Q6YYC5

UniProt ID: Q6YYC5
Organism: Oryza sativa Japonica Group
Review Status: COMPLETE
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Gene 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.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004842 ubiquitin-protein transferase activity
IBA
GO_REF:0000033 		MODIFY
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.
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
Sources checked:
PANTHER:PTN002247669 · RGLG clade node of PTHR45751 SUPPORTS TRANSFER
Q6YYC5 (SF16) descends from this node; RING retained.
UniProtKB:Q9SAL0 · AtRGLG4 SUPPORTS TRANSFER
SF16 ortholog; IDA ligase activity (PMID:22898498).
Supporting Evidence:
PMID:22898498
Both RGLG3 and RGLG4 possessed ubiquitin ligase activities
file:ORYSJ/Q6YYC5/Q6YYC5-uniprot.txt
DR InterPro; IPR001841; Znf_RING.
GO:0005634 nucleus
IBA
GO_REF:0000033 		ACCEPT
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).
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.
Supporting Evidence:
PMID:25788731
Confocal images showed that GFP-RGLG3 and GFP-RGLG4 were present in both the cytoplasm and nucleus
GO:0016567 protein ubiquitination
IBA
GO_REF:0000033 		ACCEPT
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.
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.
Supporting Evidence:
PMID:27497447
GRXS17 is ubiquitinated and degraded in an RGLG3- and RGLG4-dependent manner in planta
GO:0004842 ubiquitin-protein transferase activity
IEA
GO_REF:0000107 		MODIFY
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.
Reason: Same as the IBA row: correct but general; refine to GO:0061630 ubiquitin protein ligase activity, the E3 activity of a RING ligase.
Supporting Evidence:
PMID:22898498
Both RGLG3 and RGLG4 possessed ubiquitin ligase activities
GO:0005634 nucleus
IEA
GO_REF:0000107 		ACCEPT
Summary: Ensembl Compara transfer of the AtRGLG4 IDA nucleus annotation from the SF16 ortholog. Same claim as the IBA nucleus row.
Reason: Ortholog localization by imaging and fractionation; consistent with the PAINT node assertion.
Supporting Evidence:
PMID:25788731
FLAG-RGLG3 and FLAG-RGLG4 were detected in both fractions
GO:0005737 cytoplasm
IEA
GO_REF:0000107 		ACCEPT
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.
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).
Supporting Evidence:
PMID:25788731
Confocal images showed that GFP-RGLG3 and GFP-RGLG4 were present in both the cytoplasm and nucleus
file:ORYSJ/Q6YYC5/Q6YYC5-bioinformatics/RESULTS-rereview.md
The N-terminus therefore does not match

Core Functions

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:
ubiquitin protein ligase activity
Directly Involved In:
protein ubiquitination
Cellular Locations:
cytoplasm nucleus
Supporting Evidence:
  • PMID:22898498
    Both RGLG3 and RGLG4 possessed ubiquitin ligase activities
  • PMID:27497447
    GRXS17 is ubiquitinated and degraded in an RGLG3- and RGLG4-dependent manner in planta
  • PMID:25788731
    Confocal images showed that GFP-RGLG3 and GFP-RGLG4 were present in both the cytoplasm and nucleus
  • file:ORYSJ/Q6YYC5/Q6YYC5-uniprot.txt
    DR PANTHER; PTHR45751:SF16; E3 UBIQUITIN-PROTEIN LIGASE RGLG4; 1.

References

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Suggested Questions for Experts

Q: What are the ubiquitination substrates of Os08g0135400/Q6YYC5 in rice? Is the rice ortholog of GRXS17 a substrate, as it is for AtRGLG3/4?

Q: 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.

Q: 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

Experiment: 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.

Hypothesis: Q6YYC5 has RING-dependent E3 ubiquitin ligase activity in vitro.

Type: biochemical assay

Experiment: 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.

Hypothesis: Q6YYC5 localizes to cytoplasm and nucleus in rice cells.

Type: subcellular localization

External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

ProtNLM2 External predictions

View prediction review YAML · Q6YYC5-protnlm-predictions-review.yaml · Review status: COMPLETE

Q6YYC5 (Os08g0135400) is a rice RGLG-family RING-type E3 ubiquitin ligase in PANTHER subfamily PTHR45751:SF16 with its Arabidopsis ortholog RGLG4. The ProtNLM2 prediction of ubiquitin protein ligase activity is a correct refinement of the gene's broader ubiquitin-protein transferase activity annotation, supported by transfer from the experimentally active RGLG3/RGLG4 clade. The Lys63-linkage-specific process prediction is uncertain: K63 chain formation has been shown only for the RGLG1/RGLG2 branch, chain linkage is set by the E2/E3 pair rather than the RING domain, and no linkage assay exists for Q6YYC5 or for the RGLG3/RGLG4 clade.

Source documents: genes/ORYSJ/Q6YYC5/Q6YYC5-uniprot.txt · genes/ORYSJ/Q6YYC5/Q6YYC5-goa.tsv · genes/ORYSJ/Q6YYC5/Q6YYC5-ai-review.yaml · genes/ARATH/RGLG4/RGLG4-ai-review.yaml · interpro/panther/PTHR45751/PTHR45751-review.yaml · publications/PMID_22898498.md · publications/PMID_27497447.md · publications/PMID_17586653.md · publications/PMID_22095047.md · genes/ORYSJ/Q6YYC5/Q6YYC5-hypotheses/prediction-k63-linked-ubiquitination/openscientist.md

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0070534 protein K63-linked ubiquitination GO_BP
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: Q6YYC5 carries a RING domain and the RGLG4 subfamily assignment, so generic protein ubiquitination is supported, and the gene already carries GO:0016567 by IBA. The linkage-specific refinement has no direct support. Lys63-linked chain formation in vitro was shown for Arabidopsis RGLG2 (PMID:17586653), in the RGLG1/RGLG2 branch, whereas Q6YYC5 is sister to RGLG4 by PANTHER placement and by the OpenScientist identity and neighbor-joining analysis. The RGLG3/RGLG4 clade has ligase activity and drives GRXS17 degradation with the E2 UBC30 (PMID:27497447), but no linkage assay exists for it. Degradative outcomes do not separate the branches, because RGLG1/RGLG2 also mediate proteasomal degradation of AtERF53 (PMID:22095047). Lys63 chain formation requires a Ubc13-type E2 heterodimer, so the RING domain alone cannot settle linkage. The PANTHER family review scores this term as unresolved and the gene review leaves linkage as an open question. The prediction is neither supported nor refuted; a linkage assay with the rice cognate E2 would be needed.
Supporting Evidence:
  • file:ORYSJ/Q6YYC5/Q6YYC5-uniprot.txt: "DR InterPro; IPR001841; Znf_RING. ... DR PANTHER; PTHR45751:SF16; E3 UBIQUITIN-PROTEIN LIGASE RGLG4; 1. ... FT DOMAIN 356..389 ... FT /note="RING-type""
  • PMID:17586653: "It can form Lys-63–linked multiubiquitin chains in an in vitro reaction."
  • PMID:17586653: "The formation of Lys-63–linked chains requires a heterodimeric E2 enzyme, formed by canonical E2 Ubc13 and another UBC fold protein"
  • PMID:27497447: "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."
  • PMID:22095047: "RGLG2 and its closest sequelog, RGLG1, were shown to have E3 ligase activity and mediated AtERF53 ubiquitination for proteasome degradation."
  • file:ORYSJ/Q6YYC5/Q6YYC5-hypotheses/prediction-k63-linked-ubiquitination/openscientist.md: "the orthology used to justify it points to RGLG4, the degradative clade (F002, F004), not the K63-demonstrated RGLG1/2"
GO:0061630 ubiquitin protein ligase activity GO_MF
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: Q6YYC5 has the RGLG architecture with a C-terminal RING-type domain (residues 356-389) and is placed in PANTHER subfamily PTHR45751:SF16 with Arabidopsis RGLG4. RGLG3 and RGLG4 have experimentally demonstrated ubiquitin ligase activity (PMID:22898498), and RGLG4 with UBC30 promotes ubiquitination and degradation of GRXS17 (PMID:27497447), which justifies transfer of E3 activity within the subfamily as an inference rather than an observation on the rice protein. GOA carries only the parent term GO:0004842 ubiquitin-protein transferase activity (IBA and IEA), which GO:0061630 is_a; the gene review refines both rows to GO:0061630 and makes it the core molecular function. The prediction is therefore correct and more specific than the existing annotation, without any claim about substrate or chain linkage.
Supporting Evidence:
  • file:ORYSJ/Q6YYC5/Q6YYC5-uniprot.txt: "DR InterPro; IPR001841; Znf_RING. ... DR PANTHER; PTHR45751:SF16; E3 UBIQUITIN-PROTEIN LIGASE RGLG4; 1. ... FT DOMAIN 356..389 ... FT /note="RING-type""
  • PMID:22898498: "Both RGLG3 and RGLG4 possessed ubiquitin ligase activities"
  • PMID:27497447: "GRXS17 is ubiquitinated and degraded in an RGLG3- and RGLG4-dependent manner in planta"

Deep Research

Falcon

(Q6YYC5-deep-research-falcon.md)

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OpenScientist

(Q6YYC5-hypotheses/core-function-1-go-0061630/openscientist.md)

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OpenScientist

(Q6YYC5-hypotheses/prediction-k63-linked-ubiquitination/openscientist.md)

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📚 Additional Documentation

Notes

(Q6YYC5-notes.md)

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📄 View Raw YAML

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