id: Q6YYC5 gene_symbol: Q6YYC5 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:39947 label: Oryza sativa Japonica Group description: >- Os08g0135400 (UniProt Q6YYC5; RAP locus Os08g0135400) encodes a 401-residue rice member of the RGLG (RING domain ligase) family of plant RING-type E3 ubiquitin-protein ligases. The protein has the RGLG architecture: a central copine-type von Willebrand factor A (vWA) domain (Pfam Copine PF07002, SMART VWA) and a C-terminal RING finger (residues 356-389) whose cysteine/histidine positions are conserved with the Arabidopsis RGLGs. It lacks the C2 domains of true copines, so the copine signature reflects the shared vWA module rather than a calcium-dependent phospholipid-binding unit. PANTHER places it in subfamily PTHR45751:SF16 together with Arabidopsis RGLG4 (Q9SAL0), its ortholog, which is the same length. AtRGLG4 and its near paralog RGLG3 have ubiquitin ligase activity in vitro, work with the E2 UBC30 to ubiquitinate the glutaredoxin GRXS17 and promote its degradation in planta, are found in both cytoplasm and nucleus, and act as positive regulators of jasmonate signalling. By inheritance from that clade, Q6YYC5 is expected to be a cytoplasmic and nuclear RING E3 ligase that ubiquitinates specific substrates; no experiment has yet tested the rice protein directly, and its substrates and physiological role are unknown. references: - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PAINT/IBA pipeline. All three IBA rows descend from PANTHER node PTN002247669 (taxon Eukaryota), seeded by AT1G79380 (RGLG4), AT3G01650 (RGLG1), AT5G14420 (RGLG2) and AT5G63970 (RGLG3) for ligase activity and nucleus, and by AT3G01650 alone for protein ubiquitination (interpro/panther/PTHR45751/PTHR45751-paint.tsv). The curators did not propagate the plasma membrane IDA of RGLG1/RGLG2 or the K63-linked ubiquitination IDA of RGLG1, which is read as a deliberate restriction. (Corrected from the previous version of this review, which mislabelled AT1G79380 as RGLG1.) - id: GO_REF:0000107 title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- EnsemblPlants Compara transfer from UniProtKB:Q9SAL0 / AT1G79380, which is Arabidopsis RGLG4 (not RGLG1, as the previous version of this review stated). The donor annotations are the IDA ligase activity (PMID:22898498) and the IDA nucleus and cytoplasm localizations (PMID:25788731). - id: PMID:22898498 title: "Two novel RING-type ubiquitin ligases, RGLG3 and RGLG4, are essential for jasmonate-mediated responses in Arabidopsis." findings: - statement: >- AtRGLG3 and AtRGLG4 both have ubiquitin ligase activity and positively regulate jasmonate-mediated responses in Arabidopsis. supporting_text: "Both RGLG3 and RGLG4 possessed ubiquitin ligase activities" reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Abstract-only cache. Source of the IDA GO:0004842 annotation on AtRGLG4 (Q9SAL0), the SF16 ortholog of Q6YYC5. The jasmonate phenotypes are loss-of-function phenotypes and are not transferred. - id: PMID:27497447 title: "The Arabidopsis Iron-Sulfur Protein GRXS17 is a Target of the Ubiquitin E3 Ligases RGLG3 and RGLG4." findings: - statement: >- GRXS17 is a substrate of AtRGLG3/RGLG4; UBC30 is a cognate E2. In vitro, auto-ubiquitination was shown for RGLG3 and GRXS17 ubiquitination with UBC30; GRXS17 degradation in planta depends on RGLG3 and RGLG4. supporting_text: "GRXS17 is ubiquitinated and degraded in an RGLG3- and RGLG4-dependent manner in planta" reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Abstract-only cache. The abstract states auto-ubiquitination for RGLG3; the earlier version of this review attributed in vitro auto-ubiquitination to RGLG4, which the abstract does not state. - id: PMID:25788731 title: Hijacking of the jasmonate pathway by the mycotoxin fumonisin B1 (FB1) to initiate programmed cell death in Arabidopsis is modulated by RGLG3 and RGLG4. findings: - statement: >- GFP-RGLG4 and FLAG-RGLG4 are found in both cytoplasm and nucleus by confocal imaging and cell fractionation. supporting_text: "Confocal images showed that GFP-RGLG3 and GFP-RGLG4 were present in both the cytoplasm and nucleus" reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Full text cached. Source of the IDA nucleus and cytoplasm annotations on AtRGLG4 (Q9SAL0) that EnsemblPlants transferred to Q6YYC5. The authors note the GFP pattern resembles free GFP, and the N-terminal tag means N-terminal lipidation could not be assessed; fractionation of FLAG-RGLG4 independently supports both compartments. - id: PMID:37177781 title: "The E3 ubiquitin ligase OsRGLG5 targeted by the Magnaporthe oryzae effector AvrPi9 confers basal resistance against rice blast." findings: - statement: >- Confirmed E3 ligase activity for rice RGLG family member OsRGLG5. reference_review: relevance: LOW correctness: VERIFIED review_notes: >- OsRGLG5 is a rice paralog in a different subfamily lineage from SF16; it shows the family is enzymatically active in rice but is not used to transfer subfamily-specific functions (immunity) to Q6YYC5. - id: file:ORYSJ/Q6YYC5/Q6YYC5-hypotheses/core-function-1-go-0061630/openscientist.md title: OpenScientist hypothesis investigation - E3 ubiquitin ligase activity as core function findings: - statement: >- GO:0061630 strongly supported. Recommend upgrading from GO:0004842 (parent E2+E3 term) to GO:0061630 (E3-specific term). Multiple IDA-level demonstrations in closest ortholog AtRGLG4 and family-wide conservation. - statement: >- Q6YYC5 has a myristoylation-compatible N-terminus (MG motif) suggesting possible plasma membrane association, qualifying CC annotations but not core MF. reference_review: relevance: LOW correctness: DISPUTED review_notes: >- Retained from the earlier review but not used as support in the re-review. The myristoylation claim does not hold: Q6YYC5 has Gly at position 6, not the Ser/Thr of the N-myristoylation consensus seen in AtRGLG1/2 (file:ORYSJ/Q6YYC5/Q6YYC5-bioinformatics/RESULTS-rereview.md). - id: file:ORYSJ/Q6YYC5/Q6YYC5-deep-research-falcon.md title: Deep research report for Q6YYC5 Os08g0135400 RGLG family E3 ligase reference_review: relevance: MEDIUM correctness: LOW_QUALITY review_notes: >- Useful literature survey of rice and Arabidopsis RGLGs; confirms no direct study of Q6YYC5. Its suggestion that the copine annotation implies calcium-dependent membrane binding is not supported, since Q6YYC5 lacks C2 domains. - id: file:ORYSJ/Q6YYC5/Q6YYC5-bioinformatics/RESULTS-rereview.md title: Q6YYC5 re-review sequence comparison with Arabidopsis RGLG1-5 reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Reproducible script output: RING C/H conservation, N-terminal motif check, pairwise identities. existing_annotations: - term: id: GO:0004842 label: ubiquitin-protein transferase activity evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables review: summary: >- PAINT placed ubiquitin-protein transferase activity at PTN002247669, the RGLG-containing node of PTHR45751, from IDA evidence on Arabidopsis RGLG1-4. Q6YYC5 lies in SF16 with AtRGLG4, inside that clade, and retains the RING domain with its zinc-ligand positions. The function is sound; the term, which also covers E2 conjugating enzymes, is less specific than the E3 activity that a RING protein performs. action: MODIFY reason: >- Correct but general. A RING-domain RGLG ligase transfers ubiquitin as an E3, so the specific child GO:0061630 ubiquitin protein ligase activity is supported (AtRGLG1 in this clade carries GO:0061630 by IDA; AtRGLG3/4 have ligase activity by IDA). No change of meaning, only refinement. propagation_review: root_cause: NO_FAILURE_CORE failure_modes: - GRANULARITY_MISMATCH source_entities: - source_id: PANTHER:PTN002247669 source_label: RGLG clade node of PTHR45751 source_status: SUPPORTS_TRANSFER comment: Q6YYC5 (SF16) descends from this node; RING retained. - source_id: UniProtKB:Q9SAL0 source_label: AtRGLG4 source_status: SUPPORTS_TRANSFER comment: SF16 ortholog; IDA ligase activity (PMID:22898498). proposed_replacement_terms: - id: GO:0061630 label: ubiquitin protein ligase activity supported_by: - reference_id: PMID:22898498 supporting_text: "Both RGLG3 and RGLG4 possessed ubiquitin ligase activities" - reference_id: file:ORYSJ/Q6YYC5/Q6YYC5-uniprot.txt record_section: ["DR:InterPro"] supporting_text: "DR InterPro; IPR001841; Znf_RING." - term: id: GO:0005634 label: nucleus evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in review: summary: >- Nuclear localization was placed at PTN002247669 from Arabidopsis RGLG1-4, including the AtRGLG4 IDA (GFP imaging and nuclear fractionation). Q6YYC5 is within the clade and nothing in its sequence argues for loss of nuclear access (no transmembrane segment or signal peptide is annotated). action: ACCEPT reason: >- Inherited from an experimentally grounded PAINT node that includes the SF16 ortholog AtRGLG4. Nucleus is one of the two compartments where the ortholog is found. supported_by: - reference_id: PMID:25788731 supporting_text: "Confocal images showed that GFP-RGLG3 and GFP-RGLG4 were present in both the cytoplasm and nucleus" - term: id: GO:0016567 label: protein ubiquitination evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: >- Protein ubiquitination is the process a RING E3 ligase directly executes. The PAINT node was seeded by AtRGLG1; the SF16 ortholog AtRGLG4 ubiquitinates GRXS17 and drives its degradation in planta. Q6YYC5 performs the step itself, so this is participation, not mere requirement. action: ACCEPT reason: >- Direct consequence of the E3 activity, inherited from a node grounded in Arabidopsis experiments and consistent with the ortholog's substrate ubiquitination. Specific substrates for the rice protein are unknown, so the general process term is as precise as the evidence permits. supported_by: - reference_id: PMID:27497447 supporting_text: "GRXS17 is ubiquitinated and degraded in an RGLG3- and RGLG4-dependent manner in planta" - term: id: GO:0004842 label: ubiquitin-protein transferase activity evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: enables review: summary: >- Ensembl Compara transfer from AtRGLG4 (Q9SAL0, AT1G79380), whose ligase activity was shown by IDA. The orthology is consistent with the PANTHER SF16 placement shared by both proteins. Same claim as the IBA row. action: MODIFY reason: >- Same as the IBA row: correct but general; refine to GO:0061630 ubiquitin protein ligase activity, the E3 activity of a RING ligase. proposed_replacement_terms: - id: GO:0061630 label: ubiquitin protein ligase activity supported_by: - reference_id: PMID:22898498 supporting_text: "Both RGLG3 and RGLG4 possessed ubiquitin ligase activities" - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: located_in review: summary: >- Ensembl Compara transfer of the AtRGLG4 IDA nucleus annotation from the SF16 ortholog. Same claim as the IBA nucleus row. action: ACCEPT reason: >- Ortholog localization by imaging and fractionation; consistent with the PAINT node assertion. supported_by: - reference_id: PMID:25788731 supporting_text: "FLAG-RGLG3 and FLAG-RGLG4 were detected in both fractions" - term: id: GO:0005737 label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: located_in review: summary: >- Ensembl Compara transfer of the AtRGLG4 IDA cytoplasm annotation. AtRGLG4 is found in the cytoplasm and nucleus in protoplasts and in fractionated transgenic plants; its substrate GRXS17 is a cytosolic/nuclear glutaredoxin. action: ACCEPT reason: >- Supported by direct ortholog localization within the same PANTHER subfamily. The earlier claim, based on the N-terminus, that Q6YYC5 may instead be plasma-membrane anchored by myristoylation is not supported (residue 6 is Gly). supported_by: - reference_id: PMID:25788731 supporting_text: "Confocal images showed that GFP-RGLG3 and GFP-RGLG4 were present in both the cytoplasm and nucleus" - reference_id: file:ORYSJ/Q6YYC5/Q6YYC5-bioinformatics/RESULTS-rereview.md supporting_text: "The N-terminus therefore does not match" core_functions: - description: >- RING-type E3 ubiquitin-protein ligase of the RGLG4 subfamily (PTHR45751:SF16). The C-terminal RING finger, with its zinc-ligand cysteine/histidine positions conserved, is expected to recruit a ubiquitin-charged E2 and transfer ubiquitin to substrates bound through the vWA domain. This is inferred from the SF16 ortholog AtRGLG4, which has ligase activity and with UBC30 ubiquitinates GRXS17 for degradation, and from the PAINT node covering the Arabidopsis RGLGs. The ortholog acts in cytoplasm and nucleus. Rice substrates are unknown. molecular_function: id: GO:0061630 label: ubiquitin protein ligase activity directly_involved_in: - id: GO:0016567 label: protein ubiquitination locations: - id: GO:0005737 label: cytoplasm - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:22898498 supporting_text: "Both RGLG3 and RGLG4 possessed ubiquitin ligase activities" - reference_id: PMID:27497447 supporting_text: "GRXS17 is ubiquitinated and degraded in an RGLG3- and RGLG4-dependent manner in planta" - reference_id: PMID:25788731 supporting_text: "Confocal images showed that GFP-RGLG3 and GFP-RGLG4 were present in both the cytoplasm and nucleus" - reference_id: file:ORYSJ/Q6YYC5/Q6YYC5-uniprot.txt record_section: ["DR:PANTHER"] supporting_text: "DR PANTHER; PTHR45751:SF16; E3 UBIQUITIN-PROTEIN LIGASE RGLG4; 1." suggested_questions: - question: >- What are the ubiquitination substrates of Os08g0135400/Q6YYC5 in rice? Is the rice ortholog of GRXS17 a substrate, as it is for AtRGLG3/4? - question: >- Which rice E2 enzymes partner with Q6YYC5 (for example the rice UBC30 orthologs), and what chain linkage does the pair build? Linkage type is set by the E2/E3 pair and cannot be inferred from the RING domain alone. - question: >- Does Q6YYC5 contribute to jasmonate signalling in rice as AtRGLG3/4 do in Arabidopsis? This is a phenotype question and would not on its own establish participation in a GO process. suggested_experiments: - hypothesis: >- Q6YYC5 has RING-dependent E3 ubiquitin ligase activity in vitro. description: >- Purify recombinant Q6YYC5 and a RING-dead mutant (zinc-ligand Cys to Ser) and run in vitro ubiquitination with E1, a panel of rice E2s including UBC30 orthologs, ubiquitin and ATP. Score auto-ubiquitination and ubiquitination of candidate substrates such as rice GRXS17. experiment_type: biochemical assay - hypothesis: >- Q6YYC5 localizes to cytoplasm and nucleus in rice cells. description: >- Express C-terminally tagged Q6YYC5 (which leaves the N-terminus free) in rice protoplasts or stable lines and image with nuclear and cytoplasmic markers; confirm by subcellular fractionation. experiment_type: subcellular localization