KAR2

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005634 nucleus	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: IBA annotation to nucleus based on phylogenetic inference from Hsp70 family members. KAR2/BiP is primarily an ER lumen protein with an HDEL ER retention signal (PMID:2661018). While some Hsp70 family members are nuclear, KAR2 is not typically described as nuclear in the literature. The IBA may reflect general Hsp70 family localization rather than KAR2-specific data. Reason: KAR2 is primarily an ER lumen chaperone (PMID:2661018). The nucleus annotation is inferred from the broader Hsp70 family and is not well-supported for KAR2 specifically, but yeast ER is contiguous with the nuclear envelope so some nuclear presence is plausible. Keep as non-core. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN001834223 · PAINT ER-BiP family node SUPPORTS TRANSFER The ER-BiP node supports a broad nuclear-envelope-compatible call, but nucleus is not the primary or most informative localization for Kar2p.
GO:0005737 cytoplasm	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: IBA annotation to cytoplasm based on phylogenetic inference from cytosolic Hsp70 family members. KAR2 has an ER signal peptide and HDEL retention signal and is predominantly an ER lumen protein (PMID:2661018). This annotation likely reflects the broader Hsp70 family rather than KAR2-specific localization. Reason: The cytoplasm annotation is inherited from the broad Hsp70 family. KAR2 is an ER lumen resident (PMID:2661018). Some cytoplasmic presence before ER import is trivially true but not informative about KAR2 function. Keep as non-core. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN002321897 · PAINT broad Hsp70 family node SUPPORTS TRANSFER Cytoplasm is ontologically compatible with the ER but much less informative than Kar2p's target-specific ER-lumen localization.
GO:0016887 ATP hydrolysis activity	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for ATP hydrolysis activity, well-supported by direct experimental evidence (PMID:1325440). Purified BiP/Kar2p exhibits ATPase activity with a specific activity of 2 pmol/min/ug. The ATPase cycle is central to the chaperone mechanism. Reason: ATP hydrolysis is a core biochemical activity of KAR2/BiP, directly demonstrated by purification and biochemical assay (PMID:1325440). The IBA annotation is consistent with both experimental data and the known Hsp70 mechanism. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000452648 · PAINT conserved Hsp70 family node SUPPORTS TRANSFER ATP hydrolysis is ancestral across Hsp70s and independently demonstrated for Kar2p. Supporting Evidence: PMID:1325440 It is active as a homodimer and exhibits ATPase activity with a specific activity of 2 pmol/min/micrograms of protein.
GO:0031072 heat shock protein binding	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: IBA annotation for heat shock protein binding. KAR2/BiP interacts with multiple co-chaperones including J-domain proteins (Sec63, Scj1, Jem1) and the Hsp70 family member LHS1 (PMID:14704430). This is a well-supported annotation for an Hsp70. Reason: KAR2 interacts with J-domain co-chaperones and the ER Hsp70 family member LHS1 (PMID:14704430). Heat shock protein binding is an integral part of the Hsp70 chaperone cycle. The IBA annotation is well-supported. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000452648 · PAINT conserved Hsp70 family node SUPPORTS TRANSFER Direct Kar2p-Lhs1p interaction supports the transfer, but this generic binding term is secondary to Kar2p's ATP-dependent chaperone activity. Supporting Evidence: PMID:14704430 Lhs1p and Kar2p specifically interacted to couple, and coordinately regulate, their respective activities. file:yeast/KAR2/KAR2-deep-research-falcon.md Kar2p works with Sec63 (J-domain cochaperone) and Sls1p, which stimulates Sec63-mediated activation of Kar2p. Lhs1 and Sil1 are identified as nucleotide exchange factors/functionally linked ER lumenal factors for BiP/Kar2; Scj1 is an Hsp40 cochaperone.
GO:0044183 protein folding chaperone	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for protein folding chaperone activity. KAR2/BiP is a canonical Hsp70 that functions as an ATP-dependent protein folding chaperone in the ER lumen. This is a core function. The more specific term GO:0140662 (ATP-dependent protein folding chaperone) would be even more accurate for KAR2 since it is an ATP-dependent foldase, but GO:0044183 is the term assigned by IBA and is correct. Reason: Protein folding chaperone is a core molecular function of KAR2/BiP. As a canonical Hsp70, it assists protein folding in an ATP-dependent manner. The IBA annotation is at an appropriate level of specificity; the more specific GO:0140662 is also appropriate but GO:0044183 correctly captures the chaperone function. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000452648 · PAINT conserved Hsp70 family node SUPPORTS TRANSFER The ancestral foldase inference agrees with Kar2p's ATPase/client-binding cycle and established ER folding role. Supporting Evidence: PMID:1325440 Purification and characterization of BiP/Kar2 protein from Saccharomyces cerevisiae. file:yeast/KAR2/KAR2-deep-research-falcon.md Kar2p is an Hsp70-family molecular chaperone in the ER lumen that binds unfolded polypeptides and supports protein folding homeostasis, ER import/translocation, and quality control pathways including ER-associated degradation (ERAD).
GO:0036503 ERAD pathway	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for ERAD pathway involvement. KAR2/BiP participates in ERAD by maintaining the solubility of misfolded proteins for retrotranslocation and degradation (PMID:11381090), and as part of the luminal surveillance complex with Yos9 and Hrd3 (PMID:16873065). Reason: KAR2 involvement in ERAD is well-established by multiple experimental studies. BiP maintains ERAD substrate solubility (PMID:11381090) and is part of the Yos9/Kar2/Hrd3 luminal surveillance complex that selects misfolded glycoproteins for ERAD (PMID:16873065). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001834223 · PAINT ER-BiP family node SUPPORTS TRANSFER ERAD participation is appropriately placed on the ER-BiP branch and independently supported by yeast genetic and complex evidence. Supporting Evidence: PMID:11381090 these ERAD substrates are stabilized and aggregate in the ER at elevated temperatures when BiP, the lumenal Hsp70 molecular chaperone, is mutated PMID:16873065 Yos9p, together with Kar2p and Hrd3p, forms a luminal surveillance complex that both recruits nonnative proteins to the core ERAD machinery file:yeast/KAR2/KAR2-deep-research-falcon.md Kar2p binds unfolded or unassembled ER proteins and contributes to quality control, maintaining client solubility and promoting retrotranslocation/degradation through ERAD.
GO:0016020 membrane	IBA GO_REF:0000033	MODIFY	Summary: IBA annotation for broad membrane localization from the ER-BiP PAINT node. The node is correctly placed on BiP orthologs and Kar2p has membrane-proximal activity at the Sec61/Sec63 translocon and the Hrd1 ERAD machinery, but GO:0016020 is an uninformative parent for a soluble ER-lumen Hsp70 whose more precise ER lumen and ER membrane locations are already captured. Reason: PTN001834223 is a sound ER-BiP node, so the IBA is not a paralog leak or a stale transfer. The selected bare-membrane GO term is less informative than the accepted ER lumen and ER membrane rows for a soluble HDEL-retrieved BiP that acts peripherally at ER membrane complexes. This row should not be exported as a standalone KAR2 localization. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN001834223 · PAINT ER-BiP family node SUPPORTS TRANSFER The BiP-specific node safely transfers membrane-proximal ER activity; the defect is that GO:0016020 is a generic parent term rather than an informative localization for soluble Kar2p. Proposed replacements: endoplasmic reticulum membrane
GO:0042026 protein refolding	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for protein refolding. As an Hsp70 chaperone, KAR2/BiP assists in refolding of proteins that have become misfolded or aggregated in the ER lumen. This is consistent with its role in maintaining protein homeostasis in the ER. Reason: Protein refolding is a well-established function of Hsp70 chaperones including KAR2/BiP. The annotation is supported by the known mechanism of Hsp70-mediated protein refolding and the demonstrated role of BiP in maintaining solubility of ER proteins (PMID:11381090). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000452648 · PAINT conserved Hsp70 family node SUPPORTS TRANSFER Unlike the ribosome-specialized Ssb branch, ER BiP handles misfolded mature clients, so the ancestral refolding process is compatible with Kar2p biology.
GO:0034663 endoplasmic reticulum chaperone complex	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for ER chaperone complex membership. KAR2/BiP is a key component of ER chaperone complexes, interacting with co-chaperones (Sec63, Scj1, Jem1), nucleotide exchange factors (Lhs1, Sil1), and the luminal surveillance complex (Yos9, Hrd3) (PMID:16873065, PMID:14704430). Reason: KAR2 is a central component of ER chaperone complexes. It forms complexes with J-domain proteins and NEFs for protein translocation and folding, and is part of the luminal surveillance complex (PMID:16873065). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001834223 · PAINT ER-BiP family node SUPPORTS TRANSFER Complex participation is conserved on the ER-BiP branch and agrees with Kar2p's experimentally established luminal surveillance and cochaperone complexes.
GO:0005788 endoplasmic reticulum lumen	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for ER lumen localization. KAR2/BiP is a well-established ER lumen resident protein with an HDEL retention signal. Confirmed by IDA in PMID:2661018. Reason: ER lumen is the primary localization of KAR2/BiP, confirmed experimentally (PMID:2661018). The HDEL motif at the C-terminus ensures ER retention. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001834223 · PAINT ER-BiP family node SUPPORTS TRANSFER The node is appropriately restricted to ER BiP homologs, and Kar2p's signal peptide plus terminal HDEL independently support ER-lumen residency. Supporting Evidence: PMID:2661018 KAR2, a karyogamy gene, is the yeast homolog of the mammalian BiP/GRP78 gene. file:yeast/KAR2/KAR2-deep-research-falcon.md Soluble ER residents in budding yeast are commonly retained by C-terminal HDEL-type retrieval sequences. For Kar2p/BiP, an experimentally used retrieval motif is FEHDEL (i.e., HDEL as the terminal four residues). The H/KDEL tetrapeptide must occupy the final four residues to function, and HDEL-dependent retrieval is required for cell growth in budding yeast.
GO:0030968 endoplasmic reticulum unfolded protein response	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for ER UPR involvement. KAR2/BiP plays a central role in UPR signaling by regulating the Ire1 kinase/ribonuclease. Kar2 substrate-binding- and ATPase-domain mutants alter Kar2-Ire1 association and UPR activation (PMID:12808051). The authors present BiP dissociation as part of a supported regulatory model and explicitly describe competition between unfolded proteins and Ire1 as speculation, rather than establishing titration as the sole activation mechanism. Recent synthesis (2023 review, summarized in the falcon deep research report) refines this view: Kar2/BiP acts as an "adjustor" of Ire1 within a layered control system rather than a simple on/off switch, and Kar2 dissociation alone is not sufficient for full Ire1 activation (additional Ire1-intrinsic restraints contribute). Reason: KAR2/BiP involvement in the ER UPR is supported by the demonstrated UPR phenotypes of Kar2 substrate-binding- and ATPase-domain mutants under basal and ER-stress conditions (PMID:12808051). The paper reports strong support for a Kar2-dependent Ire1-regulation model, but its unfolded-client competition/titration explanation remains a proposed mechanism. KAR2 is also itself transcriptionally induced by UPR. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001834223 · PAINT ER-BiP family node SUPPORTS TRANSFER UPR participation is appropriately inherited within ER BiPs and independently grounded by Kar2p-Ire1 genetic evidence in yeast. Supporting Evidence: PMID:12808051 Our findings provide strong evidence in support of BiP/Kar2-dependent Ire1 regulation model and suggest that Ire1 associates with Kar2 as a chaperone substrate. PMID:12808051 cells carrying a mutation in the Kar2 ATPase domain, in which Kar2 poorly dissociated from Ire1 even in the presence of tunicamycin, a potent inducer of ER stress, were unable to activate the pathway. file:yeast/KAR2/KAR2-deep-research-falcon.md Kar2p/BiP should be viewed less as a simple “on/off inhibitor” and more as an adjustor of Ire1 activity with layered regulation
GO:0000166 nucleotide binding	IEA GO_REF:0000043	MODIFY	Summary: Retired UniProt keyword IEA annotation for broad nucleotide binding. KAR2/BiP has a well-characterized Hsp70 nucleotide-binding domain, but the current GOA export no longer carries this exact source row and ATP binding is the more specific live annotation. Reason: Nucleotide binding is true for Kar2p but too broad for the N-terminal Hsp70 nucleotide-binding domain. The row should be replaced by the specific ATP binding term that is now supplied directly by InterPro. Proposed replacements: ATP binding
GO:0005524 ATP binding	IEA GO_REF:0000120	ACCEPT	Summary: Retired combined-UniProt ATP-binding row. Kar2p ATP binding remains correct and is essential for the Hsp70 chaperone cycle, but the refreshed GOA now exports an exact InterPro2GO GO_REF:0000002 row for this same term. Reason: ATP binding is directly demonstrated for KAR2/BiP (PMID:1325440). The IEA annotation is consistent with experimental evidence.
GO:0005737 cytoplasm	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: IEA annotation for cytoplasm from ARBA machine learning. KAR2 is primarily an ER lumen protein. Duplicate of the IBA cytoplasm annotation. Reason: Consistent with the IBA annotation for the same term. KAR2 is primarily ER lumen-localized (PMID:2661018). Cytoplasm is not informative about KAR2 function. Keep as non-core.
GO:0005788 endoplasmic reticulum lumen	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation for ER lumen based on UniProt subcellular location mapping. Consistent with direct experimental evidence (PMID:2661018). Reason: ER lumen localization is well-established for KAR2/BiP. The IEA duplicates the IBA and experimental evidence but is correct.
GO:0006616 SRP-dependent cotranslational protein targeting to membrane, translocation	IEA GO_REF:0000117	ACCEPT	Summary: IEA annotation from ARBA for SRP-dependent cotranslational translocation. KAR2/BiP is required for both co- and post-translational translocation (PMID:7568189). This IEA annotation is consistent with experimental evidence. Reason: KAR2 is experimentally shown to be required for SRP-dependent cotranslational translocation (PMID:7568189). The IEA is correct. Supporting Evidence: PMID:7568189 Sec63p and Kar2p are necessary for both co- and posttranslational translocation in yeast.
GO:0016787 hydrolase activity	IEA GO_REF:0000043	MODIFY	Summary: Retired UniProt keyword IEA annotation for broad hydrolase activity. Kar2p has ATPase activity, but this parent term is much less informative than the live ATP hydrolysis activity rows. Reason: GO:0016787 is a very broad parent of ATP hydrolysis activity, which was directly demonstrated for purified Kar2p. The current UniProt keyword row is no longer live and should be replaced by GO:0016887. Proposed replacements: ATP hydrolysis activity
GO:0016887 ATP hydrolysis activity	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for ATP hydrolysis activity. Consistent with direct experimental evidence (PMID:1325440) and the IBA and IDA annotations for the same term. Reason: ATP hydrolysis is directly demonstrated for KAR2/BiP (PMID:1325440). The IEA duplicates the IBA and IDA annotations but is correct.
GO:0051082 unfolded protein binding	IEA GO_REF:0000117	MODIFY	Summary: IEA annotation for unfolded protein binding from ARBA. GO:0051082 is now formally obsolete. KAR2/BiP does bind unfolded proteins, but as an ATP-dependent foldase, the more accurate annotation is GO:0140662 (ATP-dependent protein folding chaperone) or GO:0044183 (protein folding chaperone). Reason: GO:0051082 is now formally obsolete. KAR2/BiP is an ATP-dependent protein folding chaperone; its binding to unfolded substrates is part of its chaperone mechanism, not a passive binding activity. Should be replaced with the chaperone function terms already annotated (GO:0044183 or GO:0140662). Proposed replacements: ATP-dependent protein folding chaperone protein folding chaperone
GO:0005515 protein binding	IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine...	REMOVE	Summary: Live IntAct IPI annotation to generic protein binding from a high-throughput proteome survey. The retained IDP1 interaction does not establish a more informative Kar2p molecular function. Reason: Generic protein binding is not an informative GO molecular-function annotation for an Hsp70 chaperone, and this high-throughput interaction does not support a more specific MF term. Removing the row does not reject the reported IDP1 physical interaction.
GO:0005515 protein binding	IPI PMID:16554755 Global landscape of protein complexes in the yeast Saccharom...	REMOVE	Summary: Retired IntAct IPI annotation to generic protein binding from a global protein-complex survey. Reason: The current IntAct GOA export no longer carries this exact row. In any case, generic protein binding is not an informative MF for Kar2p and the high-throughput AP-MS evidence does not support a specific replacement MF.
GO:0005515 protein binding	IPI PMID:16873065 A luminal surveillance complex that selects misfolded glycop...	REMOVE	Summary: IPI annotation for protein binding from the luminal surveillance complex study. The specific interaction is with YOS9, forming the Yos9/Kar2/Hrd3 complex (PMID:16873065). This is better captured by the luminal surveillance complex CC annotation. Reason: The interaction with YOS9 in the luminal surveillance complex (PMID:16873065) is captured by GO:0034099 (luminal surveillance complex). Generic protein binding adds no additional molecular-function information for Kar2p.
GO:0005515 protein binding	IPI PMID:19536198 An atlas of chaperone-protein interactions in Saccharomyces ...	REMOVE	Summary: Retired IntAct IPI annotation to generic protein binding from a chaperone-protein interaction atlas. Reason: The current IntAct GOA export no longer carries this exact row. The generic GO:0005515 assertion is uninformative for an Hsp70 that naturally binds many clients, and the survey does not justify a more specific MF.
GO:0005515 protein binding	IPI PMID:37968396 The social and structural architecture of the yeast protein ...	REMOVE	Summary: Retired IntAct IPI annotation to generic protein binding from a yeast interactome architecture study. Reason: The current IntAct GOA export no longer carries this exact row. Generic protein binding is not an informative GO MF for an ATP-dependent Hsp70 chaperone.
GO:0002235 detection of unfolded protein	NAS PMID:16873065 A luminal surveillance complex that selects misfolded glycop...	ACCEPT	Summary: NAS annotation for detection of unfolded protein from the luminal surveillance complex study. Kar2p is part of the Yos9/Kar2/Hrd3 complex that recognizes terminally misfolded glycoproteins for ERAD (PMID:16873065). PMID:12808051 also supports Kar2-dependent Ire1 regulation, but its proposal that unfolded clients compete with Ire1 for Kar2 binding is explicitly speculative. Reason: ACCEPT is grounded in the Yos9/Kar2/Hrd3 gatekeeper complex, which identifies terminally misfolded ERAD substrates (PMID:16873065), together with Kar2's established client-chaperone biology. Unfolded-protein titration of Kar2 away from Ire1 is an author-proposed model in PMID:12808051, not an independently established detection mechanism and not the basis of this acceptance. Supporting Evidence: PMID:16873065 Yos9p/Kar2p/Hrd3p acts as a gatekeeper, ensuring correct identification of terminally misfolded proteins PMID:12808051 We speculate that recognition of unfolded proteins is based on their competition with Ire1 for binding with BiP/Kar2. file:yeast/KAR2/KAR2-deep-research-falcon.md Kar2p binds unfolded or unassembled ER proteins and contributes to quality control, maintaining client solubility and promoting retrotranslocation/degradation through ERAD.
GO:0005789 endoplasmic reticulum membrane	NAS PMID:16873065 A luminal surveillance complex that selects misfolded glycop...	KEEP AS NON CORE	Summary: NAS annotation for ER membrane localization from the luminal surveillance complex study. KAR2/BiP is primarily in the ER lumen but associates with membrane complexes (Sec61/Sec63 translocon, Hrd1 complex) through protein-protein interactions (PMID:16873065, PMID:10367885). Reason: While KAR2 is a soluble ER lumen protein, it functionally associates with ER membrane complexes during translocation and ERAD. The NAS is reasonable but secondary to the more precise ER-lumen localization.
GO:0036503 ERAD pathway	NAS PMID:16873065 A luminal surveillance complex that selects misfolded glycop...	ACCEPT	Summary: NAS annotation for ERAD pathway from the luminal surveillance complex study. Duplicate of the IBA and IMP ERAD annotations. Well-supported. Reason: ERAD involvement is well-established (PMID:16873065, PMID:11381090). This NAS is consistent with the IBA and IMP annotations.
GO:0036503 ERAD pathway	IMP PMID:11381090 Molecular chaperones in the yeast endoplasmic reticulum main...	ACCEPT	Summary: IMP annotation for ERAD pathway. Nishikawa et al. (2001) demonstrated that ERAD substrates (CPY* and pro-alpha-factor) are stabilized and aggregate in the ER at elevated temperatures when BiP/Kar2 is mutated (kar2-159), showing that BiP maintains ERAD substrates in a retrotranslocation-competent state (PMID:11381090). Reason: Direct genetic evidence that kar2 mutations impair ERAD. This is a core function of KAR2 in ER quality control. Supporting Evidence: PMID:11381090 these ERAD substrates are stabilized and aggregate in the ER at elevated temperatures when BiP, the lumenal Hsp70 molecular chaperone, is mutated
GO:0015450 protein-transporting ATPase activity	IDA PMID:10367885 BiP acts as a molecular ratchet during posttranslational tra...	ACCEPT	Summary: IDA annotation for protein-transporting ATPase activity. Matlack et al. (1999) demonstrated in a reconstituted system that BiP/Kar2p acts as a molecular ratchet during posttranslational transport of prepro-alpha factor across the ER membrane, using ATP hydrolysis to drive translocation (PMID:10367885). Reason: This is a core molecular function of KAR2. Direct biochemical demonstration that BiP uses ATP hydrolysis to drive protein translocation across the ER membrane via a Brownian ratchet mechanism (PMID:10367885). Supporting Evidence: PMID:10367885 BiP (Kar2p), a member of the Hsp70 family resident in the ER lumen, acts as a molecular ratchet during translocation of the secretory protein prepro-alpha factor through the channel formed by the Sec complex.
GO:0070972 protein localization to endoplasmic reticulum	IMP PMID:1996357 Binding protein BiP is required for translocation of secreto...	ACCEPT	Summary: IMP annotation for protein localization to ER. The cached record for PMID:1996357 is abstract-only, but its abstract directly reports that BiP depletion blocks translocation of secretory proteins into the ER. Independent studies establish both co- and post-translational pathways (PMID:7568189, PMID:10367885). Reason: KAR2 is required for protein import into the ER, demonstrated by multiple studies (PMID:7568189, PMID:10367885). This is a core function.
GO:0070880 fungal-type cell wall beta-glucan biosynthetic process	IGI PMID:9430631 Cell wall 1,6-beta-glucan synthesis in Saccharomyces cerevis...	KEEP AS NON CORE	Summary: IGI annotation for cell wall beta-glucan biosynthesis. Simons et al. (1998) showed that double mutants defective in both BiP/Kar2p and ER glucosidases exhibited reduced 1,6-beta-glucan synthesis, abnormal cell wall morphology, and severely inhibited growth (PMID:9430631). This likely reflects the requirement of KAR2 for proper folding of cell wall biosynthetic enzymes in the ER rather than a direct role in glucan synthesis. Reason: The cell wall defect is an indirect consequence of KAR2 chaperone function in the ER rather than a direct role in glucan biosynthesis. The glucosidases and BiP/Kar2p function synergistically in protein quality control that affects cell wall synthesis (PMID:9430631). This is a pleiotropic effect of the general chaperone function. Supporting Evidence: PMID:9430631 the glucosidases function synergistically with BiP/Kar2p in this process
GO:0000742 karyogamy involved in conjugation with cellular fusion	IMP PMID:10069807 Genetic interactions between KAR7/SEC71, KAR8/JEM1, KAR5, an...	KEEP AS NON CORE	Summary: IMP annotation for karyogamy. Brizzio et al. (1999) showed genetic interactions between KAR2 and other KAR genes during nuclear fusion, and that KAR2 interacts with the DnaJ protein Jem1p for nuclear envelope fusion during mating (PMID:10069807). This is the original phenotype for which KAR2 was named (KARyogamy). Reason: Karyogamy is the original phenotype for KAR2 but represents a specialized use of its general chaperone function in nuclear envelope fusion during mating. It is not a core molecular function but a biologically important pleiotropic effect. KAR2 works with Jem1p in a nuclear envelope fusion chaperone complex (PMID:10069807). Supporting Evidence: PMID:10069807 Overexpression of KAR8/JEM1 (but not SEC63) strongly suppressed the mating defect of kar2-1, suggesting that Kar2p interacts with Kar8/Jem1p for nuclear fusion.
GO:0005783 endoplasmic reticulum	IDA PMID:2661018 KAR2, a karyogamy gene, is the yeast homolog of the mammalia...	ACCEPT	Summary: IDA annotation for ER localization from the original KAR2 characterization. Rose et al. (1989) identified KAR2 as the yeast BiP/GRP78 homolog and demonstrated its ER localization (PMID:2661018). Reason: Direct experimental demonstration of ER localization. This is the primary localization of KAR2/BiP (PMID:2661018).
GO:0006616 SRP-dependent cotranslational protein targeting to membrane, translocation	IMP PMID:7568189 BiP and Sec63p are required for both co- and posttranslation...	ACCEPT	Summary: IMP annotation for SRP-dependent cotranslational translocation. Brodsky et al. (1995) demonstrated that BiP/Kar2p and Sec63p are required for both co- and posttranslational protein translocation into the yeast ER (PMID:7568189). Reason: Direct genetic evidence that KAR2 is required for cotranslational translocation, using kar2 mutant membranes defective in invertase import (PMID:7568189). Supporting Evidence: PMID:7568189 Sec63p and Kar2p are necessary for both co- and posttranslational translocation in yeast. file:yeast/KAR2/KAR2-deep-research-falcon.md A mechanistic anchor is Sec63, a transmembrane protein whose luminal J-domain recruits Kar2p and stimulates Kar2p ATPase activity; sec63 J-domain mutants (e.g., sec63-1) are defective in Kar2p binding and accumulate untranslocated preproteins. ER microsomes from kar2 and sec63-1 mutants are defective for both post- and cotranslational translocation in vitro.
GO:0006986 response to unfolded protein	IMP PMID:12808051 Genetic evidence for a role of BiP/Kar2 that regulates Ire1 ...	ACCEPT	Summary: IMP annotation for response to unfolded protein. Kimata et al. (2003) provided genetic evidence that BiP/Kar2 regulates Ire1 in response to unfolded protein accumulation. kar2 substrate-binding domain mutants activated UPR even without ER stress, while ATPase domain mutants failed to activate UPR even with tunicamycin (PMID:12808051). Reason: KAR2/BiP is a central regulator of the UPR signaling pathway. The genetic evidence from kar2 mutants directly demonstrates BiP's role in sensing unfolded proteins and regulating Ire1 (PMID:12808051). Supporting Evidence: PMID:12808051 cells carrying a mutation in the Kar2 substrate-binding domain were incubated at the restrictive temperature, association of Kar2 to Ire1 was disrupted, and the UPR pathway was activated even in the absence of extrinsic ER stress. file:yeast/KAR2/KAR2-deep-research-falcon.md under non-stress conditions, Kar2 binds the luminal domain of Ire1 and inhibits Ire1 self-association; upon ER stress, Kar2 dissociates, enabling Ire1 oligomerization and downstream HAC1 splicing.
GO:0016887 ATP hydrolysis activity	IDA PMID:1325440 Purification and characterization of BiP/Kar2 protein from S...	ACCEPT	Summary: IDA annotation for ATP hydrolysis activity. Tokunaga et al. (1992) purified BiP/Kar2p and directly demonstrated ATPase activity with a specific activity of 2 pmol/min/ug (PMID:1325440). Reason: Direct biochemical demonstration of ATPase activity in purified KAR2/BiP protein. This is a core enzymatic activity. Supporting Evidence: PMID:1325440 It is active as a homodimer and exhibits ATPase activity with a specific activity of 2 pmol/min/micrograms of protein.
GO:0031204 post-translational protein targeting to membrane, translocation	IDA PMID:10367885 BiP acts as a molecular ratchet during posttranslational tra...	ACCEPT	Summary: IDA annotation for post-translational translocation. Matlack et al. (1999) used a reconstituted in vitro system to demonstrate that BiP/Kar2p drives posttranslational transport of prepro-alpha factor across the ER membrane via a Brownian ratchet mechanism (PMID:10367885). Reason: Direct biochemical demonstration of BiP-dependent posttranslational translocation in a reconstituted system (PMID:10367885). Core function. Supporting Evidence: PMID:10367885 BiP (Kar2p), a member of the Hsp70 family resident in the ER lumen, acts as a molecular ratchet during translocation of the secretory protein prepro-alpha factor through the channel formed by the Sec complex. file:yeast/KAR2/KAR2-deep-research-falcon.md Kar2p can function as a “molecular ratchet” during translocation, biasing client movement into the ER lumen.
GO:0031204 post-translational protein targeting to membrane, translocation	IMP PMID:7568189 BiP and Sec63p are required for both co- and posttranslation...	ACCEPT	Summary: IMP annotation for post-translational translocation. Brodsky et al. (1995) showed that kar2 mutants are defective in posttranslational translocation (PMID:7568189). Reason: Genetic evidence complementing the IDA evidence from PMID:10367885. Both co- and post-translational translocation require KAR2 (PMID:7568189). Supporting Evidence: PMID:7568189 Sec63p and Kar2p are necessary for both co- and posttranslational translocation in yeast.
GO:0034099 luminal surveillance complex	IDA PMID:16873065 A luminal surveillance complex that selects misfolded glycop...	ACCEPT	Summary: IDA annotation for luminal surveillance complex. Denic et al. (2006) demonstrated that Yos9p, Kar2p, and Hrd3p form a stable luminal surveillance complex that selects misfolded glycoproteins for ERAD (PMID:16873065). Reason: Direct biochemical demonstration that KAR2/BiP is a component of the luminal surveillance complex (PMID:16873065). This complex is important for ERAD substrate recognition. Supporting Evidence: PMID:16873065 Yos9p, together with Kar2p and Hrd3p, forms a luminal surveillance complex that both recruits nonnative proteins to the core ERAD machinery
GO:0051082 unfolded protein binding	IMP PMID:12808051 Genetic evidence for a role of BiP/Kar2 that regulates Ire1 ...	MODIFY	Summary: IMP annotation for unfolded protein binding. Kimata et al. (2003) showed that Kar2 substrate-binding domain mutants disrupted the association with Ire1, and proposed that Ire1 associates with Kar2 as a chaperone substrate (PMID:12808051). GO:0051082 is now formally obsolete; the binding activity here is part of KAR2's chaperone mechanism. Reason: GO:0051082 is now formally obsolete. The binding to unfolded proteins demonstrated in this study is part of KAR2's ATP-dependent chaperone mechanism. The appropriate replacement is GO:0140662 (ATP-dependent protein folding chaperone) or GO:0044183 (protein folding chaperone), both already annotated. Proposed replacements: ATP-dependent protein folding chaperone protein folding chaperone Supporting Evidence: PMID:12808051 Ire1 associates with Kar2 as a chaperone substrate
GO:0051082 unfolded protein binding	IDA PMID:23704572 Futile protein folding cycles in the ER are terminated by th...	MODIFY	Summary: IDA annotation for unfolded protein binding. The cached PMID:23704572 record is abstract-only and reports that O-mannosylation terminates failed folding cycles by reducing substrate engagement with the Kar2 chaperone. GO:0051082 is now formally obsolete, and this substrate interaction is better represented as chaperone activity. Reason: GO:0051082 is now formally obsolete. As for the other unfolded protein binding annotations, the activity is better described as ATP-dependent protein folding chaperone (GO:0140662). The IDA evidence likely demonstrates substrate binding as part of the chaperone cycle. Proposed replacements: ATP-dependent protein folding chaperone protein folding chaperone
GO:0140662 ATP-dependent protein folding chaperone	IDA PMID:14704430 Coordinated activation of Hsp70 chaperones.	NEW	Summary: KAR2/BiP is a canonical Hsp70 that functions as an ATP-dependent protein folding chaperone. Its substrate binding and release are coupled to ATP hydrolysis and nucleotide exchange. This term is the most specific and accurate description of KAR2's core foldase function. Reason: GO:0140662 is the most accurate MF term for KAR2/BiP. PMID:14704430 directly demonstrates nucleotide-exchange stimulation of Kar2p and coupling of the Kar2p/Lhs1p ATPase activities in the ER chaperone system. PMID:23704572 independently establishes Kar2-client engagement, while PMID:1325440 demonstrates purified Kar2p ATPase activity. Together these support replacing the obsolete passive-binding term with the ATP-dependent chaperone activity. Supporting Evidence: PMID:14704430 Lhs1p stimulated Kar2p by providing a specific nucleotide exchange activity, whereas Kar2p reciprocally activated the Lhs1p adenosine triphosphatase (ATPase). The two ATPase activities are coupled, and their coordinated regulation is essential for normal function in vivo. PMID:23704572 O-mannosylation incapacitated target molecule folding and removed them from folding cycles by reducing engagement with the Kar2 chaperone. PMID:1325440 It is active as a homodimer and exhibits ATPase activity with a specific activity of 2 pmol/min/micrograms of protein. file:yeast/KAR2/KAR2-deep-research-falcon.md Kar2p's canonical domain architecture is explicitly described as an Hsp70 with an approximately 44 kDa ATPase domain, an approximately 18 kDa peptide-binding pocket, and an approximately 10 kDa C-terminal domain.
GO:0005524 ATP binding	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO IEA annotation to ATP binding through the Hsp70 nucleotide-binding domain. This is a current exact-source row replacing the older combined UniProt ATP-binding row. Reason: Kar2p's ATP binding is inherent to the conserved N-terminal Hsp70 nucleotide-binding domain and is required for its chaperone cycle; purified Kar2p directly hydrolyzes ATP (PMID:1325440). The InterPro transfer is consistent with target-specific yeast biochemistry.
GO:0005788 endoplasmic reticulum lumen	IEA GO_REF:0000120	ACCEPT	Summary: Combined UniProt IEA annotation to ER lumen from ARBA and UniProt SubCell sources. Reason: ER lumen is Kar2p's primary localization, supported by the ER signal sequence and C-terminal HDEL retrieval signal described in the original KAR2 characterization (PMID:2661018). This current GO_REF:0000120 row replaces the older UniProt SubCell GO_REF:0000044 row for the same localization. Supporting Evidence: PMID:2661018 endoplasmic reticulum retention signal (HDEL) at the carboxyl terminus
GO:0016887 ATP hydrolysis activity	ISS GO_REF:0000024	ACCEPT	Summary: ISS transfer of ATP hydrolysis activity from human BiP/HSPA5. Reason: Human HSPA5/BiP is the direct ER Hsp70 ortholog and a safe source for ATPase activity. The same activity is independently demonstrated for purified yeast Kar2p and is central to the Hsp70 chaperone mechanism (PMID:1325440). Supporting Evidence: PMID:1325440 It is active as a homodimer and exhibits ATPase activity
GO:0030163 protein catabolic process	IEA GO_REF:0000117	MODIFY	Summary: Broad ARBA IEA annotation to protein catabolic process. Kar2p contributes to ER-associated degradation, but this parent process is too broad for its ER quality-control role. Reason: The ARBA process row points to real Kar2p biology. Kar2p helps maintain misfolded ERAD substrates in a soluble, retrotranslocation-competent state and participates in the Yos9p/Kar2p/Hrd3p luminal surveillance complex (PMID:11381090, PMID:16873065). GO:0036503 ERAD quality control pathway is the specific live term already supported by IBA, NAS, and IMP rows. Proposed replacements: ERAD quality control pathway Supporting Evidence: PMID:11381090 these ERAD substrates are stabilized and aggregate in the ER at elevated temperatures when BiP PMID:16873065 recruits nonnative proteins to the core ERAD machinery
GO:0033554 cellular response to stress	IEA GO_REF:0000117	MODIFY	Summary: Broad ARBA IEA annotation to cellular response to stress. Kar2p has a direct role in the ER unfolded protein response rather than a generic stress-response role. Reason: Genetic analysis of kar2 mutants supports a direct role for Kar2p in Ire1 regulation during ER stress (PMID:12808051). The more specific GO:0030968 endoplasmic reticulum unfolded protein response term is already present on the live IBA row and better captures the stress pathway in which Kar2p acts. Proposed replacements: endoplasmic reticulum unfolded protein response Supporting Evidence: PMID:12808051 association of BiP/Kar2 with Ire1 represses the UPR pathway
GO:0034099 luminal surveillance complex	NAS PMID:16873065 A luminal surveillance complex that selects misfolded glycop...	ACCEPT	Summary: ComplexPortal NAS annotation for Kar2p membership in the Yos9p/Kar2p/Hrd3p luminal surveillance complex. Reason: Denic et al. directly established that Yos9p, Kar2p and Hrd3p form the luminal surveillance complex that identifies terminally misfolded glycoproteins for ERAD (PMID:16873065). This ComplexPortal row is the statement-level counterpart of the older SGD IDA row for the same complex. Supporting Evidence: PMID:16873065 Yos9p, together with Kar2p and Hrd3p, forms a luminal surveillance complex
GO:0070880 fungal-type cell wall beta-glucan biosynthetic process	IGI PMID:9430631 Cell wall 1,6-beta-glucan synthesis in Saccharomyces cerevis...	KEEP AS NON CORE	Summary: Second SGD IGI annotation for fungal-type cell wall beta-glucan biosynthesis, supported by genetic interaction between KAR2 and a second ER glucosidase locus. Reason: The cell-wall 1,6-beta-glucan phenotype is real, but it is a downstream consequence of ER glycoprotein folding/quality-control defects rather than a direct Kar2p role in glucan synthesis. This row should mirror the sibling IGI row from the same paper and remain non-core. Supporting Evidence: PMID:9430631 glucosidases function synergistically with BiP/Kar2p in this process

Gene Description

Existing Annotations Review

Core Functions

Primary chaperone function - KAR2/BiP is an essential Hsp70 that assists protein folding in the ER through ATP-dependent substrate binding and release cycles, regulated by J-domain co-chaperones (Sec63, Scj1, Jem1) and nucleotide exchange factors (Lhs1, Sil1).

Protein translocation function - KAR2/BiP acts as a molecular ratchet at the Sec61/Sec63 translocon, driving both co- and post-translational protein translocation across the ER membrane via ATP hydrolysis.

ERAD quality control function - as part of the Yos9/Kar2/Hrd3 luminal surveillance complex, KAR2/BiP maintains ERAD substrate solubility for retrotranslocation and selects misfolded glycoproteins for degradation.

UPR regulatory function - KAR2/BiP association with Ire1 represses UPR signaling; Kar2p-Ire1 dissociation during ER stress permits Ire1 activation within the unfolded protein response.

References

Deep Research

Falcon

SGD

SGD gene description for KAR2 (yeast)

📚 Additional Documentation

Notes

Bioreason Rl Predictions

Bioreason Rl Review

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