SAN1 (Sir Antagonist 1) is a nuclear E3 ubiquitin-protein ligase with a central RING domain (residues 240-280) that plays a key role in nuclear protein quality control (PQC) in Saccharomyces cerevisiae. San1 directly recognizes misfolded nuclear proteins through intrinsically disordered N- and C-terminal domains containing conserved substrate-recognition sites, and ubiquitinates them for proteasomal degradation in conjunction with the E2 ubiquitin-conjugating enzymes Cdc34 and Ubc1 (PMID:15797381, PMID:21211726). San1 exhibits exquisite specificity for aberrant proteins and does not target wild-type versions of its substrates (PMID:15797381). Originally identified as a suppressor of SIR4 mutations, San1 targets mutant Sir4 and Spt16 for ubiquitin-mediated degradation (PMID:15078868). San1 also participates in cytoplasmic PQC alongside Ubr1, where misfolded cytoplasmic proteins can be delivered to nuclear San1 in a chaperone-dependent manner (PMID:20080635). San1 is primarily nuclear localized and requires nuclear localization for function (PMID:15797381). The protein is largely intrinsically disordered with a RING-type zinc finger as the only structured domain.
Definition: Recognition of misfolded protein conformation to initiate quality-control degradation. Distinct from chaperone activity in that the binding leads to ubiquitination and proteasomal degradation rather than refolding or prevention of aggregation.
Justification: E3 ubiquitin ligases like San1 (yeast) and SYVN1/HRD1 (human) directly recognize misfolded proteins, but their binding serves to target substrates for degradation rather than for chaperone-like protection. The existing terms GO:0031249 (denatured protein binding, being obsoleted) and GO:0051787 (misfolded protein binding) do not distinguish between binding for chaperoning vs. binding for degradation targeting. A new term would capture the specific molecular function of these quality control sensors.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006511 ubiquitin-dependent protein catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation from phylogenetic inference. San1 is a well-characterized E3 ubiquitin ligase that targets misfolded nuclear proteins for ubiquitin-dependent proteasomal degradation (PMID:15078868, PMID:15797381). This is a core biological process for SAN1. Reason: San1 directly promotes ubiquitin-dependent protein catabolism by ubiquitinating misfolded substrates for proteasomal degradation. This is the central downstream biological outcome of San1 activity. The IBA annotation is fully consistent with the extensive experimental evidence from IDA and IMP annotations for the same term. Supporting Evidence: PMID:15797381 San1p, a ubiquitin-protein ligase that, in conjunction with the ubiquitin-conjugating enzymes Cdc34p and Ubc1p, targets four distinct mutant nuclear proteins for ubiquitination and destruction by the proteasome PMID:15078868 mutant sir4 and spt16 proteins are unstable in SAN1 cells but are stabilized in san1Delta cells |
| GO:0061630 ubiquitin protein ligase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for ubiquitin protein ligase activity. San1 contains a RING domain and demonstrates E3 ubiquitin ligase activity both in vitro and in vivo (PMID:15078868, PMID:15797381). GO:0061630 is the preferred term for E3 ligases per GO E3 ligase annotation guidelines, and is more specific than GO:0004842. Reason: San1 is a RING-type E3 ubiquitin-protein ligase. This is the correct and preferred MF term for E3 ligases according to GO annotation guidelines. The IBA annotation is well supported by direct experimental evidence (IDA) for both GO:0004842 and GO:0061630. Supporting Evidence: PMID:15078868 We demonstrate that San1 possesses ubiquitin-protein isopeptide ligase activity in vitro, and the ubiquitin-protein isopeptide ligase activity of San1 is required for its function in vivo PMID:21211726 the yeast nuclear PQC ubiquitin ligase San1 directly recognizes its misfolded substrates via intrinsically disordered N- and C-terminal domains |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA annotation for cytoplasmic localization. While San1 is primarily a nuclear protein (PMID:15797381), it also participates in cytoplasmic protein quality control (PMID:20080635). Misfolded cytoplasmic proteins are delivered to nuclear San1 in a chaperone-dependent manner. The cytoplasmic localization may reflect the IBA being inferred from orthologs with broader localization. Reason: San1 is primarily nuclear and requires nuclear localization for function (PMID:15797381). However, San1 does participate in cytoplasmic PQC via chaperone-dependent delivery of cytoplasmic substrates (PMID:20080635). The cytoplasmic role is secondary to the primary nuclear PQC function. The IBA is consistent with the IMP annotation from PMID:20080635. Supporting Evidence: PMID:20080635 Ubr1 and San1 mediate chaperone-dependent ubiquitination of numerous misfolded cytoplasmic proteins PMID:15797381 San1p is nuclear localized and requires nuclear localization for function |
| GO:0008270 zinc ion binding | IEA GO_REF:0000043 | ACCEPT | Summary: IEA annotation inferred from UniProt keyword mapping for zinc binding. San1 contains a RING-type zinc finger domain (residues 240-280) that coordinates zinc ions, which is essential for its E3 ubiquitin ligase activity. Reason: San1 has a well-characterized RING-type zinc finger domain (PROSITE PS50089, Pfam PF13639). RING domains coordinate two zinc ions via conserved cysteine and histidine residues. This is a structural feature directly tied to San1 core E3 ligase activity. The IEA is a broader annotation than what is represented by the RING domain, but it is correct. |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | ACCEPT | Summary: IEA annotation for metal ion binding, a parent of zinc ion binding. San1 binds zinc ions through its RING domain. This is a broader annotation than the zinc ion binding annotation but is not incorrect. Reason: This is a parent term of GO:0008270 (zinc ion binding). While redundant with the more specific zinc ion binding annotation, IEA annotations at a broader level are acceptable and not incorrect. The RING domain of San1 coordinates zinc ions. |
| GO:0005777 peroxisome | HDA PMID:35563734 Pls1 Is a Peroxisomal Matrix Protein with a Role in Regulati... | REMOVE | Summary: HDA annotation from a high-throughput screen (PMID:35563734) that identified new peroxisomal proteins in yeast using overexpression of proteins under a strong TEF2 promoter. SAN1 is not directly discussed in the paper. This study focused on identifying a new peroxisomal protein Pls1 (Ynl097c-b) and its role in lysine biosynthesis. San1 may have been detected in the screen but appears to be a false positive or artifact of overexpression. Reason: San1 is a well-characterized nuclear protein that requires nuclear localization for function (PMID:15797381). No other study has reported peroxisomal localization for San1. The HDA annotation from PMID:35563734 comes from a high-throughput overexpression screen where proteins were expressed under a strong constitutive promoter, which can lead to mislocalization artifacts. San1 is not mentioned by name in the paper. Given the strong evidence for nuclear localization and the absence of any mechanistic connection to peroxisomal function, this annotation is likely artifactual. Supporting Evidence: PMID:15797381 San1p is nuclear localized and requires nuclear localization for function |
| GO:0008270 zinc ion binding | RCA PMID:30358795 The cellular economy of the Saccharomyces cerevisiae zinc pr... | ACCEPT | Summary: RCA (Reviewed Computational Analysis) annotation for zinc ion binding from a study of the yeast zinc proteome (PMID:30358795). The study used bioinformatics to identify zinc-binding proteins in yeast and characterized the zinc proteome under replete and deficient conditions. San1 was identified as a zinc-binding protein based on its RING domain. Reason: San1 contains a RING-type zinc finger domain that requires zinc for structural integrity and E3 ligase function. The RCA annotation is consistent with the domain architecture of San1 and the IEA annotation. The RING domain (residues 240-280) is a well-characterized zinc-binding fold. Supporting Evidence: PMID:30358795 The yeast zinc proteome of 582 known or potential zinc-binding proteins was identified using a bioinformatics analysis that combined global domain searches with local motif searches |
| GO:0004842 ubiquitin-protein transferase activity | IDA PMID:21211726 Disorder targets misorder in nuclear quality control degrada... | ACCEPT | Summary: IDA annotation for ubiquitin-protein transferase activity from Rosenbaum et al. 2011, which demonstrated San1 directly ubiquitinates misfolded substrates. While GO:0061630 (ubiquitin protein ligase activity) is the preferred term for E3 ligases, GO:0004842 is a broader parent that is also correct. Reason: San1 has demonstrated ubiquitin-protein transferase activity. GO:0004842 is a broader term that encompasses E3 ligase activity. While GO:0061630 is preferred for E3 ligases, duplicate annotations with the parent term are acceptable, especially when they have distinct experimental evidence. Supporting Evidence: PMID:21211726 the yeast nuclear PQC ubiquitin ligase San1 directly recognizes its misfolded substrates via intrinsically disordered N- and C-terminal domains |
| GO:0031249 denatured protein binding | IPI PMID:21211726 Disorder targets misorder in nuclear quality control degrada... | MODIFY | Summary: IPI annotation for denatured protein binding from Rosenbaum et al. 2011. This study demonstrated that San1 directly recognizes misfolded substrates through its intrinsically disordered N- and C-terminal domains. The WITH column indicates interaction with P11978 (Cdc68/Spt16). GO:0031249 is being obsoleted. For San1, the binding is for ubiquitination/degradation targeting, not for chaperone-like protection. GO:0051787 (misfolded protein binding) is a more appropriate replacement. A new term "misfolded protein sensor activity" may be even more appropriate for E3 ligases that recognize misfolded substrates for degradation. Reason: GO:0031249 (denatured protein binding) is being obsoleted. San1 directly binds misfolded proteins through its disordered N- and C-terminal domains, but this binding serves to target substrates for ubiquitin-dependent proteasomal degradation, not for chaperone-like protection or refolding. GO:0051787 (misfolded protein binding) is an existing term that better captures the substrate recognition aspect. Ideally, a new term such as "misfolded protein sensor activity" would be created to distinguish degradation-targeting recognition from chaperone-like binding. Proposed replacements: misfolded protein binding Supporting Evidence: PMID:21211726 the yeast nuclear PQC ubiquitin ligase San1 directly recognizes its misfolded substrates via intrinsically disordered N- and C-terminal domains. These disordered domains are punctuated with small segments of order and high sequence conservation that serve as substrate-recognition sites San1 uses to target its different substrates PMID:15797381 San1p has exquisite specificity for aberrant proteins and does not target the wild-type versions of its mutant substrates |
| GO:0031249 denatured protein binding | IPI PMID:21211726 Disorder targets misorder in nuclear quality control degrada... | MODIFY | Summary: Second IPI annotation for denatured protein binding from Rosenbaum et al. 2011, with additional WITH/FROM entries (P11978, P32558, P32797) indicating interaction with multiple misfolded substrate proteins. Same modification rationale as the first GO:0031249 annotation. Reason: Same as the other GO:0031249 annotation. GO:0031249 is being obsoleted. The evidence supports San1 directly recognizing misfolded substrates, but for degradation rather than chaperoning. GO:0051787 (misfolded protein binding) is the best available replacement term. Proposed replacements: misfolded protein binding |
| GO:0006511 ubiquitin-dependent protein catabolic process | IDA PMID:15078868 Sir Antagonist 1 (San1) is a ubiquitin ligase. | ACCEPT | Summary: IDA annotation from Dasgupta et al. 2004, which first demonstrated San1 is an E3 ubiquitin ligase that targets mutant Sir4 and Spt16 proteins for degradation. Mutant sir4 and spt16 proteins were shown to be unstable in SAN1 cells but stabilized in san1-delta cells. Reason: Direct experimental evidence that San1 promotes ubiquitin-dependent degradation of specific substrates (mutant Sir4 and Spt16). This is a core biological process for San1. Supporting Evidence: PMID:15078868 mutant sir4 and spt16 proteins are unstable in SAN1 cells but are stabilized in san1Delta cells |
| GO:0006511 ubiquitin-dependent protein catabolic process | IDA PMID:15797381 Degradation-mediated protein quality control in the nucleus. | ACCEPT | Summary: IDA annotation from Gardner et al. 2005, which demonstrated San1 targets four distinct mutant nuclear proteins for ubiquitination and destruction by the proteasome, working with E2 enzymes Cdc34 and Ubc1. Reason: Strong direct assay evidence for San1 role in ubiquitin-dependent protein catabolism. Gardner et al. showed San1 ubiquitinates multiple distinct aberrant nuclear proteins for proteasomal degradation. This is the core function of San1 in nuclear PQC. Supporting Evidence: PMID:15797381 San1p, a ubiquitin-protein ligase that, in conjunction with the ubiquitin-conjugating enzymes Cdc34p and Ubc1p, targets four distinct mutant nuclear proteins for ubiquitination and destruction by the proteasome |
| GO:0006511 ubiquitin-dependent protein catabolic process | IMP PMID:15797381 Degradation-mediated protein quality control in the nucleus. | ACCEPT | Summary: IMP annotation from Gardner et al. 2005, based on mutant phenotype evidence. Loss of SAN1 results in chronic stress response and accumulation of aberrant proteins, indicating its role in ubiquitin-dependent protein catabolism. Reason: Mutant phenotype evidence showing that san1-delta cells have impaired degradation of aberrant nuclear proteins. This complements the IDA evidence from the same study. Supporting Evidence: PMID:15797381 Loss of SAN1 results in a chronic stress response, underscoring its role of protein quality control in the cell |
| GO:0004842 ubiquitin-protein transferase activity | IDA PMID:15078868 Sir Antagonist 1 (San1) is a ubiquitin ligase. | ACCEPT | Summary: IDA annotation from Dasgupta et al. 2004, which first demonstrated San1 possesses ubiquitin-protein isopeptide ligase activity in vitro and that this activity is required for function in vivo. Reason: Direct biochemical demonstration of San1 ubiquitin-protein transferase activity in vitro. While GO:0061630 is the preferred E3 ligase term, this broader annotation is correct and supported by strong direct assay evidence. Supporting Evidence: PMID:15078868 We demonstrate that San1 possesses ubiquitin-protein isopeptide ligase activity in vitro, and the ubiquitin-protein isopeptide ligase activity of San1 is required for its function in vivo |
| GO:0004842 ubiquitin-protein transferase activity | IDA PMID:15797381 Degradation-mediated protein quality control in the nucleus. | ACCEPT | Summary: IDA annotation from Gardner et al. 2005, confirming San1 is a ubiquitin-protein ligase that ubiquitinates aberrant nuclear proteins in conjunction with Cdc34 and Ubc1. Reason: Independent experimental confirmation of San1 ubiquitin-protein transferase activity, demonstrating it works with specific E2 enzymes (Cdc34 and Ubc1) to ubiquitinate misfolded substrates. Supporting Evidence: PMID:15797381 San1p, a ubiquitin-protein ligase that, in conjunction with the ubiquitin-conjugating enzymes Cdc34p and Ubc1p, targets four distinct mutant nuclear proteins for ubiquitination and destruction by the proteasome |
| GO:0005634 nucleus | IDA PMID:15797381 Degradation-mediated protein quality control in the nucleus. | ACCEPT | Summary: IDA annotation for nuclear localization from Gardner et al. 2005. San1 is nuclear localized and requires nuclear localization for its protein quality control function. Reason: San1 is primarily a nuclear E3 ligase. Nuclear localization was directly demonstrated and shown to be required for San1 protein quality control function. This is the primary subcellular localization for San1. Supporting Evidence: PMID:15797381 San1p is nuclear localized and requires nuclear localization for function |
| GO:0005737 cytoplasm | IMP PMID:20080635 Cytoplasmic protein quality control degradation mediated by ... | KEEP AS NON CORE | Summary: IMP annotation for cytoplasmic localization from Heck et al. 2010. This study showed that San1 participates in cytoplasmic PQC alongside Ubr1, where misfolded cytoplasmic proteins are delivered to nuclear San1 via chaperone-dependent mechanisms. Reason: While San1 is primarily nuclear, this study demonstrated a functional role for San1 in cytoplasmic PQC. The mechanism involves chaperone-dependent delivery of misfolded cytoplasmic proteins to nuclear San1, rather than San1 itself operating in the cytoplasm. The cytoplasmic role is secondary to the core nuclear PQC function. Supporting Evidence: PMID:20080635 Ubr1 and San1 mediate chaperone-dependent ubiquitination of numerous misfolded cytoplasmic proteins |
| GO:0051788 response to misfolded protein | IMP PMID:15797381 Degradation-mediated protein quality control in the nucleus. | ACCEPT | Summary: IMP annotation for response to misfolded protein from Gardner et al. 2005. Loss of SAN1 results in a chronic stress response, indicating San1 plays a role in the cellular response to misfolded proteins. San1 specifically targets aberrant (misfolded) proteins for degradation and does not target wild-type proteins. Reason: San1 is a key component of the nuclear response to misfolded proteins. It specifically recognizes aberrant proteins and targets them for proteasomal degradation. Loss of San1 results in accumulation of misfolded proteins and chronic stress, directly demonstrating its role in this response. Supporting Evidence: PMID:15797381 San1p has exquisite specificity for aberrant proteins and does not target the wild-type versions of its mutant substrates |
| GO:0071630 nuclear protein quality control by the ubiquitin-proteasome system | IMP PMID:20080635 Cytoplasmic protein quality control degradation mediated by ... | ACCEPT | Summary: IMP annotation for nuclear protein quality control by the ubiquitin-proteasome system from Heck et al. 2010. This study, together with Gardner et al. 2005, established San1 as the defining E3 ligase of the nuclear PQC pathway. San1 ubiquitinates misfolded nuclear proteins for proteasomal degradation. Reason: This is arguably the most specific and informative BP annotation for San1. San1 is the prototypical E3 ligase of nuclear PQC via the ubiquitin-proteasome system. The term precisely captures San1 core biological role. Supporting Evidence: PMID:20080635 Ubr1 and San1 mediate chaperone-dependent ubiquitination of numerous misfolded cytoplasmic proteins PMID:15797381 We propose that San1p-mediated degradation acts as the last line of proteolytic defense against the deleterious accumulation of aberrant proteins in the nucleus |
| GO:0016567 protein ubiquitination | IDA PMID:15078868 Sir Antagonist 1 (San1) is a ubiquitin ligase. | NEW | Summary: San1 is a RING-type E3 ubiquitin ligase that ubiquitinates misfolded nuclear proteins. According to GO E3 ligase annotation guidelines, the BP for E3 ligases should include protein ubiquitination (GO:0016567) or a more specific child term. This annotation is not currently in the GOA but is warranted based on the guidelines and experimental evidence. Reason: Per GO E3 ubiquitin ligase annotation guidelines, the BP activity unit for an E3 ligase should include protein ubiquitination (GO:0016567) as a part_of annotation. San1 has been directly demonstrated to ubiquitinate substrates in vitro and in vivo (PMID:15078868, PMID:15797381, PMID:21211726). This is a core process annotation that is currently missing. Supporting Evidence: PMID:15078868 We demonstrate that San1 possesses ubiquitin-protein isopeptide ligase activity in vitro, and the ubiquitin-protein isopeptide ligase activity of San1 is required for its function in vivo |
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Download this section (compressed HTML)Q: Should a new GO molecular function term be created for "misfolded protein sensor activity" to distinguish E3 ligases that recognize misfolded substrates for degradation from chaperones that bind misfolded proteins to prevent aggregation?
Q: Is GO:0051787 (misfolded protein binding) an adequate replacement for GO:0031249 (denatured protein binding) for San1, or does the degradation-targeting context require a more specific term?
Q: Should the peroxisomal localization (HDA, PMID:35563734) be retained as a possible minor localization site, or should it be removed as an overexpression artifact?
Experiment: Map the substrate-recognition repertoire of San1 in vivo by ubiquitin-AP-MS in san1-delta vs. wild-type strains under proteostatic stress (heat shock, azetidine, canavanine) to define the physiological misfolded-substrate spectrum and test whether all substrates engage the same disordered N-/C-terminal recognition sites characterized in PMID:21211726.
Experiment: Define the structural basis of San1 misfolded-protein recognition by AlphaFold- Multimer prediction and HDX-MS of San1 disordered-domain peptides bound to model misfolded substrates (e.g., te-Spt16, sir4-9), with mutational validation of the conserved sequence segments interspersed among the disordered regions.
Experiment: Quantitatively dissect the nuclear- vs. cytoplasmic-PQC division of labor between San1 and Ubr1 (PMID:20080635) by single-cell live imaging of fluorescent reporter misfolded substrates in san1-delta, ubr1-delta, and double-deletion strains under matched stress, scoring nuclear import kinetics and degradation half-lives.
Experiment: Test whether the HDA peroxisomal signal (PMID:35563734) reflects bona fide San1 localization or an overexpression artifact by tagging endogenous SAN1 with split-GFP at the C-terminus and co-imaging with a peroxisomal marker (Pex3-mCherry) under non-stress and PQC-stress conditions.
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