# PN dossier: OTUD3

- review_batch: proteostasis-batch-2026-06-07c
- review_yaml: genes/human/OTUD3/OTUD3-ai-review.yaml
- PN workbook rows: 3

## PN row 1: Translation | Cytosolic translation | Ribosome-associated QC | Deubiquitination
- UniProt: Q5T2D3
- In branches: TR, UPS
- PN-node mapping records (path + ancestors):
    - [type] Translation|Cytosolic translation|Ribosome-associated QC|Deubiquitination
        status=mapped scope=ok_for_propagation_to_go GO=[GO:0101005 deubiquitinase activity]
        rationale: This PN RQC type denotes deubiquitinases acting in ribosome-associated quality control. Deubiquitinase activity is the shared molecular-function target.
    - [group] Translation|Cytosolic translation|Ribosome-associated QC
        status=mapped scope=ok_for_propagation_to_go GO=[GO:0006515 protein quality control for misfolded or incompletely synthesized proteins]
        rationale: The PN ribosome-associated quality-control group covers surveillance and disposal of stalled or defective nascent-chain translation products. GO lacks a dedicated ribosome-associated QC term in the local cache, so the broader protein-quality-control process is the best supported target.
    - [class] Translation|Cytosolic translation
        status=context_only scope=too_broad_to_propagate GO=[GO:0002181 cytoplasmic translation]
        rationale: The PN class Cytosolic translation is centered on the cytoplasmic translation apparatus and process, but it also houses supporting machinery such as ribosome biogenesis factors. The GO process term is a useful high-level label for the class, but propagating it to all members would over-annotate genes whose PN placement is through assembly or maturation context rather than core cytoplasmic translation.
    - [branch] Translation
        status=context_only scope=too_broad_to_propagate GO=[GO:0006412 translation]
        rationale: The PN Translation branch is organized around the translation apparatus and immediately associated cotranslational quality-control systems. GO translation is the closest high-level process label, but the PN branch also contains adjacent machinery such as ribosome biogenesis and nascent-chain handling. Keeping this relationship is useful for interpretation, but it is too broad to project safely onto every member.

## PN row 2: Ubiquitin Proteasome System | DUBs and UBL demodifiers | OTU | other
- UniProt: Q5T2D3
- In branches: TR, UPS
- Signature domains: IPR003323
- Auxiliary domains: (none)
- PN references (titles):
    - 23827681
- PN-node mapping records (path + ancestors):
    - [type] Ubiquitin Proteasome System|DUBs and UBL demodifiers|OTU|other
        status=no_mapping scope= GO=[]
        rationale: Reviewed as an OTU-family subtype. Because the family branch includes inactive or ambiguous OTU-like cases, no automatic DUB propagation is made from this subtype.
    - [group] Ubiquitin Proteasome System|DUBs and UBL demodifiers|OTU
        status=context_only scope=too_broad_to_propagate GO=[GO:0101005 deubiquitinase activity]
        rationale: This OTU-family group is DUB-related context, but the subtree includes inactive or ambiguous OTU-like cases. Direct DUB propagation should come from narrower gene-level review rather than this whole family bucket.
    - [class] Ubiquitin Proteasome System|DUBs and UBL demodifiers
        status=no_mapping scope= GO=[]
        rationale: Reviewed as a UPS taxonomy container. Its descendants mix catalytic roles, complex membership, binding domains, regulators, adaptors, and substrate-context labels, so a single propagating GO assertion would overstate the shared biology.
    - [branch] Ubiquitin Proteasome System
        status=no_mapping scope= GO=[]
        rationale: Reviewed as the top-level UPS branch. It is a project taxonomy umbrella rather than a direct GO assertion; UPS propagation must come from manually curated child nodes.

## PN row 3: Ubiquitin Proteasome System | Ubiquitin and UBL binding | DUB | OTU | UBA-like (other)
- UniProt: Q5T2D3
- In branches: TR, UPS
- Signature domains: PMID: 23827681 (likely @ 228-276)
- Auxiliary domains: IPR003323
- PN references (titles):
    - 23827681
- PN-node mapping records (path + ancestors):
    - [subtype] Ubiquitin Proteasome System|Ubiquitin and UBL binding|DUB|OTU|UBA-like (other)
        status=no_mapping scope= GO=[]
        rationale: Reviewed as a narrower UBL-binding DUB-domain subdivision. Because this subtree includes noncatalytic or pseudo-DUB cases, active DUB propagation is handled by the DUB-family branch rather than this binding-domain node.
    - [type] Ubiquitin Proteasome System|Ubiquitin and UBL binding|DUB|OTU
        status=no_mapping scope= GO=[]
        rationale: Reviewed as a narrower UBL-binding DUB-domain subdivision. Because this subtree includes noncatalytic or pseudo-DUB cases, active DUB propagation is handled by the DUB-family branch rather than this binding-domain node.
    - [group] Ubiquitin Proteasome System|Ubiquitin and UBL binding|DUB
        status=context_only scope=too_broad_to_propagate GO=[GO:0101005 deubiquitinase activity]
        rationale: This UBL-binding group is DUB-related context, but it includes noncatalytic or pseudo-DUB domain cases such as NPLOC4/USP39-like entries. Active DUB propagation is handled from the DUB-family branch.
    - [class] Ubiquitin Proteasome System|Ubiquitin and UBL binding
        status=context_only scope=too_broad_to_propagate GO=[GO:0140036 ubiquitin-modified protein reader activity]
        rationale: This class records ubiquitin/UBL-reader context, but the subtree mixes ubiquitin, SUMO, UBL-domain, domain-architecture, catalytic, signaling, trafficking, and nucleic-acid process buckets. It is useful context, not a safe direct propagation.
    - [branch] Ubiquitin Proteasome System
        status=no_mapping scope= GO=[]
        rationale: Reviewed as the top-level UPS branch. It is a project taxonomy umbrella rather than a direct GO assertion; UPS propagation must come from manually curated child nodes.

## Projected GO annotations (2)
- GO:0006515 protein quality control for misfolded or incompletely synthesized proteins | scope=ok_for_propagation_to_go | goa_status=new_to_goa | from=Translation|Cytosolic translation|Ribosome-associated QC
- GO:0101005 deubiquitinase activity | scope=ok_for_propagation_to_go | goa_status=entailed_by_goa_closure | from=Translation|Cytosolic translation|Ribosome-associated QC|Deubiquitination