id: Q6YYC5
gene_symbol: Q6YYC5
taxon:
  id: NCBITaxon:39947
  label: Oryza sativa subsp. japonica
status: COMPLETE
description: >-
  Q6YYC5 is an RGLG4-like RING-domain E3 ubiquitin ligase with support for generic
  protein ubiquitination. Its Lys63-linkage refinement is refuted as a paralog
  overannotation from the K63-demonstrated RGLG1/RGLG2 clade; Q6YYC5 instead clusters
  with the degradative RGLG3/RGLG4 clade.
source_documents:
  - genes/ORYSJ/Q6YYC5/Q6YYC5-uniprot.txt
  - genes/ORYSJ/Q6YYC5/Q6YYC5-goa.tsv
  - publications/PMID_22898498.md
  - publications/PMID_27497447.md
  - genes/ORYSJ/Q6YYC5/Q6YYC5-hypotheses/prediction-k63-linked-ubiquitination/openscientist.md
predictions:
  - source_method: ProtNLM2
    source_version: UniProt 2024_06 pilot
    predicted_term:
      id: GO:0070534
      label: protein K63-linked ubiquitination
    predicted_term_type: GO_BP
    review:
      assessment: PLI
      error_type: PARALOG_OVERANNOTATION
      confidence_score: 0
      summary: >-
        The target has a RING domain and an RGLG4 subfamily assignment. Arabidopsis RGLG3 and RGLG4 have
        experimentally demonstrated ubiquitin ligase activity (PMID:22898498), supporting general ubiquitination
        but not specifying a Lys63-linked chain for this rice protein. The focused report found that Q6YYC5
        clusters with RGLG4, in the RGLG3/RGLG4 degradative clade, rather than the RGLG1/RGLG2 clade
        tied to K63-linked ubiquitination. Chain linkage also depends on the cognate E2 and cannot be
        established by the RING domain alone. The linkage-specific process is absent from the cached
        annotations and appears to be a paralog overannotation from the K63-demonstrated RGLG1/RGLG2
        branch.
      supported_by:
        - reference_id: file:ORYSJ/Q6YYC5/Q6YYC5-uniprot.txt
          supporting_text: >-
            ID   Q6YYC5_ORYSJ            Unreviewed;       401 AA. ... DR   GO; GO:0005634; C:nucleus;
            IBA:GO_Central. ... DR   GO; GO:0004842; F:ubiquitin-protein transferase activity; IBA:GO_Central.
            ... DR   GO; GO:0016567; P:protein ubiquitination; IBA:GO_Central. ... DR   InterPro; IPR001841;
            Znf_RING. ... DR   PANTHER; PTHR45751:SF16; E3 UBIQUITIN-PROTEIN LIGASE RGLG4; 1. ... FT   DOMAIN          356..389
            ... FT                   /note="RING-type"
        - reference_id: PMID:22898498
          supporting_text: >-
            Both RGLG3 and RGLG4 possessed ubiquitin ligase activities
        - reference_id: PMID:27497447
          supporting_text: >-
            pinpoint UBC30 as a cognate E2 UBC capable of interacting with RGLG3 and RGLG4
            and mediating auto-ubiquitination of RGLG3 and ubiquitination of GRXS17 in
            vitro. Accordingly, GRXS17 is ubiquitinated and degraded in an RGLG3- and
            RGLG4-dependent manner in planta.
        - reference_id: file:ORYSJ/Q6YYC5/Q6YYC5-hypotheses/prediction-k63-linked-ubiquitination/openscientist.md
          supporting_text: >-
            the orthology used to justify it points to RGLG4, the degradative clade
            (F002, F004), not the K63-demonstrated RGLG1/2
  - source_method: ProtNLM2
    source_version: UniProt 2024_06 pilot
    predicted_term:
      id: GO:0061630
      label: ubiquitin protein ligase activity
    predicted_term_type: GO_MF
    review:
      assessment: COR
      confidence_score: 2
      summary: >-
        The target contains the RING domain and accompanying RGLG-family architecture, with a specific
        RGLG4 subfamily assignment. Ubiquitin ligase assays on Arabidopsis RGLG3/RGLG4 provide biological
        grounding for transfer of E3 activity (PMID:22898498). The target already has the broader curated
        IBA ubiquitin-protein transferase activity, but the exact E3 ligase term is absent from the cached
        annotations. The prediction is a supported refinement without a claim about substrate or ubiquitin-chain
        linkage.
      supported_by:
        - reference_id: file:ORYSJ/Q6YYC5/Q6YYC5-uniprot.txt
          supporting_text: >-
            ID   Q6YYC5_ORYSJ            Unreviewed;       401 AA. ... DR   GO; GO:0005634; C:nucleus;
            IBA:GO_Central. ... DR   GO; GO:0004842; F:ubiquitin-protein transferase activity; IBA:GO_Central.
            ... DR   GO; GO:0016567; P:protein ubiquitination; IBA:GO_Central. ... DR   InterPro; IPR001841;
            Znf_RING. ... DR   PANTHER; PTHR45751:SF16; E3 UBIQUITIN-PROTEIN LIGASE RGLG4; 1. ... FT   DOMAIN          356..389
            ... FT                   /note="RING-type"
        - reference_id: PMID:22898498
          supporting_text: >-
            Both RGLG3 and RGLG4 possessed ubiquitin ligase activities
references:
  - id: file:ORYSJ/Q6YYC5/Q6YYC5-uniprot.txt
    title: Q6YYC5-uniprot.txt
  - id: PMID:22898498
    title: Two novel RING-type ubiquitin ligases, RGLG3 and RGLG4, are essential for
      jasmonate-mediated responses in Arabidopsis.
  - id: PMID:27497447
    title: The Arabidopsis Iron-Sulfur Protein GRXS17 is a Target of the Ubiquitin
      E3 Ligases RGLG3 and RGLG4.
  - id: file:ORYSJ/Q6YYC5/Q6YYC5-hypotheses/prediction-k63-linked-ubiquitination/openscientist.md
    title: 'OpenScientist focused report: Q6YYC5 K63-linked ubiquitination'