id: P16474
gene_symbol: KAR2
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: >-
  KAR2 encodes the essential ER-resident Hsp70 chaperone BiP in S. cerevisiae. It is the yeast
  homolog of mammalian GRP78/BiP. KAR2/BiP functions as an ATP-dependent protein folding chaperone
  in the ER lumen, is required for both co- and post-translational protein translocation across
  the ER membrane (acting as a molecular ratchet via the Sec61/Sec63 translocon), participates
  in ER-associated degradation (ERAD) by maintaining substrate solubility, and plays a key role
  in the unfolded protein response (UPR) by regulating the Ire1 kinase. It also participates
  in karyogamy during mating. KAR2 is essential for viability and is one of the most abundant
  ER proteins (337,000 molecules/cell). Its chaperone cycle is regulated by J-domain co-chaperones
  (Sec63, Scj1, Jem1) that stimulate ATP hydrolysis, and by nucleotide exchange factors (Lhs1, Sil1).
existing_annotations:
# ===== IBA annotations (phylogenetic) =====
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.

- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.

- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
      - reference_id: PMID:1325440
        supporting_text: >-
          It is active as a homodimer and exhibits ATPase activity with a specific activity
          of 2 pmol/min/micrograms of protein.

- term:
    id: GO:0031072
    label: heat shock protein binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
      - reference_id: PMID:14704430
        supporting_text: >-
          Lhs1p and Kar2p specifically interacted to couple, and coordinately regulate,
          their respective activities.

- term:
    id: GO:0044183
    label: protein folding chaperone
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
      - reference_id: PMID:1325440
        supporting_text: >-
          Purification and characterization of BiP/Kar2 protein from Saccharomyces cerevisiae.

- term:
    id: GO:0036503
    label: ERAD pathway
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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).
    action: ACCEPT
    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).
    supported_by:
      - reference_id: PMID:11381090
        supporting_text: >-
          these ERAD substrates are stabilized and aggregate in the ER at elevated
          temperatures when BiP, the lumenal Hsp70 molecular chaperone, is mutated
      - reference_id: PMID:16873065
        supporting_text: >-
          Yos9p, together with Kar2p and Hrd3p, forms a luminal surveillance complex
          that both recruits nonnative proteins to the core ERAD machinery

- term:
    id: GO:0016020
    label: membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for membrane localization. KAR2/BiP is an ER lumen protein that
      associates with the ER membrane translocon complex (Sec61/Sec63) during protein
      translocation (PMID:10367885). The annotation is quite general; more specific
      CC terms (ER lumen, ER membrane) are already captured.
    action: ACCEPT
    reason: >-
      KAR2 does associate with the ER membrane, particularly during translocation
      where it interacts with the Sec61/Sec63 translocon at the membrane
      (PMID:10367885). While general, this IBA annotation is not wrong.

- term:
    id: GO:0042026
    label: protein refolding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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).

- term:
    id: GO:0034663
    label: endoplasmic reticulum chaperone complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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).
    action: ACCEPT
    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).

- term:
    id: GO:0005788
    label: endoplasmic reticulum lumen
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    reason: >-
      ER lumen is the primary localization of KAR2/BiP, confirmed experimentally
      (PMID:2661018). The HDEL motif at the C-terminus ensures ER retention.
    supported_by:
      - reference_id: PMID:2661018
        supporting_text: >-
          KAR2, a karyogamy gene, is the yeast homolog of the mammalian BiP/GRP78 gene.

- term:
    id: GO:0030968
    label: endoplasmic reticulum unfolded protein response
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for ER UPR involvement. KAR2/BiP plays a central role in UPR
      signaling by regulating the Ire1 kinase/ribonuclease. Association of BiP with
      Ire1 represses the UPR pathway; under ER stress, BiP dissociates from Ire1
      (titrated away by unfolded proteins), activating UPR signaling (PMID:12808051).
    action: ACCEPT
    reason: >-
      KAR2/BiP is a key regulator of the UPR pathway. Genetic evidence demonstrates
      that BiP association with Ire1 represses UPR, and dissociation activates it
      (PMID:12808051). KAR2 is also itself transcriptionally induced by the UPR.
    supported_by:
      - reference_id: PMID:12808051
        supporting_text: >-
          association of BiP/Kar2 with Ire1 represses the UPR pathway while under
          conditions of ER stress, BiP/Kar2 dissociation leads to activation

# ===== IEA annotations (electronic) =====
- term:
    id: GO:0000166
    label: nucleotide binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA annotation for nucleotide binding based on UniProt keyword mapping.
      KAR2/BiP has a well-characterized nucleotide binding domain (NBD) that
      binds ATP and ADP. This is a broad but correct annotation, subsumed by
      the more specific ATP binding annotation.
    action: ACCEPT
    reason: >-
      Nucleotide binding is a fundamental property of KAR2/BiP confirmed by
      biochemical studies (PMID:1325440). The IEA is broader than the more
      specific ATP binding annotation but is not incorrect.

- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for ATP binding based on InterPro and UniProt keyword mapping.
      KAR2/BiP has a conserved N-terminal nucleotide binding domain with multiple
      ATP binding residues (UniProt FT BINDING entries). ATP binding is essential
      for its chaperone cycle.
    action: ACCEPT
    reason: >-
      ATP binding is directly demonstrated for KAR2/BiP (PMID:1325440). The IEA
      annotation is consistent with experimental evidence.

- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA annotation for cytoplasm from ARBA machine learning. KAR2 is primarily
      an ER lumen protein. Duplicate of the IBA cytoplasm annotation.
    action: KEEP_AS_NON_CORE
    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.

- term:
    id: GO:0005788
    label: endoplasmic reticulum lumen
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA annotation for ER lumen based on UniProt subcellular location mapping.
      Consistent with direct experimental evidence (PMID:2661018).
    action: ACCEPT
    reason: >-
      ER lumen localization is well-established for KAR2/BiP. The IEA duplicates
      the IBA and experimental evidence but is correct.

- term:
    id: GO:0006616
    label: SRP-dependent cotranslational protein targeting to membrane, translocation
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    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.
    action: ACCEPT
    reason: >-
      KAR2 is experimentally shown to be required for SRP-dependent cotranslational
      translocation (PMID:7568189). The IEA is correct.
    supported_by:
      - reference_id: PMID:7568189
        supporting_text: >-
          Sec63p and Kar2p are necessary for both co- and posttranslational translocation
          in yeast.

- term:
    id: GO:0016787
    label: hydrolase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA annotation for hydrolase activity based on UniProt keyword mapping. KAR2/BiP
      has ATPase (hydrolase) activity. This is a very general annotation subsumed by
      the more specific ATP hydrolysis activity annotation.
    action: ACCEPT
    reason: >-
      Hydrolase activity is a parent term of ATP hydrolysis activity, which is directly
      demonstrated for KAR2 (PMID:1325440). The IEA is correct but very general.

- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for ATP hydrolysis activity. Consistent with direct experimental
      evidence (PMID:1325440) and the IBA and IDA annotations for the same term.
    action: ACCEPT
    reason: >-
      ATP hydrolysis is directly demonstrated for KAR2/BiP (PMID:1325440). The IEA
      duplicates the IBA and IDA annotations but is correct.

- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA annotation for unfolded protein binding from ARBA. GO:0051082 is proposed
      for obsoletion. 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).
    action: MODIFY
    reason: >-
      GO:0051082 is proposed for obsoletion. 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_replacement_terms:
      - id: GO:0140662
        label: ATP-dependent protein folding chaperone
      - id: GO:0044183
        label: protein folding chaperone

# ===== IPI annotations (physical interaction) =====
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16429126
  review:
    summary: >-
      IPI annotation for protein binding from high-throughput proteome survey.
      Protein binding is uninformative for a chaperone that binds many client proteins.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative for a molecular chaperone that by definition
      binds diverse protein substrates. More specific interaction annotations or
      chaperone function annotations are preferred.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16554755
  review:
    summary: >-
      IPI annotation for protein binding from global protein complex survey.
      Same issue as above: uninformative for a chaperone.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative for a molecular chaperone. The specific
      interactions (with SCJ1, PSA1, SOD1, etc.) are better captured by the
      chaperone function annotations.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16873065
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The interaction with YOS9 in the luminal surveillance complex (PMID:16873065)
      is better captured by GO:0034099 (luminal surveillance complex) than by the
      generic protein binding term.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19536198
  review:
    summary: >-
      IPI annotation for protein binding from the chaperone-protein interaction atlas.
      Again, generic protein binding is uninformative for a chaperone.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic protein binding is uninformative for an Hsp70 chaperone whose function
      is to bind diverse protein substrates.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:37968396
  review:
    summary: >-
      IPI annotation for protein binding from yeast protein interactome architecture study.
      Uninformative for a chaperone.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic protein binding is uninformative for an Hsp70 molecular chaperone.

# ===== NAS annotations =====
- term:
    id: GO:0002235
    label: detection of unfolded protein
  evidence_type: NAS
  original_reference_id: PMID:16873065
  review:
    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
      misfolded glycoproteins for ERAD (PMID:16873065). Additionally, Kar2p regulates
      Ire1 by sensing unfolded proteins (PMID:12808051).
    action: ACCEPT
    reason: >-
      KAR2/BiP detects unfolded proteins in the ER both for ERAD (via the luminal
      surveillance complex, PMID:16873065) and for UPR signaling (by titration away
      from Ire1, PMID:12808051). The NAS annotation is well-supported.
    supported_by:
      - reference_id: PMID:16873065
        supporting_text: >-
          Yos9p/Kar2p/Hrd3p acts as a gatekeeper, ensuring correct identification of
          terminally misfolded proteins
      - reference_id: PMID:12808051
        supporting_text: >-
          recognition of unfolded proteins is based on their competition with Ire1 for
          binding with BiP/Kar2

- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: NAS
  original_reference_id: PMID:16873065
  review:
    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).
    action: ACCEPT
    reason: >-
      While KAR2 is a soluble ER lumen protein, it functionally associates with ER
      membrane complexes during translocation and ERAD. The NAS is reasonable.

- term:
    id: GO:0036503
    label: ERAD pathway
  evidence_type: NAS
  original_reference_id: PMID:16873065
  review:
    summary: >-
      NAS annotation for ERAD pathway from the luminal surveillance complex study.
      Duplicate of the IBA and IMP ERAD annotations. Well-supported.
    action: ACCEPT
    reason: >-
      ERAD involvement is well-established (PMID:16873065, PMID:11381090). This NAS
      is consistent with the IBA and IMP annotations.

# ===== Experimental annotations (IMP, IDA, IGI) =====
- term:
    id: GO:0036503
    label: ERAD pathway
  evidence_type: IMP
  original_reference_id: PMID:11381090
  review:
    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).
    action: ACCEPT
    reason: >-
      Direct genetic evidence that kar2 mutations impair ERAD. This is a core
      function of KAR2 in ER quality control.
    supported_by:
      - reference_id: PMID:11381090
        supporting_text: >-
          these ERAD substrates are stabilized and aggregate in the ER at elevated
          temperatures when BiP, the lumenal Hsp70 molecular chaperone, is mutated

- term:
    id: GO:0015450
    label: protein-transporting ATPase activity
  evidence_type: IDA
  original_reference_id: PMID:10367885
  review:
    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).
    action: ACCEPT
    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).
    supported_by:
      - reference_id: PMID:10367885
        supporting_text: >-
          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.

- term:
    id: GO:0070972
    label: protein localization to endoplasmic reticulum
  evidence_type: IMP
  original_reference_id: PMID:1996357
  review:
    summary: >-
      IMP annotation for protein localization to ER. The original publication
      (PMID:1996357) is not available in the publications cache, but KAR2 is
      well-established as essential for protein import into the ER lumen via
      both co- and post-translational pathways (PMID:7568189, PMID:10367885).
    action: ACCEPT
    reason: >-
      KAR2 is required for protein import into the ER, demonstrated by multiple
      studies (PMID:7568189, PMID:10367885). This is a core function.

- term:
    id: GO:0070880
    label: fungal-type cell wall beta-glucan biosynthetic process
  evidence_type: IGI
  original_reference_id: PMID:9430631
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
      - reference_id: PMID:9430631
        supporting_text: >-
          the glucosidases function synergistically with BiP/Kar2p in this process

- term:
    id: GO:0000742
    label: karyogamy involved in conjugation with cellular fusion
  evidence_type: IMP
  original_reference_id: PMID:10069807
  review:
    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).
    action: KEEP_AS_NON_CORE
    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).
    supported_by:
      - reference_id: PMID:10069807
        supporting_text: >-
          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.

- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: PMID:2661018
  review:
    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).
    action: ACCEPT
    reason: >-
      Direct experimental demonstration of ER localization. This is the primary
      localization of KAR2/BiP (PMID:2661018).

- term:
    id: GO:0006616
    label: SRP-dependent cotranslational protein targeting to membrane, translocation
  evidence_type: IMP
  original_reference_id: PMID:7568189
  review:
    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).
    action: ACCEPT
    reason: >-
      Direct genetic evidence that KAR2 is required for cotranslational translocation,
      using kar2 mutant membranes defective in invertase import (PMID:7568189).
    supported_by:
      - reference_id: PMID:7568189
        supporting_text: >-
          Sec63p and Kar2p are necessary for both co- and posttranslational translocation
          in yeast.

- term:
    id: GO:0006986
    label: response to unfolded protein
  evidence_type: IMP
  original_reference_id: PMID:12808051
  review:
    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).
    action: ACCEPT
    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).
    supported_by:
      - reference_id: PMID:12808051
        supporting_text: >-
          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.

- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IDA
  original_reference_id: PMID:1325440
  review:
    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).
    action: ACCEPT
    reason: >-
      Direct biochemical demonstration of ATPase activity in purified KAR2/BiP
      protein. This is a core enzymatic activity.
    supported_by:
      - reference_id: PMID:1325440
        supporting_text: >-
          It is active as a homodimer and exhibits ATPase activity with a specific
          activity of 2 pmol/min/micrograms of protein.

- term:
    id: GO:0031204
    label: post-translational protein targeting to membrane, translocation
  evidence_type: IDA
  original_reference_id: PMID:10367885
  review:
    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).
    action: ACCEPT
    reason: >-
      Direct biochemical demonstration of BiP-dependent posttranslational
      translocation in a reconstituted system (PMID:10367885). Core function.
    supported_by:
      - reference_id: PMID:10367885
        supporting_text: >-
          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.

- term:
    id: GO:0031204
    label: post-translational protein targeting to membrane, translocation
  evidence_type: IMP
  original_reference_id: PMID:7568189
  review:
    summary: >-
      IMP annotation for post-translational translocation. Brodsky et al. (1995)
      showed that kar2 mutants are defective in posttranslational translocation
      (PMID:7568189).
    action: ACCEPT
    reason: >-
      Genetic evidence complementing the IDA evidence from PMID:10367885.
      Both co- and post-translational translocation require KAR2 (PMID:7568189).
    supported_by:
      - reference_id: PMID:7568189
        supporting_text: >-
          Sec63p and Kar2p are necessary for both co- and posttranslational translocation
          in yeast.

- term:
    id: GO:0034099
    label: luminal surveillance complex
  evidence_type: IDA
  original_reference_id: PMID:16873065
  review:
    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).
    action: ACCEPT
    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.
    supported_by:
      - reference_id: PMID:16873065
        supporting_text: >-
          Yos9p, together with Kar2p and Hrd3p, forms a luminal surveillance complex
          that both recruits nonnative proteins to the core ERAD machinery

- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IMP
  original_reference_id: PMID:12808051
  review:
    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 proposed for obsoletion; the binding activity here is part of
      KAR2's chaperone mechanism.
    action: MODIFY
    reason: >-
      GO:0051082 is proposed for obsoletion. 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_replacement_terms:
      - id: GO:0140662
        label: ATP-dependent protein folding chaperone
      - id: GO:0044183
        label: protein folding chaperone
    supported_by:
      - reference_id: PMID:12808051
        supporting_text: >-
          Ire1 associates with Kar2 as a chaperone substrate

- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:23704572
  review:
    summary: >-
      IDA annotation for unfolded protein binding. The publication (PMID:23704572)
      is not available in the cache but is listed as IDA evidence. GO:0051082 is
      proposed for obsoletion. KAR2 binding to unfolded proteins is part of its
      ATP-dependent chaperone mechanism, not a passive binding activity.
    action: MODIFY
    reason: >-
      GO:0051082 is proposed for obsoletion. 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_replacement_terms:
      - id: GO:0140662
        label: ATP-dependent protein folding chaperone
      - id: GO:0044183
        label: protein folding chaperone

# ===== NEW annotations =====
- term:
    id: GO:0140662
    label: ATP-dependent protein folding chaperone
  evidence_type: IDA
  original_reference_id: PMID:10367885
  review:
    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 molecular function. InterPro already annotates this via IEA (visible
      in UniProt record GO:0140662 IEA:InterPro), but experimental evidence supports
      upgrading this.
    action: NEW
    reason: >-
      GO:0140662 is the most accurate MF term for KAR2/BiP, which is an ATP-dependent
      Hsp70 chaperone. Multiple publications demonstrate the ATP-dependent chaperone
      cycle (PMID:1325440, PMID:10367885, PMID:14704430). This should be added as
      the primary replacement for GO:0051082 annotations.
    supported_by:
      - reference_id: PMID:10367885
        supporting_text: >-
          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.
      - reference_id: PMID:1325440
        supporting_text: >-
          It is active as a homodimer and exhibits ATPase activity with a specific
          activity of 2 pmol/min/micrograms of protein.

references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  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: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:10069807
  title: Genetic interactions between KAR7/SEC71, KAR8/JEM1, KAR5, and KAR2 during
    nuclear fusion in Saccharomyces cerevisiae.
  findings: []
- id: PMID:10367885
  title: BiP acts as a molecular ratchet during posttranslational transport of prepro-alpha
    factor across the ER membrane.
  findings: []
- id: PMID:11381090
  title: Molecular chaperones in the yeast endoplasmic reticulum maintain the solubility
    of proteins for retrotranslocation and degradation.
  findings: []
- id: PMID:12808051
  title: Genetic evidence for a role of BiP/Kar2 that regulates Ire1 in response to
    accumulation of unfolded proteins.
  findings: []
- id: PMID:1325440
  title: Purification and characterization of BiP/Kar2 protein from Saccharomyces
    cerevisiae.
  findings: []
- id: PMID:14704430
  title: Coordinated activation of Hsp70 chaperones.
  findings: []
- id: PMID:16429126
  title: Proteome survey reveals modularity of the yeast cell machinery.
  findings: []
- id: PMID:16554755
  title: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
  findings: []
- id: PMID:16873065
  title: A luminal surveillance complex that selects misfolded glycoproteins for ER-associated
    degradation.
  findings: []
- id: PMID:19536198
  title: 'An atlas of chaperone-protein interactions in Saccharomyces cerevisiae:
    implications to protein folding pathways in the cell.'
  findings: []
- id: PMID:1996357
  title: Binding protein BiP is required for translocation of secretory proteins into
    the endoplasmic reticulum in Saccharomyces cerevisiae.
  findings: []
- id: PMID:23704572
  title: Futile protein folding cycles in the ER are terminated by the unfolded protein
    O-mannosylation pathway.
  findings: []
- id: PMID:2661018
  title: KAR2, a karyogamy gene, is the yeast homolog of the mammalian BiP/GRP78 gene.
  findings: []
- id: PMID:37968396
  title: The social and structural architecture of the yeast protein interactome.
  findings: []
- id: PMID:7568189
  title: BiP and Sec63p are required for both co- and posttranslational protein translocation
    into the yeast endoplasmic reticulum.
  findings: []
- id: PMID:9430631
  title: Cell wall 1,6-beta-glucan synthesis in Saccharomyces cerevisiae depends on
    ER glucosidases I and II, and the molecular chaperone BiP/Kar2p.
  findings: []

core_functions:
- molecular_function:
    id: GO:0140662
    label: ATP-dependent protein folding chaperone
  directly_involved_in:
  - id: GO:0042026
    label: protein refolding
  - id: GO:0006986
    label: response to unfolded protein
  locations:
  - id: GO:0005788
    label: endoplasmic reticulum lumen
  in_complex:
    id: GO:0034663
    label: endoplasmic reticulum chaperone complex
  description: >-
    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).
- molecular_function:
    id: GO:0015450
    label: protein-transporting ATPase activity
  directly_involved_in:
  - id: GO:0006616
    label: SRP-dependent cotranslational protein targeting to membrane, translocation
  - id: GO:0031204
    label: post-translational protein targeting to membrane, translocation
  locations:
  - id: GO:0005788
    label: endoplasmic reticulum lumen
  description: >-
    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.
- molecular_function:
    id: GO:0044183
    label: protein folding chaperone
  directly_involved_in:
  - id: GO:0036503
    label: ERAD pathway
  locations:
  - id: GO:0005788
    label: endoplasmic reticulum lumen
  in_complex:
    id: GO:0034099
    label: luminal surveillance complex
  description: >-
    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.
- molecular_function:
    id: GO:0044183
    label: protein folding chaperone
  directly_involved_in:
  - id: GO:0030968
    label: endoplasmic reticulum unfolded protein response
  locations:
  - id: GO:0005788
    label: endoplasmic reticulum lumen
  description: >-
    UPR regulatory function - KAR2/BiP association with Ire1 represses UPR signaling;
    under ER stress, unfolded proteins compete for BiP binding, releasing Ire1 to
    activate UPR.