RidA (formerly YjgF) is a cytosolic homotrimeric 2-iminobutanoate/2-iminopropanoate deaminase (EC 3.5.99.10) that accelerates ammonia release from reactive enamine/imine intermediates generated by pyridoxal-phosphate-dependent enzymes such as threonine dehydratase (IlvA), thereby protecting amino-acid metabolism. During hypochlorous-acid stress, reversible N-chlorination converts RidA into an ATP-independent holdase that binds unfolded cytosolic proteins and prevents their aggregation. This antiaggregation activity is modification-dependent: untreated RidA does not suppress IlvA aggregation.
Definition: Binding to an unfolded or misfolded protein to prevent its aggregation without actively catalyzing refolding. The holdase maintains the client protein in a soluble, folding-competent state.
Justification: N-chlorinated RidA directly prevents aggregation of chemically denatured citrate synthase and IlvA without ATP. Obsolete GO:0051082 records binding but not aggregation prevention, while GO:0140309 requires escort to a defined acceptor or location that is not demonstrated for RidA.
Parent term: molecular_function
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0019239 deaminase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for deaminase activity, consistent with the primary enzymatic function of RidA as a 2-iminobutanoate/2-iminopropanoate deaminase (EC 3.5.99.10). This is the core molecular function. Reason: Deaminase activity is the well-established primary function of RidA, supported by phylogenetic inference and experimental evidence from multiple organisms. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000211014 · PANTHER:PTN000211014 SUPPORTS TRANSFER Current PTHR11803 PAINT retains GO:0019239 at this ancestral node. TAIR:locus:2092374 · TAIR:locus:2092374 SUPPORTS TRANSFER Listed as descendant evidence in the exact GOA WITH/FROM; current PAINT serializes its plant seed with an AGI locus identifier. UniProtKB:P0AF93 · UniProtKB:P0AF93 SUPPORTS TRANSFER RidA itself is descendant evidence for the node and has direct deaminase evidence. UniProtKB:P0AFQ5 · UniProtKB:P0AFQ5 SUPPORTS TRANSFER Listed descendant evidence in both the GOA trace and current node assertion. UniProtKB:P37552 · UniProtKB:P37552 SUPPORTS TRANSFER Listed descendant evidence in both the GOA trace and current node assertion. UniProtKB:Q7CP78 · UniProtKB:Q7CP78 SUPPORTS TRANSFER Listed descendant evidence in both the GOA trace and current node assertion. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for cytosol localization. Consistent with IDA evidence from proteomics studies (PMID:15911532, PMID:18304323) and UniProt annotation. Reason: Cytosolic localization is well-established for RidA. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000211014 · PANTHER:PTN000211014 SUPPORTS TRANSFER Current PTHR11803 PAINT retains GO:0005829 at this ancestral node. RGD:70940 · RGD:70940 SUPPORTS TRANSFER Listed descendant localization evidence in both the GOA trace and current PAINT. SGD:S000000859 · SGD:S000000859 SUPPORTS TRANSFER Listed descendant localization evidence in both the GOA trace and current PAINT. UniProtKB:P0AF93 · UniProtKB:P0AF93 SUPPORTS TRANSFER RidA itself supplies descendant localization evidence and is expected in the trace. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | MODIFY | Summary: IEA annotation for cytoplasm localization. Broader parent of cytosol. Consistent with UniProt subcellular location annotation. Reason: Cytoplasmic localization is correct but less informative than the directly supported cytosol localization. Replace this broad mapping with GO:0005829. Proposed replacements: cytosol |
| GO:0008652 amino acid biosynthetic process | IEA GO_REF:0000043 | MODIFY | Summary: IEA annotation for amino acid biosynthetic process. RidA detoxifies reactive enamine/imine intermediates from PLP-dependent enzymes in amino acid metabolism, supporting isoleucine biosynthesis. Reason: The annotation is biologically sound but too broad. RidA's established pathway context is branched-chain amino acid biosynthesis, represented by GO:0009082. That replacement is already present as a separate accepted GOA row, so this recommendation narrows the broad mapping rather than requesting a duplicate annotation. Proposed replacements: branched-chain amino acid biosynthetic process |
| GO:0009082 branched-chain amino acid biosynthetic process | IEA GO_REF:0000043 | ACCEPT | Summary: IEA annotation for branched-chain amino acid biosynthesis. RidA deaminates reactive intermediates from threonine dehydratase (IlvA), which is part of the isoleucine biosynthetic pathway. Reason: This is a more specific and appropriate annotation. RidA's primary biological role is in the isoleucine biosynthetic pathway via detoxification of IlvA intermediates. |
| GO:0009097 isoleucine biosynthetic process | IEA GO_REF:0000043 | MODIFY | Summary: IEA annotation to the obsolete isoleucine biosynthetic process term. RidA supports the IlvA branch of branched-chain amino acid biosynthesis. Reason: The source term is obsolete, but the pathway assertion is sound. Replace it with current GO:1901705, which preserves the supported L-isoleucine branch specificity rather than collapsing this row into the separately accepted broad branched-chain amino acid biosynthetic annotation. Proposed replacements: L-isoleucine biosynthetic process |
| GO:0009636 response to toxic substance | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: IEA annotation for response to toxic substance. RidA detoxifies reactive enamine/imine intermediates that are nucleophilic and potentially toxic. Reason: RidA's primary function is detoxification of reactive intermediates. This term is consistent with its stress-protection role, though it is contextual rather than RidA's core deaminase function. The IDA annotation from PMID:25517874 provides stronger experimental support. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000043 | MODIFY | Summary: IEA annotation for hydrolase activity. RidA is classified as EC 3.5.99.10, which is a hydrolase. This is a very broad parent of the more specific deaminase activity. Reason: Hydrolase activity is correct by EC classification but is too broad to convey RidA's chemistry. Replace it with the experimentally and reaction-mapping-supported dual imino deaminase term, which is already present as a separate accepted GOA row rather than needing a duplicate annotation. Proposed replacements: 2-iminobutanoate/2-iminopropanoate deaminase activity |
| GO:0120241 2-iminobutanoate/2-iminopropanoate deaminase activity | IEA GO_REF:0000003 | ACCEPT | Summary: IEA annotation from EC number mapping. This is the most specific and accurate molecular function term for RidA, matching its EC 3.5.99.10 classification. Reason: This is the most precise term for RidA's core enzymatic function. It accurately reflects the dual substrate specificity for both 2-iminobutanoate and 2-iminopropanoate. |
| GO:0120242 2-iminobutanoate deaminase activity | IEA GO_REF:0000116 | ACCEPT | Summary: IEA annotation from Rhea mapping for the 2-iminobutanoate-specific deaminase activity. This is one of the two specific substrate activities of RidA. Reason: Consistent with the known catalytic activity. UniProt lists the reaction 2-iminobutanoate + H2O = 2-oxobutanoate + NH4(+). |
| GO:0120243 2-iminopropanoate deaminase activity | IEA GO_REF:0000116 | ACCEPT | Summary: IEA annotation from Rhea mapping for the 2-iminopropanoate-specific deaminase activity. This is the second specific substrate activity of RidA. Reason: Consistent with the known catalytic activity. UniProt lists the reaction 2-iminopropanoate + H2O = pyruvate + NH4(+). |
| GO:0120242 2-iminobutanoate deaminase activity | ISS GO_REF:0000024 | ACCEPT | Summary: ISS annotation based on sequence similarity transfer. The 2-iminobutanoate deaminase activity was first characterized in Salmonella enterica RidA and transferred to E. coli by sequence similarity. Reason: Well-supported by sequence similarity to the experimentally characterized Salmonella enterica homolog. Consistent with the IEA annotations for the same and related terms. |
| GO:0042802 identical protein binding | IDA PMID:10595546 A test case for structure-based functional assignment -- the... | KEEP AS NON CORE | Summary: IDA annotation for identical protein binding based on the crystal structure showing RidA forms a homotrimer (PMID:10595546). Reason: The structure directly demonstrates self-association, so the annotation is valid. Identical protein binding is nevertheless an uninformative generic molecular-function term; the homotrimerization and complex annotations capture the structural biology more clearly. Supporting Evidence: PMID:10595546 The YjgF molecule is a homotrimer with exact threefold symmetry. |
| GO:0070207 protein homotrimerization | IDA PMID:10595546 A test case for structure-based functional assignment -- the... | ACCEPT | Summary: IDA annotation for protein homotrimerization based on crystal structure (PMID:10595546). RidA is a homotrimer, which is the functional form. Reason: Directly supported by the 1.2A crystal structure. UniProt confirms homotrimer subunit structure. |
| GO:0032991 protein-containing complex | IDA PMID:10595546 A test case for structure-based functional assignment -- the... | ACCEPT | Summary: IDA annotation for protein-containing complex. RidA forms a homotrimeric complex. Reason: The homotrimer is the functional complex. This is a broad CC term consistent with the structural evidence. |
| GO:0009636 response to toxic substance | IDA PMID:25517874 Activation of RidA chaperone function by N-chlorination. | KEEP AS NON CORE | Summary: IDA annotation for response to toxic substance from Mueller et al. (2014). ridA deletion mutants are sensitive to HOCl stress, showing prolonged lag phase at medium HOCl concentrations (1-2 mM). RidA plays a role in protecting E. coli against HOCl-mediated stress. Reason: The ridA mutant is sensitive to HOCl, demonstrating a secondary stress-response role rather than the constitutive core deaminase function. This is supported by growth assays in the presence of HOCl (PMID:25517874). Note that this response involves the HOCl-activated chaperone function, not the deaminase activity. Supporting Evidence: PMID:25517874 Deletion of ridA results in an HOCl-sensitive phenotype. |
| GO:0019239 deaminase activity | IDA PMID:23696645 Redox proteomics uncovers peroxynitrite-sensitive proteins t... | ACCEPT | Summary: IDA annotation for deaminase activity based on experimental evidence. Reason: Direct experimental evidence for deaminase activity. This is the core molecular function of RidA. The cached paper is abstract-only and identifies in-vitro activity without exposing the full assay details, so the curator's IDA judgment is retained without claiming more detail than the cache supports. Supporting Evidence: PMID:23696645 In in vitro studies, we could show that the activity of RidA, a recently discovered enamine/imine deaminase, is regulated in a specific manner by the modification of its single conserved cysteine. |
| GO:0051082 unfolded protein binding | IDA PMID:25517874 Activation of RidA chaperone function by N-chlorination. | MODIFY | Summary: PMID:25517874 directly demonstrates that N-chlorinated RidA binds unfolded clients and prevents their aggregation without ATP. The activity is a genuine, reversible stress-activated holdase function, but GO:0051082 is obsolete and does not express aggregation prevention. Reason: Retain the demonstrated biology but replace the obsolete binding term with the project's general holdase chaperone activity NTR. GO:0140309 does not fit because the experiment shows in-situ aggregation prevention without escort to a defined acceptor or destination. The evidence is explicitly conditional on HOCl- or chloramine-mediated N-chlorination; untreated RidA did not prevent IlvA aggregation. See go-ontology#30962 and file:projects/UNFOLDED_PROTEIN_BINDING.md. Proposed replacements: holdase chaperone activity (NTR needed; GO:0140309 does not fit -- carrier-specific) Supporting Evidence: PMID:25517874 The addition of ATP did not enhance chaperone activity, consistent with a holdase function of HOCl-treated RidA PMID:25517874 In contrast, incubation of IlvA with a 10-fold molar excess of untreated RidA had no effect on IlvA’s aggregation behaviour file:projects/UNFOLDED_PROTEIN_BINDING.md GO:0051082 is now formally obsolete |
| GO:0005829 cytosol | IDA PMID:15911532 Localization, annotation, and comparison of the Escherichia ... | ACCEPT | Summary: IDA annotation for cytosol localization from proteomics study by Corbin et al. (2003). Reason: Proteomics-based experimental evidence for cytosol localization. |
| GO:0005829 cytosol | IDA PMID:18304323 Protein abundance profiling of the Escherichia coli cytosol. | ACCEPT | Summary: IDA annotation for cytosol localization from proteomics study by Ishihama et al. (2008). Reason: Independent proteomics confirmation of cytosol localization. |
| GO:0019239 deaminase activity | ISO PMID:22094463 Conserved YjgF protein family deaminates reactive enamine/im... | ACCEPT | Summary: ISO annotation for deaminase activity based on ortholog evidence. Lambrecht et al. (2012) showed that conserved YjgF/RidA family proteins deaminate reactive enamine/imine intermediates of PLP-dependent enzymes. Reason: Consistent with the core function of RidA. The study demonstrates the conserved deaminase function across the RidA family. |
| GO:0016020 membrane | HDA PMID:16858726 A complexomic study of Escherichia coli using two-dimensiona... | KEEP AS NON CORE | Summary: HDA annotation for membrane localization from a complexomics study. This is unexpected given that RidA is a soluble cytoplasmic protein with no signal peptide or transmembrane domain. Reason: Retain the experimental high-throughput observation out of curator deference, but not as a core location. The cached paper is abstract-only and does not permit independent assessment of genuine membrane association versus fractionation carryover. The publisher's supporting table records yjgF under legacy accession P39330, which the cached UniProt record identifies as a secondary accession of P0AF93, but that provenance does not resolve the biological interpretation. Multiple independent annotations and the soluble structure establish cytosol as RidA's primary location. |
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Q: How should a modification-dependent moonlighting holdase activity be represented once the general holdase chaperone activity NTR is created?
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