TNFAIP3

id: P21580
gene_symbol: TNFAIP3
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  TNFAIP3 (also known as A20) encodes a 790-amino acid ubiquitin-editing enzyme that serves
  as the central negative feedback regulator of NF-kB signaling. The protein has a dual enzymatic
  architecture: an N-terminal OTU (ovarian tumor) domain (aa 92-263) with cysteine-type deubiquitinase
  activity (catalytic residues Cys103, His256), and seven C-terminal A20-type zinc finger domains
  (ZnF1-7). The OTU domain removes K63-linked polyubiquitin chains from key signaling adaptors
  (RIPK1, TRAF6, NEMO/IKBKG, MALT1), while ZnF4 mediates E3 ubiquitin ligase activity that adds
  K48-linked chains to target substrates (notably RIPK1) for proteasomal degradation. ZnF7 binds
  linear (M1-linked) polyubiquitin chains non-catalytically, contributing to IKK complex inhibition.
  A20 is an NF-kB-inducible gene, forming a negative feedback loop that terminates inflammatory
  signaling downstream of TNFR1, TLR2/3/4/5, NOD1/2, and CD40 receptors. It also suppresses
  NLRP3 inflammasome activation and modulates RIPK1-dependent cell death checkpoints.
  A20 functions in the cytoplasm at receptor-proximal signaling complexes, with some localization
  to the nucleus and lysosomes. It forms a complex with TAX1BP1, RNF11, and ITCH for efficient
  NF-kB termination. Heterozygous loss-of-function variants cause A20 haploinsufficiency (HA20),
  an early-onset autoinflammatory disease with Behcet-like features. Common variants at the
  TNFAIP3 locus are associated with susceptibility to SLE, RA, and IBD.

existing_annotations:
# =====================
# IBA ANNOTATIONS (8)
# =====================
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for nuclear localization. A20 is predominantly cytoplasmic but has been
      detected in the nucleus by immunofluorescence (PMID:11463333). The IDA annotation from
      PMID:11463333 also supports this. However, the nucleus is not the primary site of A20 function.
    action: ACCEPT
    reason: >-
      Nuclear localization is supported by direct experimental evidence (IDA from PMID:11463333)
      and is phylogenetically conserved per IBA. While cytoplasm is the primary functional site,
      nuclear localization is reproducibly observed.
    supported_by:
      - reference_id: PMID:11463333
        supporting_text: "The zinc finger molecule A20 is an important negative regulator of NF-kappa B"

- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for cytoplasmic localization. A20 functions at cytoplasmic receptor-proximal
      signaling complexes (TNFR, TLR signalosomes) where it edits ubiquitin chains on RIPK1,
      TRAF6, and NEMO. Well-supported by UniProt subcellular location and multiple experimental studies.
    action: ACCEPT
    reason: >-
      Core site of A20 function. Cytoplasmic localization is the primary location where A20
      carries out deubiquitination and ubiquitin ligase activities at receptor-proximal complexes.
      Strongly supported by multiple lines of evidence.
    supported_by:
      - reference_id: PMID:15258597
        supporting_text: "De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling"

- term:
    id: GO:0004842
    label: ubiquitin-protein transferase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for E3 ubiquitin ligase activity. A20 ZnF4 domain mediates ubiquitin-protein
      transferase activity, catalyzing addition of K48-linked polyubiquitin chains to substrates
      including RIPK1, targeting them for proteasomal degradation (PMID:15258597).
    action: ACCEPT
    reason: >-
      Core enzymatic function. The E3 ubiquitin ligase activity via ZnF4 is one of the two
      defining enzymatic activities of A20, experimentally demonstrated by Wertz et al. (2004).
      IBA is consistent with phylogenetic conservation and IDA evidence.
    supported_by:
      - reference_id: PMID:15258597
        supporting_text: "De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling"

- term:
    id: GO:0043124
    label: negative regulation of canonical NF-kappaB signal transduction
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for negative regulation of NF-kB. This is the single most important biological
      process annotation for A20. A20 terminates NF-kB signaling by deubiquitinating K63-Ub chains
      on RIPK1/TRAF6/NEMO and adding K48-Ub chains to target them for degradation. Multiple IDA
      evidence lines confirm this (PMID:15258597, PMID:11463333, PMID:18223652, PMID:21127049).
    action: ACCEPT
    reason: >-
      Core function. A20 is the prototypical negative feedback regulator of NF-kB signaling.
      This is the most extensively validated function of A20, supported by multiple independent
      experimental approaches and confirmed by phylogenetic analysis.
    supported_by:
      - reference_id: PMID:15258597
        supporting_text: "De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling"
      - reference_id: PMID:8692885
        supporting_text: "The tumor necrosis factor-inducible zinc finger protein A20 interacts with TRAF1/TRAF2 and inhibits NF-kappaB activation"

- term:
    id: GO:0045824
    label: negative regulation of innate immune response
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation. A20 negatively regulates innate immune signaling downstream of TLRs and
      NOD1/2 receptors by editing ubiquitin chains on pathway components. Supported by ISS from
      mouse ortholog (Q60769) and extensive mouse knockout studies showing lethal inflammation.
    action: ACCEPT
    reason: >-
      Core function. A20 restrains innate immune activation through its deubiquitinase and
      E3 ligase activities targeting TLR and NLR pathway components. Mouse A20 knockouts
      develop severe multi-organ inflammation and die prematurely.
    supported_by:
      - reference_id: PMID:15142865
        supporting_text: "A20 may function as a negative regulator of TLR-mediated inflammatory responses in the airway"

- term:
    id: GO:0050728
    label: negative regulation of inflammatory response
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation. A20 is a master negative regulator of inflammation. Loss of A20 leads to
      unchecked NF-kB activation, excessive cytokine production, and multi-organ inflammation.
      HA20 patients exhibit chronic inflammation.
    action: ACCEPT
    reason: >-
      Core function. Negative regulation of inflammation is the primary biological consequence
      of A20 enzymatic activity. Supported by mouse knockout phenotypes and human HA20 disease.
    supported_by:
      - reference_id: PMID:15258597
        supporting_text: "De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling"

- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for cysteine-type DUB activity. The OTU domain of A20 is a cysteine protease
      with catalytic triad Cys103/His256 that cleaves ubiquitin chains. Demonstrated by multiple
      crystal structures and biochemical assays (PMID:14748687, PMID:17961127, PMID:18164316,
      PMID:23827681). A20 can cleave K11, K48, and K63 chains in vitro.
    action: ACCEPT
    reason: >-
      Core enzymatic function. The OTU deubiquitinase activity is one of the two defining
      enzymatic activities of A20, with extensive structural and biochemical characterization.
    supported_by:
      - reference_id: PMID:14748687
        supporting_text: "Zinc-finger protein A20, a regulator of inflammation and cell survival, has de-ubiquitinating activity"
      - reference_id: PMID:23827681
        supporting_text: "OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis"

- term:
    id: GO:0071947
    label: protein deubiquitination involved in ubiquitin-dependent protein catabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation. A20 deubiquitinates RIPK1 (removing K63 chains) as part of the ubiquitin
      editing process that subsequently leads to K48-linked ubiquitination and proteasomal
      degradation of RIPK1. This couples deubiquitination to protein catabolism.
    action: ACCEPT
    reason: >-
      Accurately captures the coupling of A20 deubiquitinase activity to proteasomal
      degradation of signaling adaptors. The sequential removal of K63 chains followed by
      addition of K48 chains on RIPK1 is the canonical A20 ubiquitin-editing mechanism.
    supported_by:
      - reference_id: PMID:15258597
        supporting_text: "De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling"

# =====================
# IEA ANNOTATIONS - UniProt/ARBA (23)
# =====================
- term:
    id: GO:0002376
    label: immune system process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA annotation from ARBA. Very broad term. A20 is indeed involved in immune system
      processes but more specific terms are already annotated.
    action: ACCEPT
    reason: >-
      While very broad, this IEA is not wrong. More specific immune-related annotations
      (negative regulation of innate immune response, negative regulation of NF-kB) are
      also present and represent the core function.

- term:
    id: GO:0003677
    label: DNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA based on InterPro A20-type zinc finger domain mapping to DNA binding. This is
      misleading. A20 zinc fingers bind ubiquitin, not DNA. The original A20 name "putative
      DNA-binding protein" was based on the zinc finger motif, but no DNA binding activity
      has been demonstrated. A20 functions entirely through ubiquitin editing in the cytoplasm.
    action: REMOVE
    reason: >-
      Incorrect annotation. A20 zinc fingers are A20-type zinc fingers specialized for
      ubiquitin binding, not DNA binding. No experimental evidence supports DNA binding
      activity for A20. The InterPro mapping is erroneous for this protein.

- term:
    id: GO:0003824
    label: catalytic activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA for generic catalytic activity. A20 has well-characterized catalytic activities
      (deubiquitinase and ubiquitin ligase) but this term is too broad to be informative.
    action: ACCEPT
    reason: >-
      Correct but very broad. More specific catalytic activity terms (cysteine-type deubiquitinase
      activity, ubiquitin-protein transferase activity) are already present.

- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000003
  review:
    summary: >-
      IEA from EC number mapping (EC:3.4.19.12). Consistent with experimental evidence
      and IBA/IDA annotations for the same term.
    action: ACCEPT
    reason: >-
      Correct. A20 OTU domain has well-characterized cysteine-type deubiquitinase activity.
      Redundant with IBA and IDA annotations but correctly derived from EC mapping.

- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA from UniProt subcellular location. Consistent with IBA and IDA annotations.
    action: ACCEPT
    reason: >-
      Correct. Nuclear localization supported by UniProt subcellular location and IDA evidence.

- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA for cytoplasm. Consistent with IBA and multiple experimental evidence lines.
    action: ACCEPT
    reason: >-
      Correct. Cytoplasm is the primary functional location of A20.

- term:
    id: GO:0005764
    label: lysosome
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA from UniProt subcellular location. A20 has been shown to target TRAF2 to lysosomes
      for degradation (PMID:18952128), and the C-terminal region (aa 697-790) is required
      for lysosomal localization per UniProt.
    action: ACCEPT
    reason: >-
      Correct. Lysosomal localization is documented in UniProt based on PMID:18952128 showing
      A20 targets TRAF2 to lysosomes for degradation.
    supported_by:
      - reference_id: PMID:18952128
        supporting_text: "The zinc finger protein A20 targets TRAF2 to the lysosomes for degradation"

- term:
    id: GO:0006508
    label: proteolysis
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA from UniProt keyword mapping (KW-0645 Protease). A20 is a thiol protease
      (deubiquitinase) that cleaves isopeptide bonds in polyubiquitin chains.
    action: ACCEPT
    reason: >-
      Correct but very broad. A20 performs proteolysis in the form of ubiquitin chain cleavage.
      More specific terms (protein deubiquitination) are also annotated.

- term:
    id: GO:0006915
    label: apoptotic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA from UniProt keyword (KW-0053 Apoptosis). A20 inhibits programmed cell death,
      particularly extrinsic apoptosis via death domain receptors. More specific terms
      for the anti-apoptotic role are annotated.
    action: ACCEPT
    reason: >-
      Broadly correct. A20 is described in UniProt as an "Inhibitor of programmed cell death."
      More specific annotations (negative regulation of extrinsic apoptotic signaling pathway
      via death domain receptors) capture this more precisely.

- term:
    id: GO:0006954
    label: inflammatory response
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA from UniProt keyword (KW-0395 Inflammatory response). A20 is a key negative
      regulator of inflammation. More specific terms are annotated.
    action: ACCEPT
    reason: >-
      Correct but broad. More specific negative regulation of inflammatory response terms
      are already present.

- term:
    id: GO:0008233
    label: peptidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA from UniProt keyword. A20 OTU domain is indeed a peptidase (cleaves isopeptide bonds).
      More specific cysteine-type deubiquitinase activity is annotated.
    action: ACCEPT
    reason: >-
      Correct but broad. Parent term of more specific annotations already present.

- term:
    id: GO:0008234
    label: cysteine-type peptidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA from UniProt keyword (KW-0788 Thiol protease). A20 uses Cys103 as the catalytic
      nucleophile. More specific cysteine-type deubiquitinase activity is annotated.
    action: ACCEPT
    reason: >-
      Correct. A20 OTU domain is a cysteine-type peptidase. Parent of cysteine-type
      deubiquitinase activity which is also annotated.

- term:
    id: GO:0008270
    label: zinc ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA from InterPro/UniProt keyword. A20 has seven A20-type zinc finger domains, each
      coordinating zinc ions. This is structurally confirmed.
    action: ACCEPT
    reason: >-
      Correct. A20 has seven zinc finger domains that bind zinc ions, confirmed by crystal
      structures and NMR.

- term:
    id: GO:0016740
    label: transferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA from UniProt keyword (KW-0808 Transferase). A20 has ubiquitin-protein transferase
      (E3 ligase) activity via its ZnF4 domain.
    action: ACCEPT
    reason: >-
      Correct but very broad. More specific ubiquitin-protein transferase activity is annotated.

- term:
    id: GO:0016787
    label: hydrolase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA from UniProt keyword (KW-0378 Hydrolase). The OTU deubiquitinase domain hydrolyzes
      isopeptide bonds.
    action: ACCEPT
    reason: >-
      Correct but very broad. More specific terms (cysteine-type deubiquitinase activity)
      are annotated.

- term:
    id: GO:0019899
    label: enzyme binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA from ARBA. A20 interacts with multiple enzymes including TRAF6, TRAF2, MALT1 paracaspase,
      and E2 enzymes UBE2N and UBE2D3. However, 'enzyme binding' is a vague term.
    action: ACCEPT
    reason: >-
      Broadly correct but uninformative. A20 does bind multiple enzymes. More specific binding
      annotations (protease binding, ubiquitin binding, kinase binding) are also present.

- term:
    id: GO:0039532
    label: negative regulation of cytoplasmic pattern recognition receptor signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA from ARBA. A20 negatively regulates NOD1 and NOD2 signaling pathways (cytoplasmic
      PRRs) by deubiquitinating RIPK2. This is supported by Ensembl orthology (mouse) and
      Reactome pathway annotation.
    action: ACCEPT
    reason: >-
      Correct. A20 negatively regulates cytoplasmic PRR signaling, specifically NOD1/NOD2.
      Supported by more specific annotations for NOD1 and NOD2 pathway regulation.

- term:
    id: GO:0042127
    label: regulation of cell population proliferation
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA from ARBA. A20 affects cell proliferation indirectly through NF-kB regulation.
      Specific effects on smooth muscle cell proliferation and hepatocyte proliferation
      are annotated with better evidence.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Overly broad annotation. While A20 affects proliferation indirectly through NF-kB,
      this is not a direct molecular function. More specific proliferation annotations
      (smooth muscle cell, hepatocyte) are present.

- term:
    id: GO:0045732
    label: positive regulation of protein catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA from ARBA. A20 promotes proteasomal degradation of signaling substrates (RIPK1,
      TRAF2, UBE2N, UBE2D3) by adding K48-linked ubiquitin chains. Supported by IDA from
      PMID:21127049.
    action: ACCEPT
    reason: >-
      Correct. A20 ubiquitin-editing promotes K48-linked ubiquitination and subsequent
      proteasomal degradation of substrates. Consistent with IDA evidence.

- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA from UniProt keyword (KW-0479 Metal-binding). A20 binds zinc ions through seven
      zinc finger domains.
    action: ACCEPT
    reason: >-
      Correct but very broad. More specific zinc ion binding is also annotated.

- term:
    id: GO:0070536
    label: protein K63-linked deubiquitination
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA from ARBA. K63-linked deubiquitination is a core function of A20 OTU domain,
      targeting K63-polyUb chains on RIPK1, TRAF6, NEMO, and MALT1. Supported by IDA
      from PMID:15258597.
    action: ACCEPT
    reason: >-
      Correct and important. K63-linked deubiquitination is the primary in vivo
      deubiquitinase specificity of A20. Consistent with IDA evidence.

- term:
    id: GO:1901701
    label: cellular response to oxygen-containing compound
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA from ARBA. A20 responds to hydrogen peroxide (supported by ISS annotation).
      This is a very broad parent term of more specific annotations.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Overly broad. More specific cellular response to hydrogen peroxide is annotated.
      This broad parent does not add useful information.

# =====================
# IPI PROTEIN BINDING ANNOTATIONS (40)
# =====================
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11389905
  review:
    summary: >-
      IPI protein binding from high-throughput protein interaction study.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is too vague. A20 has well-characterized specific interactions
      (with TRAF2, TAX1BP1, TNIP1, IKBKG, RIPK1) that are more informative. These
      should be captured by more specific MF terms.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15169888
  review:
    summary: >-
      IPI protein binding.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative for A20. More specific interaction-based annotations
      are preferred.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15231748
  review:
    summary: >-
      IPI protein binding from proteomics mapping study.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative. More specific binding terms are available.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19060883
  review:
    summary: >-
      IPI protein binding, interactor is CASP8 (Q14790). A20 interaction with CASP8 may relate
      to its role in modulating death receptor signaling and apoptosis.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative. The specific interaction with CASP8 is potentially
      relevant to A20 anti-apoptotic function but should be annotated more specifically.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19131965
  review:
    summary: >-
      IPI protein binding with RNF11 (Q9Y3C5). A20 requires RNF11 to form the ubiquitin-editing
      complex with TAX1BP1 and ITCH for NF-kB downregulation.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative. The A20-RNF11 interaction is functionally significant
      but should be captured by more specific terms.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20936779
  review:
    summary: >-
      IPI protein binding with YWHAG (P61981), from MAP kinase interactome study.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21988832
  review:
    summary: >-
      IPI protein binding from liver protein interaction study. Multiple interactors (YWHAE,
      TNIP1, IKBKG).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative. Multiple protein binding annotations from this
      study do not add functional insight beyond what more specific terms provide.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:23032186
  review:
    summary: >-
      IPI protein binding with IKBKG (Q9Y6K9). A20 ZnF7 binds linear polyubiquitin on NEMO
      to inhibit IKK complex activation.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative. The A20-NEMO interaction is core to A20 function
      but should use more specific terms.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25416956
  review:
    summary: >-
      IPI protein binding from proteome-scale interactome study. Multiple interactors.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative. High-throughput interactome data.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:30561431
  review:
    summary: >-
      IPI protein binding. Multiple interactors including TRAF2, TAX1BP1, TNIP1, TNIP2, IKBKG.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative. These are functionally important interactions
      but the generic term adds no value.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:31015422
  review:
    summary: >-
      IPI protein binding with ATG16L1 isoform 1 (Q676U5-1).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:31515488
  review:
    summary: >-
      IPI protein binding from study of genetic variant effects on protein interactions.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  review:
    summary: >-
      IPI protein binding from reference human binary interactome. Multiple interactors.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative. High-throughput interactome study.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33961781
  review:
    summary: >-
      IPI protein binding with TAX1BP1 (Q86VP1) from dual proteome study.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:36931259
  review:
    summary: >-
      IPI protein binding with 14-3-3 proteins (YWHAG, YWHAE). A20 interacts with 14-3-3
      proteins, though A20 inhibits NF-kB independently of 14-3-3 binding (PMID:9299557).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:9299557
  review:
    summary: >-
      IPI protein binding with YWHAH (14-3-3 eta). Early study showing A20 binds 14-3-3
      proteins but NF-kB inhibition is independent of this interaction.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative. The 14-3-3 interaction was shown to be dispensable
      for A20 NF-kB inhibitory function.
    supported_by:
      - reference_id: PMID:9299557
        supporting_text: "A20 inhibits NF-kappaB activation independently of binding to 14-3-3 proteins"

# IPI identical protein binding
- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:11389905
  review:
    summary: >-
      IPI for A20 homodimerization. UniProt confirms A20 is a homodimer (IntAct: 9 experiments).
    action: ACCEPT
    reason: >-
      A20 homodimerization is well-supported. UniProt SUBUNIT states "Homodimer" and IntAct
      records 9 experiments confirming self-interaction. More informative than generic
      protein binding.

- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:25416956
  review:
    summary: >-
      Additional evidence for A20 homodimerization from proteome-scale interactome.
    action: ACCEPT
    reason: >-
      Corroborates A20 self-interaction. Redundant with other identical protein binding
      annotations but supported by independent study.

- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:25502805
  review:
    summary: >-
      Additional evidence for A20 homodimerization from massively parallel cloning study.
    action: ACCEPT
    reason: >-
      Corroborates A20 self-interaction with independent approach.

- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:30561431
  review:
    summary: >-
      Additional evidence for A20 homodimerization.
    action: ACCEPT
    reason: >-
      Consistent with established A20 homodimer formation.

- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:31515488
  review:
    summary: >-
      Additional evidence for A20 homodimerization from genetic variant study.
    action: ACCEPT
    reason: >-
      Consistent with A20 self-interaction.

- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  review:
    summary: >-
      Additional evidence for A20 homodimerization from reference interactome.
    action: ACCEPT
    reason: >-
      Consistent with A20 self-interaction.

# =====================
# IEA ENSEMBL ORTHOLOG ANNOTATIONS (20)
# =====================
- term:
    id: GO:0001922
    label: B-1 B cell homeostasis
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara orthology to mouse A20 (Q60769). Mouse A20 knockout shows
      B-1 B cell abnormalities. Also annotated with ISS evidence.
    action: KEEP_AS_NON_CORE
    reason: >-
      This is a downstream effect of A20 function in immune regulation rather than a core
      molecular function. Supported by mouse data but reflects pleiotropic immune consequences.

- term:
    id: GO:0002237
    label: response to molecule of bacterial origin
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA from combined automated methods. A20 responds to bacterial molecules through
      TLR signaling. Also annotated with IDA from PMID:19912257.
    action: ACCEPT
    reason: >-
      Correct. A20 is induced by and functions in response to bacterial products through
      TLR pathways. Consistent with IDA evidence.

- term:
    id: GO:0002634
    label: regulation of germinal center formation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. Mouse A20 deficiency affects germinal center formation.
      Also annotated with ISS evidence.
    action: KEEP_AS_NON_CORE
    reason: >-
      Downstream effect of A20 immune regulation. Not a core molecular function but a
      pleiotropic consequence in the adaptive immune system.

- term:
    id: GO:0002677
    label: negative regulation of chronic inflammatory response
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. A20 prevents chronic inflammation, as demonstrated by
      mouse knockouts developing severe chronic inflammation and HA20 patients showing
      chronic autoinflammatory disease.
    action: ACCEPT
    reason: >-
      Correct. A20 prevents chronic inflammation through its NF-kB regulatory activity.
      Central to A20 function.

- term:
    id: GO:0016579
    label: protein deubiquitination
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. Protein deubiquitination is a core enzymatic activity.
      Also annotated with TAS from PMID:20392859 and Reactome.
    action: ACCEPT
    reason: >-
      Correct. Core enzymatic activity of A20 OTU domain. Consistent with multiple other
      evidence lines.

- term:
    id: GO:0019900
    label: kinase binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. A20 interacts with IKK complex (IKKbeta/IKBKG) and RIPK1.
      IKK phosphorylates A20. RIPK1 is a serine/threonine kinase.
    action: ACCEPT
    reason: >-
      Correct. A20 binds RIPK1 (a kinase) and interacts with IKK complex. More specific
      than generic protein binding.

- term:
    id: GO:0032495
    label: response to muramyl dipeptide
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. A20 negatively regulates NOD2 signaling, and muramyl dipeptide
      (MDP) is the NOD2 ligand. A20 likely deubiquitinates RIPK2 in the NOD2 pathway.
    action: KEEP_AS_NON_CORE
    reason: >-
      Downstream of NOD2 signaling pathway regulation. A20 responds indirectly to MDP
      through its role in NOD2 pathway negative regulation.

- term:
    id: GO:0032691
    label: negative regulation of interleukin-1 beta production
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA from combined automated methods. A20 inhibits IL-1beta production by suppressing
      NF-kB and NLRP3 inflammasome activation. Also annotated with IMP from PMID:28094437.
    action: KEEP_AS_NON_CORE
    reason: >-
      Downstream effect of NF-kB and inflammasome suppression. Not a direct molecular function
      but a well-documented pleiotropic consequence. Supported by IMP evidence.

- term:
    id: GO:0032715
    label: negative regulation of interleukin-6 production
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. A20 inhibits IL-6 production through NF-kB suppression.
      Also annotated with ISS. HA20 patients show elevated IL-6.
    action: KEEP_AS_NON_CORE
    reason: >-
      Downstream effect of NF-kB regulation. IL-6 is an NF-kB target gene, so A20
      indirectly suppresses its production.

- term:
    id: GO:0032720
    label: negative regulation of tumor necrosis factor production
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. A20 suppresses TNF production via NF-kB inhibition.
      Also annotated with ISS.
    action: KEEP_AS_NON_CORE
    reason: >-
      Downstream effect. TNF is an NF-kB target gene. A20 indirectly reduces TNF
      production by terminating NF-kB signaling.

- term:
    id: GO:0034148
    label: negative regulation of toll-like receptor 5 signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. A20 likely negatively regulates TLR5 signaling similar to
      its regulation of TLR2, TLR3, and TLR4 pathways.
    action: ACCEPT
    reason: >-
      Consistent with A20 general role as negative regulator of TLR signaling. Supported
      by mouse ortholog data and analogous to experimentally confirmed TLR2/3/4 regulation.

- term:
    id: GO:0043124
    label: negative regulation of canonical NF-kappaB signal transduction
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA from combined automated methods. Redundant with IBA and multiple IDA annotations.
    action: ACCEPT
    reason: >-
      Correct. Core function of A20. Consistent with multiple higher-quality evidence codes.

- term:
    id: GO:0045824
    label: negative regulation of innate immune response
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. Redundant with IBA and ISS annotations.
    action: ACCEPT
    reason: >-
      Correct. Core function. Consistent with IBA and ISS evidence.

- term:
    id: GO:0050728
    label: negative regulation of inflammatory response
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. Redundant with IBA and ISS annotations.
    action: ACCEPT
    reason: >-
      Correct. Core function. Consistent with IBA and ISS evidence.

- term:
    id: GO:0050869
    label: negative regulation of B cell activation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. A20 negatively regulates B cell activation through NF-kB
      suppression. Mouse knockouts show B cell abnormalities.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic consequence of NF-kB regulation in B cells. Not core molecular function
      but documented in mouse.

- term:
    id: GO:0070301
    label: cellular response to hydrogen peroxide
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. A20 expression or function may be modulated by hydrogen
      peroxide. Also annotated with ISS.
    action: KEEP_AS_NON_CORE
    reason: >-
      Not a core function. Response to oxidative stress is a secondary aspect of A20 biology.

- term:
    id: GO:0070429
    label: negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. A20 negatively regulates NOD1 signaling, likely by
      deubiquitinating RIPK2 in the NOD1 pathway.
    action: ACCEPT
    reason: >-
      Consistent with A20 role in negative regulation of PRR signaling. NOD1 pathway
      regulation is part of A20 core innate immune regulatory function.

- term:
    id: GO:0070433
    label: negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. A20 negatively regulates NOD2 signaling. Reactome annotates
      A20 in the NOD1/2 signaling pathway. A20 deubiquitinates RIPK2 downstream of NOD2.
    action: ACCEPT
    reason: >-
      Consistent with A20 core function in innate immune signaling regulation. Supported
      by Reactome pathway annotation.

- term:
    id: GO:2000347
    label: positive regulation of hepatocyte proliferation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara. A20 protects hepatocytes from TNF-induced death, which
      may indirectly promote hepatocyte survival/proliferation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic downstream effect. Hepatocyte proliferation regulation is an indirect
      consequence of A20 anti-apoptotic/anti-inflammatory function.

- term:
    id: GO:2001237
    label: negative regulation of extrinsic apoptotic signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA from combined automated methods. A20 inhibits extrinsic apoptosis by editing
      ubiquitin chains on RIPK1, preventing death complex formation. More specific
      annotation via death domain receptors is also present (IDA).
    action: ACCEPT
    reason: >-
      Correct. A20 inhibits extrinsic apoptotic signaling through RIPK1 ubiquitin editing.
      Consistent with IDA annotation for the more specific via death domain receptors term.

# =====================
# TAS/REACTOME ANNOTATIONS (14)
# =====================
- term:
    id: GO:0010803
    label: regulation of tumor necrosis factor-mediated signaling pathway
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5357905
  review:
    summary: >-
      TAS from Reactome pathway "Regulation of TNFR1 signaling". A20 is a key component of
      TNFR1 signaling regulation, editing ubiquitin chains on RIPK1 in the TNF receptor complex.
    action: ACCEPT
    reason: >-
      Core function. A20 directly regulates TNFR1 signaling through ubiquitin editing of RIPK1.
      Well-supported by Reactome pathway analysis.

- term:
    id: GO:0016579
    label: protein deubiquitination
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5688426
  review:
    summary: >-
      TAS from Reactome "Deubiquitination" pathway. Core enzymatic function.
    action: ACCEPT
    reason: >-
      Correct. Core enzymatic activity of A20.

- term:
    id: GO:0035872
    label: nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-168638
  review:
    summary: >-
      TAS from Reactome "NOD1/2 Signaling Pathway". A20 participates in NLR signaling by
      negatively regulating NOD1/2 pathway activation.
    action: ACCEPT
    reason: >-
      Correct. A20 is a component of NLR signaling pathway as a negative regulator.
      Reactome places A20 in the NOD1/2 pathway for RIPK2 deubiquitination.

- term:
    id: GO:0043124
    label: negative regulation of canonical NF-kappaB signal transduction
  evidence_type: IDA
  original_reference_id: PMID:18223652
  review:
    summary: >-
      IDA from PMID:18223652. MALT1 paracaspase cleavage of A20 during TCR stimulation
      disrupts A20 NF-kB inhibitory function, leading to increased NF-kB activation.
      This demonstrates A20 is required for NF-kB suppression during T cell activation.
    action: ACCEPT
    reason: >-
      Core function. The fact that MALT1 cleaves A20 to relieve NF-kB inhibition
      during T cell activation confirms A20 as an active NF-kB suppressor.
    supported_by:
      - reference_id: PMID:18223652
        supporting_text: "T cell antigen receptor stimulation induces MALT1 paracaspase-mediated cleavage of the NF-kappaB inhibitor A20"

- term:
    id: GO:0061578
    label: K63-linked deubiquitinase activity
  evidence_type: EXP
  original_reference_id: PMID:14748687
  review:
    summary: >-
      EXP evidence for K63-linked deubiquitinase activity. Evans et al. (2004) first demonstrated
      A20 deubiquitinase activity using biochemical assays. Cys103 was identified as the
      catalytic residue.
    action: ACCEPT
    reason: >-
      Core enzymatic function. This is the first experimental demonstration of A20 deubiquitinase
      activity. K63-linked chain cleavage is the primary in vivo specificity.
    supported_by:
      - reference_id: PMID:14748687
        supporting_text: "Zinc-finger protein A20, a regulator of inflammation and cell survival, has de-ubiquitinating activity"

- term:
    id: GO:0061578
    label: K63-linked deubiquitinase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5357845
  review:
    summary: >-
      TAS from Reactome "K63polyUb-RIPK1 is deubiquitinated". A20 removes K63-linked
      polyubiquitin from RIPK1.
    action: ACCEPT
    reason: >-
      Correct. Reactome pathway annotation consistent with experimental evidence for
      K63-linked DUB activity on RIPK1.

- term:
    id: GO:0061578
    label: K63-linked deubiquitinase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5690856
  review:
    summary: >-
      TAS from Reactome "TNFAIP3 (A20) deubiquitinates K63polyUb-RIPK1".
    action: ACCEPT
    reason: >-
      Correct. Consistent with EXP and other TAS evidence.

- term:
    id: GO:0061578
    label: K63-linked deubiquitinase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-8869506
  review:
    summary: >-
      TAS from Reactome "TNFAIP3 in OTUD7B:TNFAIP3:ZRANB1 deubiquitinates K63polyUb-TRAF6".
      A20 also deubiquitinates K63-linked chains on TRAF6 as part of a complex.
    action: ACCEPT
    reason: >-
      Correct. TRAF6 is a well-characterized substrate for A20 K63-linked deubiquitination.

- term:
    id: GO:0032691
    label: negative regulation of interleukin-1 beta production
  evidence_type: IMP
  original_reference_id: PMID:28094437
  review:
    summary: >-
      IMP evidence. A20 mutations lead to increased IL-1beta production, demonstrating
      A20 negatively regulates IL-1beta. This is consistent with A20 suppression of
      NF-kB and NLRP3 inflammasome.
    action: KEEP_AS_NON_CORE
    reason: >-
      Downstream consequence of NF-kB and inflammasome regulation. Supported by mutant
      phenotype but represents a pleiotropic effect rather than direct molecular function.

- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: IMP
  original_reference_id: PMID:15258597
  review:
    summary: >-
      IMP from Wertz et al. Nature 2004. Mutagenesis of Cys103 abolished deubiquitinase
      activity, and mutations in zinc finger cysteines abolished ubiquitin ligase activity.
      This landmark paper established the dual enzymatic nature of A20.
    action: ACCEPT
    reason: >-
      Core enzymatic function. The Wertz et al. 2004 paper is the definitive study establishing
      A20 as a ubiquitin-editing enzyme with both DUB and E3 activities.
    supported_by:
      - reference_id: PMID:15258597
        supporting_text: "De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling"

# TAS cytosol annotations (10 Reactome references)
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5357845
  review:
    summary: >-
      TAS from Reactome. A20 functions in the cytosol at receptor-proximal signaling complexes.
    action: ACCEPT
    reason: >-
      Correct. Cytosol is the specific subcellular compartment where A20 edits ubiquitin
      chains on signaling adaptors.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5690827
  review:
    summary: >-
      TAS from Reactome "TNFAIP3 (A20) ubiquitinates RIPK1".
    action: ACCEPT
    reason: >-
      Correct. Consistent with cytosolic localization.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5690845
  review:
    summary: >-
      TAS from Reactome "TNIPs bind TNFAIP3 (A20)".
    action: ACCEPT
    reason: >-
      Correct. A20-TNIP interaction occurs in the cytosol.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5690856
  review:
    summary: >-
      TAS from Reactome for K63polyUb-RIPK1 deubiquitination in cytosol.
    action: ACCEPT
    reason: >-
      Correct. Cytosolic deubiquitination of RIPK1.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5690870
  review:
    summary: >-
      TAS from Reactome for TRAF6 deubiquitination in cytosol.
    action: ACCEPT
    reason: >-
      Correct.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5693055
  review:
    summary: >-
      TAS from Reactome "TAX1BP1:TNFAIP3(A20) binds RIPK1-containing complexes".
    action: ACCEPT
    reason: >-
      Correct. TAX1BP1-A20 complex functions in cytosol.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5693108
  review:
    summary: >-
      TAS from Reactome for K48-linked ubiquitination of RIPK1 in cytosol.
    action: ACCEPT
    reason: >-
      Correct.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-688136
  review:
    summary: >-
      TAS from Reactome "TNFAIP3 (A20) deubiquitinates RIP2".
    action: ACCEPT
    reason: >-
      Correct. A20 deubiquitinates RIPK2 in the cytosol during NOD signaling.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-8869506
  review:
    summary: >-
      TAS from Reactome for TRAF6 deubiquitination complex in cytosol.
    action: ACCEPT
    reason: >-
      Correct.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-937337
  review:
    summary: >-
      TAS from Reactome "TAX1BP1:A20 inhibit TBK1/IKKi K63-polyubiquitination".
    action: ACCEPT
    reason: >-
      Correct. A20-TAX1BP1 complex inhibits TBK1/IKKi ubiquitination in cytosol, relevant
      to antiviral innate immune signaling regulation.

# =====================
# EXPERIMENTAL ANNOTATIONS (IDA, IMP, EXP, IPI)
# =====================
- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: IDA
  original_reference_id: PMID:23827681
  review:
    summary: >-
      IDA from Mevissen et al. Cell 2013. Comprehensive characterization of OTU family DUB
      specificity showing A20 can cleave K11, K48, and K63 chains. This study used ubiquitin
      chain restriction analysis to demonstrate linkage specificity.
    action: ACCEPT
    reason: >-
      Core enzymatic function. Detailed biochemical characterization of A20 DUB specificity
      using purified enzyme and defined ubiquitin chain substrates.
    supported_by:
      - reference_id: PMID:23827681
        supporting_text: "OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis"

- term:
    id: GO:0035871
    label: protein K11-linked deubiquitination
  evidence_type: IDA
  original_reference_id: PMID:23827681
  review:
    summary: >-
      IDA from Mevissen et al. 2013. A20 can cleave K11-linked ubiquitin chains in vitro.
      However, the in vivo relevance of K11 chain cleavage is less clear than K63 chain cleavage.
    action: ACCEPT
    reason: >-
      Experimentally demonstrated. While K63 cleavage is the primary in vivo activity,
      K11 chain cleavage is a validated biochemical activity of A20 OTU domain.
    supported_by:
      - reference_id: PMID:23827681
        supporting_text: "OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis"

- term:
    id: GO:0071108
    label: protein K48-linked deubiquitination
  evidence_type: IDA
  original_reference_id: PMID:23827681
  review:
    summary: >-
      IDA from Mevissen et al. 2013. A20 can cleave K48-linked chains in vitro. UniProt
      confirms A20 can deubiquitinate K48 chains in vitro.
    action: ACCEPT
    reason: >-
      Experimentally demonstrated biochemical activity, though K63 cleavage is the primary
      in vivo specificity. K48 chain cleavage may contribute to ubiquitin editing function.
    supported_by:
      - reference_id: PMID:23827681
        supporting_text: "OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis"

- term:
    id: GO:0070062
    label: extracellular exosome
  evidence_type: HDA
  original_reference_id: PMID:20458337
  review:
    summary: >-
      HDA (high-throughput direct assay) detection of A20 in B-cell exosomes by mass
      spectrometry. This is from a proteomic analysis of exosome contents.
    action: KEEP_AS_NON_CORE
    reason: >-
      Detection in exosomes by mass spectrometry may reflect passive incorporation rather
      than functional localization. Not a core functional location.

- term:
    id: GO:1902042
    label: negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
  evidence_type: IDA
  original_reference_id: PMID:12167698
  review:
    summary: >-
      IDA from PMID:12167698. A20 protects cells from death receptor-mediated apoptosis.
      A20 edits ubiquitin chains on RIPK1 in the TNFR1 complex, preventing formation of
      the death-inducing signaling complex (DISC).
    action: ACCEPT
    reason: >-
      Important function. A20 prevents TNFR1-mediated apoptosis by ubiquitin editing of
      RIPK1, which is part of its core NF-kB/cell death regulatory function.

- term:
    id: GO:0045824
    label: negative regulation of innate immune response
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS from mouse A20 (Q60769). Core function confirmed in mouse.
    action: ACCEPT
    reason: >-
      Core function. Mouse A20 knockout has severe innate immune dysregulation.

- term:
    id: GO:0070301
    label: cellular response to hydrogen peroxide
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS from mouse A20. A20 responds to oxidative stress signals.
    action: KEEP_AS_NON_CORE
    reason: >-
      Not core. Response to H2O2 is a secondary/stress-related function.

- term:
    id: GO:0072573
    label: tolerance induction to lipopolysaccharide
  evidence_type: IMP
  original_reference_id: PMID:21220427
  review:
    summary: >-
      IMP evidence. A20 is required for LPS tolerance induction -- the phenomenon where
      prior LPS exposure renders cells refractory to subsequent LPS stimulation. A20 is
      required for LPS-induced cytokine and IFN-beta production in LPS-tolerized macrophages.
    action: ACCEPT
    reason: >-
      Important specific function. LPS tolerance is a key innate immune regulatory mechanism,
      and A20 has a specific required role in this process.

- term:
    id: GO:2000349
    label: negative regulation of CD40 signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:12885753
  review:
    summary: >-
      IMP from PMID:12885753. A20 protects endothelial cells from CD40-CD40L-mediated
      activation. A20 overexpression inhibited CD40-mediated NF-kB activation.
    action: ACCEPT
    reason: >-
      Consistent with A20 core function of NF-kB suppression. CD40 signals through TRAF2/TRAF6
      to NF-kB, and A20 targets these adaptors.
    supported_by:
      - reference_id: PMID:12885753
        supporting_text: "A20 protects from CD40-CD40 ligand-mediated endothelial cell activation and apoptosis"

- term:
    id: GO:2000352
    label: negative regulation of endothelial cell apoptotic process
  evidence_type: IDA
  original_reference_id: PMID:12885753
  review:
    summary: >-
      IDA from PMID:12885753. A20 protects endothelial cells from CD40-mediated apoptosis.
    action: KEEP_AS_NON_CORE
    reason: >-
      Cell-type specific effect. A20 anti-apoptotic function in endothelial cells is a
      downstream consequence of NF-kB regulation rather than a core molecular function.
    supported_by:
      - reference_id: PMID:12885753
        supporting_text: "A20 protects from CD40-CD40 ligand-mediated endothelial cell activation and apoptosis"

- term:
    id: GO:0002237
    label: response to molecule of bacterial origin
  evidence_type: IDA
  original_reference_id: PMID:19912257
  review:
    summary: >-
      IDA evidence. A20 is induced by and responds to bacterial molecules through TLR signaling.
    action: ACCEPT
    reason: >-
      A20 is an NF-kB-inducible gene that is directly induced by bacterial products via TLR
      signaling and functions to terminate the resulting inflammatory response.

- term:
    id: GO:0071222
    label: cellular response to lipopolysaccharide
  evidence_type: IDA
  original_reference_id: PMID:19912257
  review:
    summary: >-
      IDA evidence for cellular response to LPS. A20 is rapidly induced by LPS stimulation
      and functions to terminate TLR4-NF-kB signaling.
    action: ACCEPT
    reason: >-
      Core pathway involvement. A20 is a canonical LPS-responsive gene induced as negative
      feedback to terminate TLR4-NF-kB signaling.

- term:
    id: GO:0002020
    label: protease binding
  evidence_type: IPI
  original_reference_id: PMID:18223652
  review:
    summary: >-
      IPI for binding to MALT1 paracaspase (Q9UDY8). A20 is a substrate of MALT1 paracaspase,
      which cleaves A20 upon TCR stimulation to relieve NF-kB inhibition.
    action: ACCEPT
    reason: >-
      Functionally significant interaction. A20 binding to MALT1 is important for TCR signaling
      regulation. More informative than generic protein binding.
    supported_by:
      - reference_id: PMID:18223652
        supporting_text: "T cell antigen receptor stimulation induces MALT1 paracaspase-mediated cleavage of the NF-kappaB inhibitor A20"

- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: TAS
  original_reference_id: PMID:20392859
  review:
    summary: >-
      TAS from review article PMID:20392859 documenting A20 DUB activity.
    action: ACCEPT
    reason: >-
      Correct. Core enzymatic function. Consistent with IDA and IBA evidence.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15142865
  review:
    summary: >-
      IPI protein binding with ITCH (Q8IUC6). A20 interacts with ITCH E3 ligase as part
      of the ubiquitin-editing complex (A20-TAX1BP1-RNF11-ITCH).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative. The A20-ITCH interaction is functionally significant
      but should use more specific terms.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15474016
  review:
    summary: >-
      IPI protein binding with TNIP1, TNIP2, TAX1BP1, IKBKG. These are key functional
      partners of A20 in the NF-kB regulatory complex.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative. These interactions are core to A20 function but
      generic protein binding adds no value.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20392859
  review:
    summary: >-
      IPI protein binding with IRF7 (Q92985). A20 may modulate interferon regulatory
      factor signaling.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative.

- term:
    id: GO:0016579
    label: protein deubiquitination
  evidence_type: TAS
  original_reference_id: PMID:20392859
  review:
    summary: >-
      TAS from review. Protein deubiquitination is a core function.
    action: ACCEPT
    reason: >-
      Correct. Core enzymatic function.

- term:
    id: GO:0031397
    label: negative regulation of protein ubiquitination
  evidence_type: IDA
  original_reference_id: PMID:20392859
  review:
    summary: >-
      IDA evidence. A20 promotes disassembly of E2-E3 ubiquitin ligase complexes, negatively
      regulating ubiquitination of signaling proteins in the TNFR1 and IL-1R pathways.
    action: ACCEPT
    reason: >-
      Important aspect of A20 function. A20 not only deubiquitinates substrates but also
      disrupts E2-E3 complexes (TRAF6, TRAF2, BIRC2 with UBE2N and UBE2D3), preventing
      further ubiquitination.

- term:
    id: GO:0032703
    label: negative regulation of interleukin-2 production
  evidence_type: IMP
  original_reference_id: PMID:18223652
  review:
    summary: >-
      IMP evidence. MALT1 cleavage of A20 during TCR signaling leads to increased IL-2
      production, demonstrating A20 normally suppresses IL-2 production.
    action: KEEP_AS_NON_CORE
    reason: >-
      Downstream consequence of NF-kB regulation during T cell activation. IL-2 is an NF-kB
      target gene, so A20 indirectly suppresses its production.
    supported_by:
      - reference_id: PMID:18223652
        supporting_text: "T cell antigen receptor stimulation induces MALT1 paracaspase-mediated cleavage of the NF-kappaB inhibitor A20"

- term:
    id: GO:0034136
    label: negative regulation of toll-like receptor 2 signaling pathway
  evidence_type: NAS
  original_reference_id: PMID:15142865
  review:
    summary: >-
      NAS from PMID:15142865. A20 negatively regulates TLR2 signaling as part of its broad
      role in TLR pathway regulation.
    action: ACCEPT
    reason: >-
      Consistent with A20 core function as negative regulator of TLR signaling. TLR2 signals
      through TRAF6, a known A20 substrate.

- term:
    id: GO:0034140
    label: negative regulation of toll-like receptor 3 signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:15474016
  review:
    summary: >-
      IDA evidence for A20 negative regulation of TLR3 signaling.
    action: ACCEPT
    reason: >-
      Core function. TLR3 pathway regulation is part of A20 broad innate immune regulatory function.

- term:
    id: GO:0034144
    label: negative regulation of toll-like receptor 4 signaling pathway
  evidence_type: NAS
  original_reference_id: PMID:15142865
  review:
    summary: >-
      NAS from PMID:15142865. A20 negatively regulates TLR4 signaling. LPS (TLR4 ligand)
      is one of the most studied A20 activating stimuli.
    action: ACCEPT
    reason: >-
      Core function. TLR4-LPS signaling is one of the best-characterized pathways
      regulated by A20.

- term:
    id: GO:0043130
    label: ubiquitin binding
  evidence_type: IPI
  original_reference_id: PMID:19285159
  review:
    summary: >-
      IPI for ubiquitin binding with ubiquitin (P0CG48). A20 ZnF4 and ZnF7 bind polyubiquitin
      chains. ZnF4 recognizes K63-linked chains; ZnF7 binds linear (M1-linked) chains.
      This non-catalytic ubiquitin binding is essential for A20 function.
    action: ACCEPT
    reason: >-
      Core function. Ubiquitin binding via zinc fingers is essential for A20 regulatory
      activity, both for substrate recognition and for non-catalytic IKK inhibition.
    supported_by:
      - reference_id: PMID:19285159
        supporting_text: "known NF-kappaB regulators including NEMO, A20, ABIN-1, ABIN-2, optineurin and p62 were also identified"

- term:
    id: GO:0050691
    label: regulation of defense response to virus by host
  evidence_type: NAS
  original_reference_id: PMID:15142865
  review:
    summary: >-
      NAS evidence. A20 modulates antiviral signaling by regulating TLR3 and RIG-I/MDA5
      pathways that sense viral nucleic acids.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic consequence of A20 innate immune regulation. Antiviral defense regulation
      is an indirect effect of TLR/RLR pathway modulation.

- term:
    id: GO:0071222
    label: cellular response to lipopolysaccharide
  evidence_type: IDA
  original_reference_id: PMID:21220427
  review:
    summary: >-
      IDA evidence for LPS response, specifically in the context of LPS tolerance.
      A20 is required for LPS tolerance.
    action: ACCEPT
    reason: >-
      Correct. A20 mediates LPS tolerance response. Important and specific function.

- term:
    id: GO:0001922
    label: B-1 B cell homeostasis
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS from mouse A20 (Q60769). Mouse A20 deficiency causes B-1 B cell abnormalities.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic immune consequence of A20 deficiency. Not core molecular function.

- term:
    id: GO:0002634
    label: regulation of germinal center formation
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS from mouse. A20 regulates germinal center formation through immune cell regulation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic downstream effect in adaptive immunity.

- term:
    id: GO:0032715
    label: negative regulation of interleukin-6 production
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS from mouse. A20 deficiency leads to elevated IL-6.
    action: KEEP_AS_NON_CORE
    reason: >-
      Downstream effect of NF-kB regulation. IL-6 is an NF-kB target gene.

- term:
    id: GO:0032720
    label: negative regulation of tumor necrosis factor production
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS from mouse. A20 deficiency leads to elevated TNF production.
    action: KEEP_AS_NON_CORE
    reason: >-
      Downstream effect. TNF is an NF-kB target gene. A20 suppresses TNF production
      indirectly through NF-kB inhibition.

- term:
    id: GO:0043124
    label: negative regulation of canonical NF-kappaB signal transduction
  evidence_type: IDA
  original_reference_id: PMID:21127049
  review:
    summary: >-
      IDA evidence for negative regulation of NF-kB. A20 inhibits RANKL-induced
      NF-kB activation in osteoclasts.
    action: ACCEPT
    reason: >-
      Core function. Additional experimental evidence confirming A20 NF-kB suppression
      in a different cell type context.

- term:
    id: GO:0045732
    label: positive regulation of protein catabolic process
  evidence_type: IDA
  original_reference_id: PMID:21127049
  review:
    summary: >-
      IDA evidence. A20 promotes proteasomal degradation of signaling substrates through
      K48-linked ubiquitination.
    action: ACCEPT
    reason: >-
      Correct. A20 E3 ligase activity adds K48 chains to promote proteasomal degradation.

- term:
    id: GO:0045779
    label: negative regulation of bone resorption
  evidence_type: NAS
  original_reference_id: PMID:21127049
  review:
    summary: >-
      NAS evidence. A20 inhibits RANKL-induced osteoclast formation, which would reduce
      bone resorption.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic tissue-specific effect. Bone resorption regulation is an indirect
      consequence of NF-kB suppression in osteoclasts.

- term:
    id: GO:0048662
    label: negative regulation of smooth muscle cell proliferation
  evidence_type: IDA
  original_reference_id: PMID:16816117
  review:
    summary: >-
      IDA evidence. A20 inhibits smooth muscle cell proliferation, relevant to vascular
      biology and neointima formation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic tissue-specific effect. SMC proliferation regulation is an indirect
      consequence of NF-kB suppression in vascular cells.

- term:
    id: GO:0050728
    label: negative regulation of inflammatory response
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS from mouse A20. Core anti-inflammatory function.
    action: ACCEPT
    reason: >-
      Core function. Consistent with IBA evidence.

- term:
    id: GO:0050869
    label: negative regulation of B cell activation
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS from mouse. A20 regulates B cell activation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic immune consequence. B cell regulation is downstream of NF-kB suppression.

- term:
    id: GO:0061043
    label: regulation of vascular wound healing
  evidence_type: NAS
  original_reference_id: PMID:16816117
  review:
    summary: >-
      NAS evidence. A20 regulates vascular wound healing by inhibiting smooth muscle cell
      proliferation and NF-kB-driven inflammatory responses in vascular cells.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic tissue-specific effect. Vascular wound healing regulation is an indirect
      consequence of A20 anti-inflammatory function.

- term:
    id: GO:0071222
    label: cellular response to lipopolysaccharide
  evidence_type: IDA
  original_reference_id: PMID:21127049
  review:
    summary: >-
      IDA evidence for LPS response in context of osteoclast biology.
    action: ACCEPT
    reason: >-
      Correct. A20 is induced by and responds to LPS.

- term:
    id: GO:0090291
    label: negative regulation of osteoclast proliferation
  evidence_type: NAS
  original_reference_id: PMID:21127049
  review:
    summary: >-
      NAS evidence. A20 inhibits osteoclast proliferation/formation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic tissue-specific effect. Osteoclast regulation is downstream of NF-kB
      suppression by A20.

# IDA from Wertz et al. 2004 (PMID:15258597) - landmark paper
- term:
    id: GO:0004842
    label: ubiquitin-protein transferase activity
  evidence_type: IDA
  original_reference_id: PMID:15258597
  review:
    summary: >-
      IDA from Wertz et al. Nature 2004. ZnF4 domain mediates E3 ubiquitin ligase activity,
      adding K48-linked polyubiquitin chains to RIPK1. Mutations in ZnF4 cysteines (C624, C627)
      abolished this activity.
    action: ACCEPT
    reason: >-
      Core enzymatic function. The E3 ligase activity of ZnF4 is one of the two defining
      enzymatic activities of A20, experimentally demonstrated by mutagenesis.
    supported_by:
      - reference_id: PMID:15258597
        supporting_text: "De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling"

- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: IDA
  original_reference_id: PMID:15258597
  review:
    summary: >-
      IDA from Wertz et al. 2004. Cys103 mutation abolished DUB activity.
    action: ACCEPT
    reason: >-
      Core enzymatic function. Definitive experimental demonstration.
    supported_by:
      - reference_id: PMID:15258597
        supporting_text: "De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling"

- term:
    id: GO:0043124
    label: negative regulation of canonical NF-kappaB signal transduction
  evidence_type: IDA
  original_reference_id: PMID:15258597
  review:
    summary: >-
      IDA from Wertz et al. 2004. Both DUB and E3 domains contribute to NF-kB suppression.
    action: ACCEPT
    reason: >-
      Core function. The landmark paper establishing the mechanism of A20 NF-kB regulation.
    supported_by:
      - reference_id: PMID:15258597
        supporting_text: "De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling"

- term:
    id: GO:0070536
    label: protein K63-linked deubiquitination
  evidence_type: IDA
  original_reference_id: PMID:15258597
  review:
    summary: >-
      IDA from Wertz et al. 2004. A20 OTU domain removes K63-linked polyubiquitin from RIPK1.
    action: ACCEPT
    reason: >-
      Core enzymatic function. K63-linked deubiquitination of RIPK1 is the primary in vivo
      DUB activity of A20.
    supported_by:
      - reference_id: PMID:15258597
        supporting_text: "De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling"

- term:
    id: GO:0070936
    label: protein K48-linked ubiquitination
  evidence_type: IDA
  original_reference_id: PMID:15258597
  review:
    summary: >-
      IDA from Wertz et al. 2004. A20 ZnF4 adds K48-linked polyubiquitin to RIPK1, targeting
      it for proteasomal degradation. This is the ubiquitin ligase arm of the ubiquitin-editing
      mechanism.
    action: ACCEPT
    reason: >-
      Core enzymatic function. K48-linked ubiquitination by ZnF4 is the E3 ligase arm of
      A20 ubiquitin-editing, complementing the OTU deubiquitinase activity.
    supported_by:
      - reference_id: PMID:15258597
        supporting_text: "De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling"

# IPI and IDA from PMID:11463333
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11463333
  review:
    summary: >-
      IPI protein binding with TRAF4 (Q9Y4K3). From the study that also established A20
      nuclear/cytoplasmic localization.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is uninformative.

- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:11463333
  review:
    summary: >-
      IDA for nuclear localization. Evans et al. (2001) showed A20 localizes to both cytoplasm
      and nucleus using immunofluorescence.
    action: ACCEPT
    reason: >-
      Primary experimental evidence for nuclear localization. While cytoplasm is the main
      functional location, nuclear localization is directly demonstrated.
    supported_by:
      - reference_id: PMID:11463333
        supporting_text: "The zinc finger molecule A20 is an important negative regulator of NF-kappa B"

- term:
    id: GO:0043124
    label: negative regulation of canonical NF-kappaB signal transduction
  evidence_type: IDA
  original_reference_id: PMID:11463333
  review:
    summary: >-
      IDA for NF-kB negative regulation from Evans et al. 2001.
    action: ACCEPT
    reason: >-
      Core function. Additional experimental support for A20 NF-kB suppression.

references:
- id: GO_REF:0000003
  title: Gene Ontology annotation based on Enzyme Commission mapping
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- 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:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to
    orthologs using Ensembl Compara
  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:8692885
  title: The tumor necrosis factor-inducible zinc finger protein A20 interacts with
    TRAF1/TRAF2 and inhibits NF-kappaB activation.
  findings:
    - statement: A20 interacts with TRAF1 and TRAF2 and inhibits NF-kB activation
      supporting_text: >-
        TRAF1 and TRAF2 interact with A20, a zinc finger protein, whose expression is induced by
        agents that activate NF-kappaB. Mutational analysis revealed that the N-terminal
        half of A20 interacts with the conserved C-terminal TRAF domain of TRAF1 and
        TRAF2. In cotransfection experiments, A20 blocked TRAF2-mediated NF-kappaB
        activation.
- id: PMID:9299557
  title: A20 inhibits NF-kappaB activation independently of binding to 14-3-3 proteins.
  findings:
    - statement: A20 interacts with YWHAZ and YWHAH but inhibits NF-kB independently
      supporting_text: >-
        different isoforms of 14-3-3
        proteins, viz. eta and zeta, are able to bind A20, involving the 14-3-3-binding
        motif RSKSDP located between zinc fingers 3 and 4. However, A20 mutants that no
        longer associated with 14-3-3 proteins could still fully inhibit NF-kappaB
        activation induced by tumor necrosis factor, interleukin-1beta or phorbol
        12-myristate 13-acetate, thus excluding a crucial role for 14-3-3 interaction in
        this A20 function.
- id: PMID:11389905
  title: Functional redundancy of the zinc fingers of A20 for inhibition of NF-kappaB activation and protein-protein interactions.
  findings: []
- id: PMID:11463333
  title: Isolation and characterization of two novel A20-like proteins.
  findings:
    - statement: A20 localizes to cytoplasm and nucleus; NF-kB inhibitory activity demonstrated
      supporting_text: >-
        The zinc finger molecule A20 is an important negative regulator of
        NF-kappa B. The mechanism utilized by A20 is not fully understood, but A20 has
        been shown to bind to tumour-necrosis-factor-receptor-associated factor (TRAF)
        molecules, which are necessary for pro-inflammatory cytokine signalling.
- id: PMID:12167698
  title: A20 inhibits tumor necrosis factor (TNF) alpha-induced apoptosis by disrupting
    recruitment of TRADD and RIP to the TNF receptor 1 complex in Jurkat T cells.
  findings:
    - statement: A20 inhibits extrinsic apoptotic signaling via death domain receptors
      supporting_text: >-
        the zinc finger protein A20 is an NF-kappaB-inducible
        gene that can protect the IKKgamma-deficient cells from TNF-induced apoptosis by
        disrupting the recruitment of the death domain signaling molecules TRADD and RIP
        to the receptor signaling complex.
- id: PMID:12885753
  title: A20 protects from CD40-CD40 ligand-mediated endothelial cell activation and
    apoptosis.
  findings:
    - statement: A20 protects endothelial cells from CD40-mediated NF-kB activation and apoptosis
      supporting_text: >-
        Coexpression of A20
        inhibits NF-kappaB and upregulation of IkappaBalpha and E-Selectin but not TF,
        suggesting that CD40 induces TF in a non-NF-kappaB-dependent manner. In human
        coronary artery ECs (HCAECs), adenovirus-mediated overexpression of A20 blocks
        physiological, CD40-induced activation of NF-kappaB, upstream of IkappaBalpha
        degradation
- id: PMID:14748687
  title: Zinc-finger protein A20, a regulator of inflammation and cell survival, has
    de-ubiquitinating activity.
  findings:
    - statement: First demonstration of A20 deubiquitinase activity; Cys103 identified as catalytic residue
      supporting_text: >-
        Here we demonstrate that A20 is a de-ubiquitinating enzyme. It
        contains an N-terminal catalytic domain that belongs to the ovarian-tumour
        superfamily of cysteine proteases. A20 cleaved ubiquitin monomers from branched
        polyubiquitin chains linked through Lys48 or Lys63 and bound covalently to a
        thiol-group-reactive, ubiquitin-derived probe. Mutation of a conserved cysteine
        residue in the catalytic site (Cys103) abolished these activities.
- id: PMID:15142865
  title: A20 inhibits toll-like receptor 2- and 4-mediated interleukin-8 synthesis in
    airway epithelial cells.
  findings:
    - statement: A20 negatively regulates TLR2 and TLR4 signaling pathways
      supporting_text: >-
        overexpression of
        A20 inhibited activation of both NF-kappaB and the IL-8 promoter by PGN or LPS
        in these cells. Taken together, our results suggest that A20 may function as a
        negative regulator of TLR-mediated inflammatory responses in the airway, thereby
        protecting the host against harmful overresponses to pathogens.
- id: PMID:15169888
  title: ABIN-2 forms a ternary complex with TPL-2 and NF-kappa B1 p105 and is essential
    for TPL-2 protein stability.
  findings: []
- id: PMID:15231748
  title: Functional proteomics mapping of a human signaling pathway.
  findings: []
- id: PMID:15258597
  title: De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB
    signalling.
  findings:
    - statement: Landmark paper establishing A20 as dual ubiquitin-editing enzyme with OTU DUB and ZnF4 E3 ligase activities
      supporting_text: >-
        A20 downregulates NF-kappaB signalling through the cooperative activity of its
        two ubiquitin-editing domains. The amino-terminal domain of A20, which is a
        de-ubiquitinating (DUB) enzyme of the OTU (ovarian tumour) family, removes
        lysine-63 (K63)-linked ubiquitin chains from receptor interacting protein (RIP),
        an essential mediator of the proximal TNF receptor 1 (TNFR1) signalling complex.
        The carboxy-terminal domain of A20, composed of seven C2/C2 zinc fingers, then
        functions as a ubiquitin ligase by polyubiquitinating RIP with K48-linked
        ubiquitin chains, thereby targeting RIP for proteasomal degradation.
    - statement: A20 removes K63-linked polyubiquitin from RIPK1 and adds K48-linked chains targeting RIPK1 for proteasomal degradation
      supporting_text: >-
        The amino-terminal domain of A20, which is a
        de-ubiquitinating (DUB) enzyme of the OTU (ovarian tumour) family, removes
        lysine-63 (K63)-linked ubiquitin chains from receptor interacting protein (RIP),
        an essential mediator of the proximal TNF receptor 1 (TNFR1) signalling complex.
        The carboxy-terminal domain of A20, composed of seven C2/C2 zinc fingers, then
        functions as a ubiquitin ligase by polyubiquitinating RIP with K48-linked
        ubiquitin chains, thereby targeting RIP for proteasomal degradation.
- id: PMID:15474016
  title: A20 is a potent inhibitor of TLR3- and Sendai virus-induced activation of NF-kappaB
    and ISRE and IFN-beta promoter.
  findings:
    - statement: A20 negatively regulates TLR3 signaling pathway
      supporting_text: >-
        A20, a NF-kappaB-inducible zinc finger protein that has been
        demonstrated to be an inhibitor of TNF-induced NF-kappaB activation and a
        physiological suppressor of inflammatory response, potently inhibited TLR3- and
        Sendai virus-mediated activation of ISRE and NF-kappaB and IFN-beta promoter in
        reporter gene assays.
- id: PMID:16684768
  title: ABIN-1 binds to NEMO/IKKgamma and co-operates with A20 in inhibiting NF-kappaB.
  findings:
    - statement: A20 cooperates with TNIP1/ABIN-1 and interacts with IKBKG/NEMO to inhibit NF-kB
      supporting_text: >-
        ABIN-1
        physically links A20 to NEMO/IKKgamma and facilitates A20-mediated
        de-ubiquitination of NEMO/IKKgamma, thus resulting in inhibition of NF-kappaB.
- id: PMID:16816117
  title: A20, a modulator of smooth muscle cell proliferation and apoptosis, prevents
    and induces regression of neointimal hyperplasia.
  findings:
    - statement: A20 inhibits smooth muscle cell proliferation and regulates vascular wound healing
      supporting_text: >-
        A20
        inhibits SMC proliferation via increased expression of cyclin-dependent kinase
        inhibitors p21waf1 and p27kip1. Surprisingly, A20 sensitizes SMC to cytokine-
        and Fas-mediated apoptosis through a novel NO-dependent mechanism.
- id: PMID:17961127
  title: Structure of the A20 OTU domain and mechanistic insights into deubiquitination.
  findings:
    - statement: Crystal structure of A20 OTU domain at 3.2A; catalytic mechanism elucidated
      supporting_text: >-
        we describe the crystal
        structure of the N-terminal OTU (ovarian tumour) deubiquitinase domain of A20,
        which differs from other deubiquitinases but shares the minimal catalytic core
        with otubain-2. Analysis of conserved surface regions allows prediction of
        ubiquitin-binding sites for the proximal and distal ubiquitin molecules.
        Structural and biochemical analysis suggests a novel architecture of the
        catalytic triad
- id: PMID:18164316
  title: Molecular basis for the unique deubiquitinating activity of the NF-kappaB inhibitor A20.
  findings:
    - statement: Crystal structure at 2.5A; active site residues Asp70, Cys103, His256 characterized
      supporting_text: >-
        To elucidate the molecular basis for
        the DUB activity of A20, we determined its crystal structure and performed a
        series of biochemical and cell biological studies. The structure reveals the
        potential catalytic mechanism of A20, which may be significantly different from
        papain-like cysteine proteases.
- id: PMID:18223652
  title: T cell antigen receptor stimulation induces MALT1 paracaspase-mediated cleavage
    of the NF-kappaB inhibitor A20.
  findings:
    - statement: MALT1 cleaves A20 during TCR stimulation, relieving NF-kB inhibition and increasing IL-2 production
      supporting_text: >-
        T cell antigen receptor stimulation induced recruitment of the
        NF-kappaB inhibitor A20 into a complex of MALT1 and the adaptor protein Bcl-10,
        leading to MALT1-mediated processing of A20. API2-MALT1 expression likewise
        resulted in cleavage of A20. MALT1 cleaved human A20 after arginine 439 and
        impaired its NF-kappaB-inhibitory function.
- id: PMID:18952128
  title: The zinc finger protein A20 targets TRAF2 to the lysosomes for degradation.
  findings:
    - statement: A20 targets TRAF2 to lysosomes for degradation
      supporting_text: >-
        A20 is capable of targeting an associated signaling molecule
        such as TRAF2 to the lysosomes for degradation. This process is dependent on the
        membrane tethering zinc finger domains of A20, but does not require A20
        ubiquitin modifying activity.
- id: PMID:19060883
  title: ABIN-1 is a ubiquitin sensor that restricts cell death and sustains embryonic
    development.
  findings: []
- id: PMID:19131965
  title: The ubiquitin-editing enzyme A20 requires RNF11 to downregulate NF-kappaB
    signalling.
  findings:
    - statement: A20 requires RNF11 and interacts with TAX1BP1 and RIPK1 for NF-kB downregulation
      supporting_text: >-
        RNF11 interacted
        with the NF-kappaB inhibitor A20 and its regulatory protein TAX1BP1 in a
        stimulus-dependent manner. RNF11 negatively regulated RIP1 and TRAF6
        ubiquitination upon stimulation with TNF and LPS, respectively. Furthermore,
        RNF11 was required for A20 to interact with and inactivate RIP1 to inhibit
        TNF-mediated NF-kappaB activation.
- id: PMID:19285159
  title: Identification of polyubiquitin binding proteins involved in NF-kappaB signaling
    using protein arrays.
  findings:
    - statement: A20 binds polyubiquitin chains through zinc finger domains
      supporting_text: >-
        known NF-kappaB regulators including NEMO, A20, ABIN-1, ABIN-2, optineurin
        and p62 were also identified
- id: PMID:19494296
  title: A20 negatively regulates T cell receptor signaling to NF-kappaB by cleaving
    Malt1 ubiquitin chains.
  findings:
    - statement: A20 deubiquitinates K63-polyubiquitin chains on MALT1 during TCR signaling
      supporting_text: >-
        A20 regulates the strength and duration of the IKK/NF-kappaB response
        upon TCR/CD28 costimulation. By catalyzing the removal of K63-linked ubiquitin
        chains from Malt1, A20 prevents sustained interaction between ubiquitinated
        Malt1 and the IKK complex and thus serves as a negative regulator of inducible
        IKK activity.
- id: PMID:19912257
  title: A20 is an early responding negative regulator of Toll-like receptor 5 signalling
    in intestinal epithelial cells during inflammation.
  findings:
    - statement: A20 is induced by and responds to molecules of bacterial origin
      supporting_text: >-
        A20 is an early response negative regulator of TLR-5 signalling in IECs that
        functions during intestinal inflammation.
- id: PMID:20392859
  title: The A20 deubiquitinase activity negatively regulates LMP1 activation of IRF7.
  findings:
    - statement: Review documenting A20 DUB activity and role in ubiquitin editing
      supporting_text: >-
        A20 negatively regulates IRF7 transcriptional activity induced by LMP1.
        Deletion or mutation of A20 C-terminal zinc finger motifs had no effect on the
        inhibition of IRF7 activity, whereas DUB-deficient truncation or point mutation
        ablated the ability of A20 to inhibit IRF7.
- id: PMID:20458337
  title: MHC class II-associated proteins in B-cell exosomes and potential functional
    implications for exosome biogenesis.
  findings: []
- id: PMID:20936779
  title: A human MAP kinase interactome.
  findings: []
- id: PMID:21095585
  title: "Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling."
  findings:
    - statement: Crystal structure of ZnF4-ubiquitin complex; ZnF4 ubiquitin binding required for NF-kB modulation
      supporting_text: >-
        A20 zinc finger 4 (ZnF4) does not directly interact with E2 enzymes but instead
        can bind mono-Ub and K63-linked poly-Ub. Mutations to the A20 ZnF4 Ub-binding
        surface result in decreased A20-mediated ubiquitination and impaired regulation
        of NF-κB signaling.
- id: PMID:21127049
  title: Role of the A20-TRAF6 axis in lipopolysaccharide-mediated osteoclastogenesis.
  findings:
    - statement: A20 inhibits RANKL-induced NF-kB activation and osteoclast formation
      supporting_text: >-
        Silencing of A20 restored TRAF6 expression and
        NF-κB activation and resulted in increased bone resorption in LPS-treated
        cultures. A20 appeared important in the control of bone resorption and could
        represent a therapeutic target to treat patients with bone resorption associated
        with inflammatory diseases.
- id: PMID:21220427
  title: Endotoxin tolerance impairs IL-1 receptor-associated kinase (IRAK) 4 and TGF-beta-activated
    kinase 1 activation, K63-linked polyubiquitination and assembly of IRAK1, TNF receptor-associated
    factor 6, and IkappaB kinase gamma and increases A20 expression.
  findings:
    - statement: A20 is required for LPS tolerance induction in macrophages
      supporting_text: >-
        Deficiencies in these signaling events in LPS-tolerant cells coincided with
        increased expression of A20, an essential deubiquitination enzyme, and sustained
        A20-IRAK1 associations
- id: PMID:21988832
  title: Toward an understanding of the protein interaction network of the human liver.
  findings: []
- id: PMID:22099304
  title: Direct, noncatalytic mechanism of IKK inhibition by A20.
  findings:
    - statement: A20 ZnF7 binds polyubiquitin to inhibit IKK through a noncatalytic mechanism
- id: PMID:23032186
  title: "A20 inhibits LUBAC-mediated NF-κB activation by binding linear polyubiquitin
    chains via its zinc finger 7."
  findings:
    - statement: ZnF7 binds linear/M1-linked polyubiquitin chains to inhibit LUBAC-mediated NF-kB activation
- id: PMID:23827681
  title: OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin
    chain restriction analysis.
  findings:
    - statement: A20 OTU domain can cleave K11, K48, and K63 linked ubiquitin chains
- id: PMID:25416956
  title: A proteome-scale map of the human interactome network.
  findings: []
- id: PMID:25502805
  title: A massively parallel pipeline to clone DNA variants and examine molecular
    phenotypes of human disease mutations.
  findings: []
- id: PMID:26642243
  title: Loss-of-function mutations in TNFAIP3 leading to A20 haploinsufficiency cause
    an early-onset autoinflammatory disease.
  findings:
    - statement: Heterozygous loss-of-function TNFAIP3 variants cause HA20, an autoinflammatory disease
- id: PMID:27732584
  title: Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne.
  findings:
    - statement: Crystal structure of A20 OTU domain with catalytic activity characterization
- id: PMID:28094437
  title: The deubiquitinating enzyme, ubiquitin-specific peptidase 50, regulates inflammasome
    activation by targeting the ASC adaptor protein.
  findings:
    - statement: A20 mutations lead to increased IL-1beta production
- id: PMID:30561431
  title: "A protein-protein interaction map of the TNF-induced NF-κB signal transduction
    pathway."
  findings: []
- id: PMID:31015422
  title: Physical and functional interaction between A20 and ATG16L1-WD40 domain in
    the control of intestinal homeostasis.
  findings: []
- id: PMID:31515488
  title: Extensive disruption of protein interactions by genetic variants across the
    allele frequency spectrum in human populations.
  findings: []
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
- id: PMID:33961781
  title: Dual proteome-scale networks reveal cell-specific remodeling of the human
    interactome.
  findings: []
- id: PMID:36931259
  title: A central chaperone-like role for 14-3-3 proteins in human cells.
  findings: []
- id: Reactome:R-HSA-168638
  title: NOD1/2 Signaling Pathway
  findings: []
- id: Reactome:R-HSA-5357845
  title: K63polyUb-RIPK1 is deubiquitinated
  findings: []
- id: Reactome:R-HSA-5357905
  title: Regulation of TNFR1 signaling
  findings: []
- id: Reactome:R-HSA-5688426
  title: Deubiquitination
  findings: []
- id: Reactome:R-HSA-5690827
  title: TNFAIP3 (A20) ubiquitinates RIPK1
  findings: []
- id: Reactome:R-HSA-5690845
  title: TNIPs bind TNFAIP3 (A20)
  findings: []
- id: Reactome:R-HSA-5690856
  title: TNFAIP3 (A20) deubiquitinates K63polyUb-RIPK1
  findings: []
- id: Reactome:R-HSA-5690870
  title: OTUD7B,TNFAIP3 deubiquitinates TRAF6
  findings: []
- id: Reactome:R-HSA-5693055
  title: TAX1BP1:TNFAIP3(A20) binds RIPK1-containing complexes
  findings: []
- id: Reactome:R-HSA-5693108
  title: 'TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains '
  findings: []
- id: Reactome:R-HSA-688136
  title: TNFAIP3 (A20) deubiquitinates RIP2
  findings: []
- id: Reactome:R-HSA-8869506
  title: TNFAIP3 in OTUD7B:TNFAIP3:ZRANB1 deubiquitinates K63polyUb-TRAF6
  findings: []
- id: Reactome:R-HSA-937337
  title: TAX1BP1:A20 inhibit TBK1/IKKi K63-polyubiquitination
  findings: []

core_functions:
- molecular_function:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  description: >-
    A20 OTU domain (aa 92-263) is a cysteine-type deubiquitinase with catalytic triad
    Cys103/His256 that cleaves K63-, K48-, and K11-linked polyubiquitin chains. The primary
    in vivo substrates are K63-linked chains on RIPK1, TRAF6, NEMO/IKBKG, and MALT1 in
    the TNFR1, TLR, NOD1/2, and TCR signaling pathways.
  directly_involved_in:
    - id: GO:0070536
      label: protein K63-linked deubiquitination
    - id: GO:0043124
      label: negative regulation of canonical NF-kappaB signal transduction
  locations:
    - id: GO:0005829
      label: cytosol

- molecular_function:
    id: GO:0004842
    label: ubiquitin-protein transferase activity
  description: >-
    A20 ZnF4 domain (aa 601-636) mediates E3 ubiquitin ligase activity, adding K48-linked
    polyubiquitin chains to RIPK1 and other substrates, targeting them for proteasomal
    degradation. This complements the OTU deubiquitinase to form the ubiquitin-editing
    mechanism.
  directly_involved_in:
    - id: GO:0070936
      label: protein K48-linked ubiquitination
    - id: GO:0043124
      label: negative regulation of canonical NF-kappaB signal transduction
  locations:
    - id: GO:0005829
      label: cytosol

- molecular_function:
    id: GO:0061578
    label: K63-linked deubiquitinase activity
  description: >-
    A20 preferentially cleaves K63-linked polyubiquitin chains in vivo, targeting RIPK1
    in the TNFR1 complex and TRAF6 in TLR/NLR pathways. K63 chain removal terminates
    signaling scaffold assembly required for IKK activation.
  directly_involved_in:
    - id: GO:0043124
      label: negative regulation of canonical NF-kappaB signal transduction
  locations:
    - id: GO:0005829
      label: cytosol

- molecular_function:
    id: GO:0043130
    label: ubiquitin binding
  description: >-
    A20 zinc finger domains bind polyubiquitin non-catalytically. ZnF4 recognizes K63-linked
    chains for substrate targeting; ZnF7 binds linear (M1-linked) chains on NEMO to inhibit
    IKK activation through a noncatalytic mechanism.
  directly_involved_in:
    - id: GO:0043124
      label: negative regulation of canonical NF-kappaB signal transduction
  locations:
    - id: GO:0005829
      label: cytosol