processed
        upon translocation across the plasma membrane. Translocation is dependent
        on the H(+)-gradient, ATP, SecA, and SecY
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: PMID:1838129
  title: Skp is a periplasmic Escherichia coli protein requiring SecA and SecY for
    export.
  findings:
  - statement: Skp is synthesized as a precursor with a signal peptide and exported
      to the periplasm via the Sec pathway
    supporting_text: Skp is synthesized as a larger precursor that is processed upon
      translocation across the plasma membrane. Translocation is dependent on the
      H(+)-gradient, ATP, SecA, and SecY
- id: PMID:8730870
  title: A periplasmic protein (Skp) of Escherichia coli selectively binds a class
    of outer membrane proteins.
  findings:
  - statement: Skp selectively binds OMPs (OmpA, OmpC, OmpF, LamB) and skp deletion
      reduces OMP levels
    supporting_text: it could be demonstrated that it bound outer membrane proteins,
      following SDS-PAGE, with high selectivity. Among these were OmpA, OmpC, OmpF
      and the maltoporin LamB
- id: PMID:9914480
  title: Affinity of the periplasmic chaperone Skp of Escherichia coli for phospholipids,
    lipopolysaccharides and non-native outer membrane proteins. Role of Skp in the
    biogenesis of outer membrane protein.
  findings:
  - statement: Skp interacts specifically with non-native OMPs and associates with
      phospholipid membranes and LPS
    supporting_text: it interacts specifically with outer membrane proteins that are
      in their non-native state
- id: PMID:10455120
  title: Skp, a molecular chaperone of gram-negative bacteria, is required for the
    formation of soluble periplasmic intermediates of outer membrane proteins.
  findings:
  - statement: Skp is required for release of newly translocated OMPs from the inner
      membrane and maintenance of their solubility in the periplasm
    supporting_text: Skp is a molecular chaperone involved in generating and maintaining
      the solubility of early folding intermediates of outer membrane proteins in
      the periplasmic space of Gram-negative bacteria
- id: PMID:11278858
  title: The early interaction of the outer membrane protein phoe with the periplasmic
    chaperone Skp occurs at the cytoplasmic membrane.
  findings:
  - statement: Skp captures PhoE at the inner membrane during translocation
    supporting_text: Newly translocated PhoE protein could be cross-linked to the
      periplasmic chaperone Skp at the periplasmic side of the inner membrane
- id: PMID:11698367
  title: Genetic evidence for parallel pathways of chaperone activity in the periplasm
    of Escherichia coli.
  findings:
  - statement: Skp and DegP function in a parallel chaperone pathway to SurA for OMP
      biogenesis
    supporting_text: we propose that Skp and DegP are components of the same pathway
      and that SurA is a component of a separate pathway
- id: PMID:12509434
  title: Folding and insertion of the outer membrane protein OmpA is assisted by the
    chaperone Skp and by lipopolysaccharide.
  findings:
  - statement: Skp and LPS together facilitate OmpA folding and insertion into lipid
      bilayers in vitro
    supporting_text: unfolded OmpA in complex with Skp and LPS folded faster into
      phospholipid bilayers than urea-unfolded OmpA
- id: PMID:15304217
  title: Crystal structure of Skp, a prefoldin-like chaperone that protects soluble
    and membrane proteins from aggregation.
  findings:
  - statement: Skp forms a jellyfish-like trimer with a central cavity for substrate
      binding and has an LPS binding site
    supporting_text: The structure of the Skp trimer resembles a jellyfish with alpha-helical
      tentacles protruding from a beta barrel body defining a central cavity
- id: PMID:16858726
  title: A complexomic study of Escherichia coli using two-dimensional blue native/SDS
    polyacrylamide gel electrophoresis.
  findings: []
- id: PMID:17908933
  title: Defining the roles of the periplasmic chaperones SurA, Skp, and DegP in Escherichia
    coli.
  findings:
  - statement: SurA is the primary OMP chaperone; Skp/DegP rescue OMPs that fall off
      the SurA pathway
    supporting_text: SurA is the primary chaperone responsible for the periplasmic
      transit of the bulk mass of OMPs to the YaeT complex. The role of Skp and DegP
      is amplified in the absence of SurA
- id: PMID:17928002
  title: The trimeric periplasmic chaperone Skp of Escherichia coli forms 1:1 complexes
    with outer membrane proteins via hydrophobic and electrostatic interactions.
  findings:
  - statement: Skp trimer forms stable 1:1 complexes with multiple bacterial OMPs
      with nanomolar affinity
    supporting_text: The Skp trimer formed 1:1 complexes, OMP.Skp(3), with bacterial
      OMPs, independent of their size or origin. The dissociation constants of these
      OMP.Skp(3) complexes were all in the nanomolar range
- id: PMID:19181847
  title: The cavity-chaperone Skp protects its substrate from aggregation but allows
    independent folding of substrate domains.
  findings:
  - statement: Skp holds OmpA beta-barrel unfolded in its cavity while allowing the
      periplasmic domain to fold independently
    supporting_text: while bound to Skp, the beta-barrel domain of OmpA is maintained
      in an unfolded state, whereas the periplasmic domain is folded in its native
      conformation
- id: PMID:23796519
  title: Dissecting the effects of periplasmic chaperones on the in vitro folding
    of the outer membrane protein PagP.
  findings:
  - statement: Skp rescues aggregation-prone PagP and delivers it for membrane insertion
      via electrostatic interactions
    supporting_text: the key role of Skp in holding aggregation-prone OMPs prior to
      their direct or indirect delivery to the membrane
- id: PMID:24077225
  title: Conformation and dynamics of the periplasmic membrane-protein-chaperone complexes
    OmpX-Skp and tOmpA-Skp.
  findings:
  - statement: OMP substrates bound to Skp populate a dynamic conformational ensemble
      enabling energy-independent release
    supporting_text: The dynamic state allows for energy-independent substrate release
      and provides a general paradigm for the conformation of OMP polypeptides bound
      to energy-independent chaperones
core_functions:
- description: Unfolded protein carrier activity -- escorts unfolded outer membrane
    proteins (OMPs) from the Sec translocon at the inner membrane across the periplasm
    to the BAM complex for insertion into the outer membrane
  molecular_function:
    id: GO:0140309
    label: unfolded protein carrier activity
  directly_involved_in:
  - id: GO:0043165
    label: Gram-negative-bacterium-type cell outer membrane assembly
  locations:
  - id: GO:0030288
    label: outer membrane-bounded periplasmic space
  supported_by:
  - reference_id: PMID:10455120
    supporting_text: Skp is a molecular chaperone involved in generating and maintaining
      the solubility of early folding intermediates of outer membrane proteins in
      the periplasmic space of Gram-negative bacteria
  - reference_id: PMID:19181847
    supporting_text: This domain-based chaperoning mechanism allows the transport
      of beta-barrels across the periplasm in an unfolded state, which may be important
      for efficient insertion into the outer membrane
- description: Homotrimerization -- Skp forms a functional homotrimer with a jellyfish-like
    architecture that creates the central cavity required for substrate binding
  molecular_function:
    id: GO:0042802
    label: identical protein binding
  locations:
  - id: GO:0030288
    label: outer membrane-bounded periplasmic space
  supported_by:
  - reference_id: PMID:15304217
    supporting_text: The structure of the Skp trimer resembles a jellyfish with alpha-helical
      tentacles protruding from a beta barrel body defining a central cavity
- description: Lipopolysaccharide binding -- Skp binds LPS which is required for efficient
    Skp-assisted folding and insertion of OMPs into membranes
  molecular_function:
    id: GO:0001530
    label: lipopolysaccharide binding
  directly_involved_in:
  - id: GO:0043165
    label: Gram-negative-bacterium-type cell outer membrane assembly
  supported_by:
  - reference_id: PMID:15304217
    supporting_text: Skp can interact directly with membrane lipids and lipopolysaccharide
      (LPS). These interactions are needed for efficient Skp-assisted folding of membrane
      proteins
  - reference_id: PMID:12509434
    supporting_text: Skp alone was not sufficient to facilitate membrane insertion
      and folding of OmpA. In addition, lipopolysaccharide (LPS) was required

Skp

Gene Description

Existing Annotations Review

Core Functions

Unfolded protein carrier activity -- escorts unfolded outer membrane proteins (OMPs) from the Sec translocon at the inner membrane across the periplasm to the BAM complex for insertion into the outer membrane

Homotrimerization -- Skp forms a functional homotrimer with a jellyfish-like architecture that creates the central cavity required for substrate binding

Lipopolysaccharide binding -- Skp binds LPS which is required for efficient Skp-assisted folding and insertion of OMPs into membranes

References

📚 Additional Documentation

Deep Research Bioreason

BioReason Chat Export

Thinking Trace

Functional Summary

UniProt Summary

InterPro Domains

GO Terms

Deep Research Bioreason Rl

BioReason Chat Export

Thinking Trace

Functional Summary

UniProt Summary

InterPro Domains

GO Terms

Bioreason Rl Review

BioReason-Pro RL Review: Skp (E. coli)

Functional Summary Review

Notes on thinking trace

📄 View Raw YAML