Uch2 (SPBC409.06) is the fission-yeast member of the UCH37/UCHL5 branch of the peptidase C12 ubiquitin C-terminal hydrolases. The 300-residue protein has an N-terminal UCH catalytic domain with the conserved Gln-Cys-His-Asp catalytic residues and a C-terminal ULD extension that mediates its association with the 26S proteasome. Uch2 is the major deubiquitinating enzyme associated with the fission-yeast 26S proteasome, co-purifies the 19S and 20S particles, interacts with Rpn10 and localizes, like the proteasome, to the nucleus and predominantly the nuclear periphery. There it acts as a cysteine-type deubiquitinase that hydrolyses ubiquitin conjugates on proteasome-bound substrates, contributing to ubiquitin-dependent proteasomal degradation. uch2 is non-essential and deletion has no obvious effect on bulk ubiquitin-dependent proteolysis, consistent with redundancy among proteasomal deubiquitinases, although loss of uch2 partially suppresses a temperature-sensitive exocyst sec3 allele that is degraded by a proteasome-dependent quality-control pathway. Purified Uch2 also cleaves NEDD8-AMC in vitro, but deletion of uch2 does not alter cullin neddylation in vivo.
IDA PMID:23496905 Nedd8 processing enzymes in Schizosaccharomyces pombe.
MARK AS OVER ANNOTATED
Summary: The cited paper shows that purified GST-Uch2 cleaves the model substrate NEDD8-AMC, but deletion of uch2 (alone or with uch1) has no effect on cullin neddylation in vivo.
Reason: Protein deneddylation is removal of NEDD8 from a conjugated target protein. The paper (full text read) demonstrates only cleavage of the fluorogenic NEDD8-AMC amide in vitro, and explicitly reports that deleting uch2 and uch1 together does not change Cul1 neddylation. No Uch2-dependent deconjugation of a NEDD8-protein conjugate is shown, and the authors interpret Uch2 as at most a minor contributor of NEDD8 precursor-processing activity. The in vitro activity is captured on the molecular-function row; participation in the cellular deneddylation process is not supported.
While incubation with GST alone does not result in cleavage of Nedd8-AMC, GST-Uch1, GST-Uch2, GST-Nep1 and GST-Nep2 can all cleave Nedd8-AMC (n = 5, S.E.M. shown as error bars).
HDA PMID:20838651 A global census of fission yeast deubiquitinating enzyme loc...
ACCEPT
Summary: Tandem-affinity purification of Uch2 recovers all 19S and 20S proteasome subunits; independent studies identify Uch2 as a proteasome-associated subunit.
Reason: Uch2 co-purifies the complete 26S proteasome in stoichiometric amounts (PMID:20838651), was previously shown by glycerol-gradient and co-immunoprecipitation to associate with the 26S proteasome through its C-terminal extension (PMID:10872838), and is the major proteasome-associated DUB in fission yeast (PMID:15533439). This is the conserved UCH37/UCHL5 branch property (PANTHER PTHR10589:SF16).
Rpn11 and Uch2 co-purified all of the 26S proteasome subunits (19S regulatory particle and 20S core particle) in quantities similar to those of the bait (Table S1)
Rpn11 and Uch2 co-purified all of the 26S proteasome subunits (19S regulatory particle and 20S core particle) in quantities similar to those of the bait (Table S1)
file:SCHPO/uch2/uch2-uniprot.txt
Component of the 26S proteasome. Interacts with rpn10.
Summary: PAINT places cysteine-type deubiquitinase activity at the PTHR10589 root node (PTN000063280), seeded by UCHL1/3/5, BAP1, Yuh1 and Uch2 itself; Uch2 retains the catalytic triad.
Reason: The activity is ancestral to the whole UCH family and Uch2 sits inside that clade in the UCHL5 subfamily (PTHR10589:SF16). Its catalytic residues (Gln77, Cys83 nucleophile, His159, Asp174) are intact, and Uch2 is directly characterised as the major proteasomal DUB. Uch2 appearing among the seeds reflects its own experimental grounding, not circularity.
Summary: Domain-based inference (Peptidase C12 UCH, UCH37-type) agrees with the IBA and with direct Uch2 characterisation.
Reason: Same core claim as the IBA row; UCH domain and UCH37-subtype signatures plus an intact catalytic site support cysteine-type deubiquitinase activity.
IGI PMID:28765280 The exocyst subunit Sec3 is regulated by a protein quality c...
ACCEPT
Summary: PomBase genetic-interaction annotation from the Sec3 quality-control study, in which uch2 deletion suppresses sec3-913 temperature sensitivity.
Reason: The genetic interaction on its own does not demonstrate catalysis, but the claim (Uch2 is a cysteine-type DUB) is well established by family membership, intact catalytic residues and the biochemical proteasome studies, so this row is consistent with the other rows for the same term.
HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ...
ACCEPT
Summary: Genome-wide ORFeome GFP localisation places Uch2 in the nucleus, matching targeted studies.
Reason: Three independent studies (ORFeome screen, DUB census, and the original Uch2 characterisation) agree that Uch2 is nuclear with enrichment at the nuclear periphery, where fission-yeast proteasomes concentrate.
Summary: Cytoplasmic activity is placed at the PTHR10589 root node, seeded mostly by small UCHs (UCHL1, UCHL3) and mammalian UCHL5; target-specific imaging places Uch2 in the nucleus only.
Reason: The IBD is at the family root (PTN000063280), so it reflects an ancestral property largely contributed by the cytosolic small UCHs; no Schizosaccharomyces donor is among its seeds. For Uch2 itself, three independent localisation studies report nuclear and nuclear-periphery signal, and the targeted census states it is exclusively nuclear; its proteasome tethering via the C-terminal extension concentrates it with nuclear-envelope proteasomes, and C-terminally truncated protein becomes diffuse. A minor cytoplasmic proteasome-bound pool is not excluded, but the term overstates where Uch2 is known to act.
Propagation Review
Root cause:PROPAGATION BAD
Failure modes:COMPARTMENT OR COMPLEX MISMATCH
Sources checked:
PANTHER:PTN000063280SUPPORTS SOURCE BUT NOT TARGET
Family-root node of PTHR10589; cytoplasmic seeds are dominated by small UCHs (UCHL1/UCHL3) and mammalian UCHL5, whereas S. pombe Uch2 is reported exclusively nuclear.
The GFP-tagged Uch2p is localized predominantly to the nuclear periphery, which is similar to the 26S proteasome localization.
GO:0006511 ubiquitin-dependent protein catabolic process
IEA GO_REF:0000002
MODIFY
Summary: Correct but general; Uch2 acts within proteasome-mediated ubiquitin-dependent degradation.
Reason: As a ubiquitin-chain-processing subunit of the 26S proteasome, Uch2 participates in the proteasomal branch of ubiquitin-dependent catabolism. GO:0043161 is an is_a child of both this term and the already-annotated GO:0010498, so it is the precise term supported. Deletion viability reflects redundancy among proteasomal DUBs rather than absence of participation.
Rpn11 and Uch2 co-purified all of the 26S proteasome subunits (19S regulatory particle and 20S core particle) in quantities similar to those of the bait (Table S1)
NAS PMID:20838651 A global census of fission yeast deubiquitinating enzyme loc...
ACCEPT
Summary: ComplexPortal-derived process annotation for 26S proteasome components.
Reason: Uch2 is a proteasome-associated DUB that processes ubiquitin conjugates on proteasome-bound substrates; it does not degrade the substrate polypeptide itself, but its activity is part of the proteasomal degradation process. The more precise ubiquitin-dependent child GO:0043161 is proposed on the GO:0006511 row; this term remains a true parent.
Rpn11 and Uch2 co-purified all of the 26S proteasome subunits (19S regulatory particle and 20S core particle) in quantities similar to those of the bait (Table S1)
file:SCHPO/uch2/uch2-deep-research-falcon.md
Thus Uch2 should not be annotated as the protease that destroys the protein substrate itself.
Summary: UCH37-type domain inference; Uch2 removes ubiquitin from proteasome-bound conjugates.
Reason: Protein deubiquitination is the direct process outcome of the core cysteine-type DUB activity, supported by family membership and the major proteasomal DUB activity attributed to Uch2.
IDA PMID:23496905 Nedd8 processing enzymes in Schizosaccharomyces pombe.
KEEP AS NON CORE
Summary: Purified GST-Uch2 cleaves NEDD8-AMC in vitro, a standard assay for NEDD8 C-terminal hydrolase activity.
Reason: The in vitro activity is directly demonstrated (full text read) and NEDD8-AMC hydrolysis is the conventional assay used by curators for this activity, as Ub-AMC is for DUB activity; UCH-family enzymes are known to accept NEDD8 owing to its similarity to ubiquitin. However, the substrate is a model amide rather than a NEDD8-protein isopeptide conjugate, and uch2 deletion does not affect cullin neddylation in vivo. The activity is therefore retained as a real but peripheral biochemical property, not a core physiological function.
While incubation with GST alone does not result in cleavage of Nedd8-AMC, GST-Uch1, GST-Uch2, GST-Nep1 and GST-Nep2 can all cleave Nedd8-AMC (n = 5, S.E.M. shown as error bars).
The GFP-tagged Uch2p is localized predominantly to the nuclear periphery, which is similar to the 26S proteasome localization.
GO:0071629 cytoplasm protein quality control by the ubiquitin-proteasome system
IGI PMID:28765280 The exocyst subunit Sec3 is regulated by a protein quality c...
KEEP AS NON CORE
Summary: In the Sec3 quality-control study, uch2 deletion partially suppresses the temperature-sensitive growth defect of sec3-913, more weakly than ubp3 deletion.
Reason: The full text (PMC5602385, read online; the local cache is abstract-only) reports that both uch2 and ubp3 deletions suppress sec3-913 temperature sensitivity, the uch2 effect being weaker, and interprets the proteasome-associated DUBs Uch2 and Ubp3 as stimulating degradation of the misfolded Sec3 variant. This is genetic-suppression evidence for a contribution of Uch2, as a proteasome subunit, to proteasomal turnover of a cytosolic quality-control substrate. It is a specific substrate context of the core proteasomal function rather than a distinct role, and Uch2 itself is nuclear, so it is kept as non-core.
HDA PMID:20838651 A global census of fission yeast deubiquitinating enzyme loc...
MODIFY
Summary: Uch2 is a UCH-family cysteine protease, not a JAMM metalloprotease; the metal-dependent term likely reflects activity of the co-purified proteasome (Rpn11).
Reason: The census paper itself classifies UCH enzymes as cysteine proteases and JAMM enzymes (Rpn11) as metalloproteases. Uch2 has the C12 Cys-His catalytic site and no JAMM/MPN motif, and its pulldowns contain the whole proteasome including Rpn11, so a metal-dependent activity of the purified material cannot be attributed to Uch2. The supported molecular function is cysteine-type deubiquitinase activity.
Rpn11 and Uch2 co-purified all of the 26S proteasome subunits (19S regulatory particle and 20S core particle) in quantities similar to those of the bait (Table S1)
file:SCHPO/uch2/uch2-uniprot.txt
Belongs to the peptidase C12 family.
Core Functions
Proteasome-associated cysteine-type deubiquitinase that hydrolyses ubiquitin conjugates on proteasome-bound substrates during ubiquitin-dependent proteasomal degradation, tethered to the 26S proteasome at the nuclear periphery through its C-terminal extension.
Rpn11 and Uch2 co-purified all of the 26S proteasome subunits (19S regulatory particle and 20S core particle) in quantities similar to those of the bait (Table S1)
Q: Which physiological NEDD8-conjugated proteins, if any, are direct Uch2 substrates, as distinct from cleavage of NEDD8 precursors or NEDD8-AMC in vitro?
Q: Does fission-yeast Uch2 share the Lys48-branch-specific debranching activity reported for mammalian UCH37/UCHL5, and is it activated by S. pombe Rpn13 as UCH37 is?
Suggested Experiments
Experiment: Reconstitute purified wild-type and C83A Uch2 with S. pombe Rpn13 and test hydrolysis of unbranched and branched K48/K63 ubiquitin chains to establish linkage and branch specificity.
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.
The single ProtNLM2 prediction, ubiquitin-dependent protein catabolic process, is correct for this 26S proteasome-associated UCH37-family deubiquitinase but less precise than the supported proteasome-mediated and quality-control descendants of that term.
Review rationale: Fission-yeast Uch2 is directly characterized as the major deubiquitinating enzyme associated with the 26S proteasome, and proteomic work shows it co-purifies the complete proteasome. Processing ubiquitin conjugates at this complex is part of proteasome-mediated ubiquitin-dependent protein turnover, even though the DUB removes ubiquitin rather than degrading the substrate polypeptide itself. The predicted term is not novel; GOA already carries it (InterPro2GO), and the gene review treats it as correct but general, refining it to GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process. GOA also carries the descendant GO:0071629 cytoplasm protein quality control by the ubiquitin-proteasome system (IGI, kept as non-core), an is_a descendant of GO:0006511 per OLS4. The prediction is therefore correct but less precise than supported annotations; viable deletion phenotypes reflect redundancy among proteasomal DUBs and do not negate participation.
Supporting Evidence:
PMID:15533439: "We report that the subunit Uch2/Uch37 is the major deubiquitinating enzyme associated with the fission yeast 26S proteasome."
PMID:20838651: "Rpn11 and Uch2 co-purified all of the 26S proteasome subunits (19S regulatory particle and 20S core particle) in quantities similar to those of the bait (Table S1)"