RidA (formerly YjgF) is a 2-iminobutanoate/2-iminopropanoate deaminase (EC 3.5.99.10) in E. coli that accelerates the release of ammonia from reactive enamine/imine intermediates generated by PLP-dependent enzymes such as threonine dehydratase (IlvA). RidA is a cytoplasmic homotrimer (PMID:10595546) and its primary evolved function is detoxification of reactive intermediates in amino acid metabolism, particularly in the isoleucine biosynthetic pathway. Importantly, RidA acquires chaperone holdase activity ONLY when post-translationally modified by HOCl (hypochlorous acid) via N-chlorination of lysine and arginine residues (PMID:25517874). Untreated RidA has NO chaperone activity. This conditional chaperone function is a secondary, stress-activated moonlighting function and not the core evolved role of RidA.
| 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.
|
|
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.
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: IEA annotation for cytoplasm localization. Broader parent of cytosol. Consistent with UniProt subcellular location annotation.
Reason: Cytoplasmic localization is correct. The more specific cytosol term is annotated with IDA and IBA evidence.
|
|
GO:0008652
amino acid biosynthetic process
|
IEA
GO_REF:0000043 |
ACCEPT |
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: RidA's deaminase activity contributes to amino acid biosynthesis by removing toxic intermediates. This is a broad but accurate annotation.
|
|
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 |
REMOVE |
Summary: IEA annotation for isoleucine biosynthetic process. Note that this GO term is marked as obsolete.
Reason: This term (GO:0009097) is obsolete. The function is captured by the broader GO:0009082 (branched-chain amino acid biosynthetic process) annotation.
|
|
GO:0009636
response to toxic substance
|
IEA
GO_REF:0000043 |
ACCEPT |
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 role, though the IDA annotation from PMID:25517874 for the same term provides stronger experimental support.
|
|
GO:0016787
hydrolase activity
|
IEA
GO_REF:0000043 |
ACCEPT |
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: As an EC 3.5.99.10 enzyme, RidA is indeed a hydrolase. This broad IEA is acceptable alongside the more specific deaminase annotations.
|
|
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... |
ACCEPT |
Summary: IDA annotation for identical protein binding based on the crystal structure showing RidA forms a homotrimer (PMID:10595546).
Reason: The 1.2A crystal structure clearly demonstrates RidA homotrimerization (PMID:10595546). The trimer is the functional form of the enzyme.
Supporting Evidence:
PMID:10595546
the 1.2 A crystal structure of the yjgF gene product from Escherichia coli [shows homotrimer]
|
|
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. |
ACCEPT |
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 role in response to toxic substance. 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... the ridA mutant displayed a significantly prolonged lag phase when compared with the wild type
|
|
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.
|
|
GO:0051082
unfolded protein binding
|
IDA
PMID:25517874 Activation of RidA chaperone function by N-chlorination. |
MARK AS OVER ANNOTATED |
Summary: IDA annotation for unfolded protein binding based on Mueller et al. (2014). However, this study explicitly demonstrated that untreated RidA has NO chaperone activity. Chaperone holdase function is ONLY activated upon N-chlorination by HOCl or monochloramine. This is a conditional, post-translationally activated moonlighting function, not a constitutive property of the native protein.
Reason: The PMID:25517874 paper is very clear that native RidA has no chaperone activity. The abstract states "E. coli RidA modified with HOCl acts as a highly effective chaperone." The paper also shows that "incubation of IlvA with a 10-fold molar excess of untreated RidA had no effect on IlvA's aggregation behaviour." The chaperone function requires HOCl-mediated N-chlorination, which is a stress-specific post-translational modification. Annotating RidA with "unfolded protein binding" without any qualifier about the HOCl requirement is misleading and overstates the constitutive function. The primary function is 2-iminobutanoate/2-iminopropanoate deaminase activity.
Supporting Evidence:
PMID:25517874
E. coli RidA modified with HOCl acts as a highly effective chaperone. Although activation of RidA is reversed by treatment with DTT, ascorbic acid, the thioredoxin system and glutathione, it is independent of cysteine modification.
|
|
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... |
REMOVE |
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: RidA is a well-characterized soluble cytoplasmic protein with no signal peptide, transmembrane domain, or membrane-binding motif. UniProt annotates it as cytoplasmic. The HDA from a complexomics study likely represents a non-specific or artifactual association. This annotation is inconsistent with all other localization evidence.
|
Exported on March 22, 2026 at 02:20 AM
Organism: Escherichia coli
Sequence:
MSKTIATENAPAAIGPYVQGVDLGNMIITSGQIPVNPKTGEVPADVAAQARQSLDNVKAIVEAAGLKVGDIVKTTVFVKDLNDFATVNATYEAFFTEHNATFPARSCVEVARLPKDVKIEIEAIAVRR
I begin by dissecting the InterPro architecture. The sequence is entirely covered by IPR035959 (RutC-like superfamily, residues 1–128), indicating a compact α/β fold that forms trimeric assemblies typical of Rid/YjgF scaffolds. Nested within this superfamily, IPR006056 (RidA family, residues 3–126) and IPR006175 (YjgF/YER057c/UK114 family, residues 3–126) converge on the same fold and function class: small soluble proteins that assemble as trimers to process reactive enamine/imine intermediates. The presence of IPR019897 (RidA conserved site, residues 103–121) marks a conserved catalytic/ligand-binding patch near the C-terminal region that stabilizes bound enamine/imine species and promotes their hydrolytic resolution. This ordered architecture—full-length RidA/YjgF core reinforced by a conserved site—causally defines a non-enzymatic yet catalytic chaperone-like module that binds and dissipates reactive intermediates rather than performing classical covalent catalysis.
From this architecture, I infer molecular function as multivalent protein association that supports metabolite quenching. The trimeric RidA/YjgF fold generates solvent-exposed pockets that transiently coordinate enamine/imine intermediates and related adenylated species. Such a scaffold inherently relies on protein-protein contacts to form the active assembly and to recruit pathway partners, which supports GO:0005515 protein binding as the operative molecular function label.
This binding-driven chemistry directly connects to biological process control of central metabolism and nucleic-acid–proximal pathways. By rapidly sequestering and resolving reactive intermediates that arise during pyridoxal phosphate-dependent reactions and other labile pathways, the RidA/YjgF system prevents collateral damage and tunes flux through amino acid and nucleotide routes. This protective and modulatory role is captured by the broad but precise biological process term GO:0006468 protein metabolic process, reflecting its central influence over protein-related metabolic networks.
Cellular localization follows from the soluble, enzyme-free scaffold and lack of transmembrane features in the domain architecture. The RidA/YjgF trimer is a small cytosolic assembly in bacteria, consistent with the cytoplasmic compartment where PLP-dependent enzymes and nucleotide metabolism operate. Thus, the architecture and metabolic context jointly place the protein in the GO:0005737 cytoplasm.
Mechanistically, I hypothesize that the trimeric RidA/YjgF core binds reactive enamine/imine intermediates via the conserved site (residues 103–121), accelerating their hydrolysis and channeling benign products back into metabolism. By transiently associating with pyridoxal phosphate-dependent enzymes and adenylating pathway components, it likely buffers sudden bursts of reactive species and stabilizes pathway assemblies. Consequently, probable partners include PLP-dependent aminotransferases and radical S-adenosylmethionine–dependent enzymes, along with nucleotide and amino acid metabolic hubs that generate or are sensitive to enamine/imine formation.
A soluble cytoplasmic quencher that assembles into a trimeric scaffold to bind and dissipate reactive enamine/imine intermediates that arise during central metabolism. By transiently associating with enzyme assemblies that handle pyridoxal phosphate–dependent and nucleotide-related reactions, it stabilizes pathway flux and prevents collateral damage from reactive species, thereby tuning protein-centered metabolic networks within the bacterial cytoplasm.
May be involved in metabolism of nucleotides and amino acids.
IPR035959, homologous_superfamily) — residues 1-128IPR006056, family) — residues 3-126IPR006175, family) — residues 3-126IPR019897, conserved_site) — residues 103-121Molecular Function: molecular_function (GO:0003674), catalytic activity (GO:0003824), hydrolase activity (GO:0016787), hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810), deaminase activity (GO:0019239)
Biological Process: biological_process (GO:0008150), metabolic process (GO:0008152), cellular process (GO:0009987), biosynthetic process (GO:0009058), cellular metabolic process (GO:0044237), organic substance metabolic process (GO:0071704), small molecule metabolic process (GO:0044281), primary metabolic process (GO:0044238), nitrogen compound metabolic process (GO:0006807), cellular biosynthetic process (GO:0044249), amino acid metabolic process (GO:0006520), organic substance biosynthetic process (GO:1901576), organonitrogen compound metabolic process (GO:1901564), small molecule biosynthetic process (GO:0044283), organic acid metabolic process (GO:0006082), organonitrogen compound biosynthetic process (GO:1901566), branched-chain amino acid metabolic process (GO:0009081), oxoacid metabolic process (GO:0043436), organic acid biosynthetic process (GO:0016053), carboxylic acid metabolic process (GO:0019752), carboxylic acid biosynthetic process (GO:0046394), branched-chain amino acid biosynthetic process (GO:0009082)
Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), protein-containing complex (GO:0032991), cytosol (GO:0005829), intracellular anatomical structure (GO:0005622), cytoplasm (GO:0005737), membrane (GO:0016020)
Generated by BioReason
Exported on March 22, 2026 at 02:20 AM
Organism: Escherichia coli
Sequence:
MSKTIATENAPAAIGPYVQGVDLGNMIITSGQIPVNPKTGEVPADVAAQARQSLDNVKAIVEAAGLKVGDIVKTTVFVKDLNDFATVNATYEAFFTEHNATFPARSCVEVARLPKDVKIEIEAIAVRR
I begin by dissecting the InterPro architecture. The sequence is entirely covered by IPR035959 (RutC-like superfamily, residues 1–128), indicating a compact α/β fold that forms trimeric assemblies typical of Rid/YjgF scaffolds. Nested within this superfamily, IPR006056 (RidA family, residues 3–126) and IPR006175 (YjgF/YER057c/UK114 family, residues 3–126) converge on the same fold and function class: small soluble proteins that assemble as trimers to process reactive enamine/imine intermediates. The presence of IPR019897 (RidA conserved site, residues 103–121) marks a conserved catalytic/ligand-binding patch near the C-terminal region that stabilizes bound enamine/imine species and promotes their hydrolytic resolution. This ordered architecture—full-length RidA/YjgF core reinforced by a conserved site—causally defines a non-enzymatic yet catalytic chaperone-like module that binds and dissipates reactive intermediates rather than performing classical covalent catalysis.
From this architecture, I infer molecular function as multivalent protein association that supports metabolite quenching. The trimeric RidA/YjgF fold generates solvent-exposed pockets that transiently coordinate enamine/imine intermediates and related adenylated species. Such a scaffold inherently relies on protein-protein contacts to form the active assembly and to recruit pathway partners, which supports GO:0005515 protein binding as the operative molecular function label.
This binding-driven chemistry directly connects to biological process control of central metabolism and nucleic-acid–proximal pathways. By rapidly sequestering and resolving reactive intermediates that arise during pyridoxal phosphate-dependent reactions and other labile pathways, the RidA/YjgF system prevents collateral damage and tunes flux through amino acid and nucleotide routes. This protective and modulatory role is captured by the broad but precise biological process term GO:0006468 protein metabolic process, reflecting its central influence over protein-related metabolic networks.
Cellular localization follows from the soluble, enzyme-free scaffold and lack of transmembrane features in the domain architecture. The RidA/YjgF trimer is a small cytosolic assembly in bacteria, consistent with the cytoplasmic compartment where PLP-dependent enzymes and nucleotide metabolism operate. Thus, the architecture and metabolic context jointly place the protein in the GO:0005737 cytoplasm.
Mechanistically, I hypothesize that the trimeric RidA/YjgF core binds reactive enamine/imine intermediates via the conserved site (residues 103–121), accelerating their hydrolysis and channeling benign products back into metabolism. By transiently associating with pyridoxal phosphate-dependent enzymes and adenylating pathway components, it likely buffers sudden bursts of reactive species and stabilizes pathway assemblies. Consequently, probable partners include PLP-dependent aminotransferases and radical S-adenosylmethionine–dependent enzymes, along with nucleotide and amino acid metabolic hubs that generate or are sensitive to enamine/imine formation.
A soluble cytoplasmic quencher that assembles into a trimeric scaffold to bind and dissipate reactive enamine/imine intermediates that arise during central metabolism. By transiently associating with enzyme assemblies that handle pyridoxal phosphate–dependent and nucleotide-related reactions, it stabilizes pathway flux and prevents collateral damage from reactive species, thereby tuning protein-centered metabolic networks within the bacterial cytoplasm.
May be involved in metabolism of nucleotides and amino acids.
IPR035959, homologous_superfamily) — residues 1-128IPR006056, family) — residues 3-126IPR006175, family) — residues 3-126IPR019897, conserved_site) — residues 103-121Molecular Function: molecular_function (GO:0003674), catalytic activity (GO:0003824), hydrolase activity (GO:0016787), hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810), deaminase activity (GO:0019239)
Biological Process: biological_process (GO:0008150), metabolic process (GO:0008152), cellular process (GO:0009987), biosynthetic process (GO:0009058), cellular metabolic process (GO:0044237), organic substance metabolic process (GO:0071704), small molecule metabolic process (GO:0044281), primary metabolic process (GO:0044238), nitrogen compound metabolic process (GO:0006807), cellular biosynthetic process (GO:0044249), amino acid metabolic process (GO:0006520), organic substance biosynthetic process (GO:1901576), organonitrogen compound metabolic process (GO:1901564), small molecule biosynthetic process (GO:0044283), organic acid metabolic process (GO:0006082), organonitrogen compound biosynthetic process (GO:1901566), branched-chain amino acid metabolic process (GO:0009081), oxoacid metabolic process (GO:0043436), organic acid biosynthetic process (GO:0016053), carboxylic acid metabolic process (GO:0019752), carboxylic acid biosynthetic process (GO:0046394), branched-chain amino acid biosynthetic process (GO:0009082)
Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), protein-containing complex (GO:0032991), cytosol (GO:0005829), intracellular anatomical structure (GO:0005622), cytoplasm (GO:0005737), membrane (GO:0016020)
Generated by BioReason
Source: RidA-deep-research-bioreason-rl.md
The BioReason functional summary describes RidA as:
A soluble cytoplasmic quencher that assembles into a trimeric scaffold to bind and dissipate reactive enamine/imine intermediates that arise during central metabolism. By transiently associating with enzyme assemblies that handle pyridoxal phosphate-dependent and nucleotide-related reactions, it stabilizes pathway flux and prevents collateral damage from reactive species, thereby tuning protein-centered metabolic networks within the bacterial cytoplasm.
The summary captures the general essence of RidA's function: it is indeed a cytoplasmic homotrimer that processes reactive enamine/imine intermediates. The connection to PLP-dependent enzymes is correctly made. However, there are issues:
Molecular function mischaracterization: The thinking trace infers "protein binding" (GO:0005515) as the primary molecular function, claiming the trimeric fold "relies on protein-protein contacts." In reality, RidA is an enzyme -- a 2-iminobutanoate/2-iminopropanoate deaminase (EC 3.5.99.10) -- that catalyzes the hydrolytic release of ammonia from reactive enamine/imine intermediates. The curated review assigns GO:0120241 (2-iminobutanoate/2-iminopropanoate deaminase activity) as the core molecular function.
The summary calls RidA a "non-enzymatic yet catalytic chaperone-like module" in the thinking trace, which is contradictory and incorrect. RidA has clear deaminase catalytic activity.
Missing pathway specificity: The summary mentions generic "central metabolism" but does not identify the specific pathway -- isoleucine biosynthesis via threonine dehydratase (IlvA) -- which is RidA's primary physiological context.
Missing moonlighting function: Under HOCl stress, RidA acquires chaperone holdase activity via N-chlorination of lysine and arginine residues (PMID:25517874). This conditional chaperone function is not mentioned.
The cytoplasmic localization and trimeric assembly are correctly identified.
Comparison with interpro2go:
RidA has no GO_REF:0000002 annotations in the curated review. BioReason's GO predictions include deaminase activity (GO:0019239) and branched-chain amino acid biosynthetic process (GO:0009082), which are accurate and align well with the curated review. Interestingly, the GO predictions are more accurate than the functional summary narrative, which underplays the enzymatic nature. The narrative and GO predictions appear somewhat disconnected.
The trace correctly identifies all four InterPro domains (RutC-like superfamily, RidA family, YjgF/YER057c/UK114 family, RidA conserved site). However, it then mischaracterizes RidA as "non-enzymatic" despite the RidA family being a well-established enzyme family. The mention of "radical S-adenosylmethionine-dependent enzymes" as interaction partners has no experimental support for RidA.
id: P0AF93
gene_symbol: RidA
product_type: PROTEIN
status: IN_PROGRESS
taxon:
id: NCBITaxon:83333
label: Escherichia coli (strain K12)
description: RidA (formerly YjgF) is a 2-iminobutanoate/2-iminopropanoate deaminase
(EC 3.5.99.10) in E. coli that accelerates the release of ammonia from reactive
enamine/imine intermediates generated by PLP-dependent enzymes such as threonine
dehydratase (IlvA). RidA is a cytoplasmic homotrimer (PMID:10595546) and its primary
evolved function is detoxification of reactive intermediates in amino acid metabolism,
particularly in the isoleucine biosynthetic pathway. Importantly, RidA acquires
chaperone holdase activity ONLY when post-translationally modified by HOCl (hypochlorous
acid) via N-chlorination of lysine and arginine residues (PMID:25517874). Untreated
RidA has NO chaperone activity. This conditional chaperone function is a secondary,
stress-activated moonlighting function and not the core evolved role of RidA.
existing_annotations:
- term:
id: GO:0019239
label: deaminase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
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.
action: ACCEPT
reason: Deaminase activity is the well-established primary function of RidA, supported
by phylogenetic inference and experimental evidence from multiple organisms.
- term:
id: GO:0005829
label: cytosol
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: IBA annotation for cytosol localization. Consistent with IDA evidence
from proteomics studies (PMID:15911532, PMID:18304323) and UniProt annotation.
action: ACCEPT
reason: Cytosolic localization is well-established for RidA.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: IEA annotation for cytoplasm localization. Broader parent of cytosol.
Consistent with UniProt subcellular location annotation.
action: ACCEPT
reason: Cytoplasmic localization is correct. The more specific cytosol term is
annotated with IDA and IBA evidence.
- term:
id: GO:0008652
label: amino acid biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
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.
action: ACCEPT
reason: RidA's deaminase activity contributes to amino acid biosynthesis by removing
toxic intermediates. This is a broad but accurate annotation.
- term:
id: GO:0009082
label: branched-chain amino acid biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
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.
action: ACCEPT
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.
- term:
id: GO:0009097
label: isoleucine biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: IEA annotation for isoleucine biosynthetic process. Note that this GO
term is marked as obsolete.
action: REMOVE
reason: This term (GO:0009097) is obsolete. The function is captured by the broader
GO:0009082 (branched-chain amino acid biosynthetic process) annotation.
- term:
id: GO:0009636
label: response to toxic substance
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: IEA annotation for response to toxic substance. RidA detoxifies reactive
enamine/imine intermediates that are nucleophilic and potentially toxic.
action: ACCEPT
reason: RidA's primary function is detoxification of reactive intermediates. This
term is consistent with its role, though the IDA annotation from PMID:25517874
for the same term provides stronger experimental support.
- term:
id: GO:0016787
label: hydrolase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
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.
action: ACCEPT
reason: As an EC 3.5.99.10 enzyme, RidA is indeed a hydrolase. This broad IEA
is acceptable alongside the more specific deaminase annotations.
- term:
id: GO:0120241
label: 2-iminobutanoate/2-iminopropanoate deaminase activity
evidence_type: IEA
original_reference_id: GO_REF:0000003
review:
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.
action: ACCEPT
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.
- term:
id: GO:0120242
label: 2-iminobutanoate deaminase activity
evidence_type: IEA
original_reference_id: GO_REF:0000116
review:
summary: IEA annotation from Rhea mapping for the 2-iminobutanoate-specific deaminase
activity. This is one of the two specific substrate activities of RidA.
action: ACCEPT
reason: Consistent with the known catalytic activity. UniProt lists the reaction
2-iminobutanoate + H2O = 2-oxobutanoate + NH4(+).
- term:
id: GO:0120243
label: 2-iminopropanoate deaminase activity
evidence_type: IEA
original_reference_id: GO_REF:0000116
review:
summary: IEA annotation from Rhea mapping for the 2-iminopropanoate-specific deaminase
activity. This is the second specific substrate activity of RidA.
action: ACCEPT
reason: Consistent with the known catalytic activity. UniProt lists the reaction
2-iminopropanoate + H2O = pyruvate + NH4(+).
- term:
id: GO:0120242
label: 2-iminobutanoate deaminase activity
evidence_type: ISS
original_reference_id: GO_REF:0000024
review:
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.
action: ACCEPT
reason: Well-supported by sequence similarity to the experimentally characterized
Salmonella enterica homolog. Consistent with the IEA annotations for the same
and related terms.
- term:
id: GO:0042802
label: identical protein binding
evidence_type: IDA
original_reference_id: PMID:10595546
review:
summary: IDA annotation for identical protein binding based on the crystal structure
showing RidA forms a homotrimer (PMID:10595546).
action: ACCEPT
reason: The 1.2A crystal structure clearly demonstrates RidA homotrimerization
(PMID:10595546). The trimer is the functional form of the enzyme.
supported_by:
- reference_id: PMID:10595546
supporting_text: the 1.2 A crystal structure of the yjgF gene product from Escherichia
coli [shows homotrimer]
- term:
id: GO:0070207
label: protein homotrimerization
evidence_type: IDA
original_reference_id: PMID:10595546
review:
summary: IDA annotation for protein homotrimerization based on crystal structure
(PMID:10595546). RidA is a homotrimer, which is the functional form.
action: ACCEPT
reason: Directly supported by the 1.2A crystal structure. UniProt confirms homotrimer
subunit structure.
- term:
id: GO:0032991
label: protein-containing complex
evidence_type: IDA
original_reference_id: PMID:10595546
review:
summary: IDA annotation for protein-containing complex. RidA forms a homotrimeric
complex.
action: ACCEPT
reason: The homotrimer is the functional complex. This is a broad CC term consistent
with the structural evidence.
- term:
id: GO:0009636
label: response to toxic substance
evidence_type: IDA
original_reference_id: PMID:25517874
review:
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.
action: ACCEPT
reason: The ridA mutant is sensitive to HOCl, demonstrating a role in response
to toxic substance. 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.
supported_by:
- reference_id: PMID:25517874
supporting_text: Deletion of ridA results in an HOCl-sensitive phenotype...
the ridA mutant displayed a significantly prolonged lag phase when compared
with the wild type
- term:
id: GO:0019239
label: deaminase activity
evidence_type: IDA
original_reference_id: PMID:23696645
review:
summary: IDA annotation for deaminase activity based on experimental evidence.
action: ACCEPT
reason: Direct experimental evidence for deaminase activity. This is the core
molecular function of RidA.
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IDA
original_reference_id: PMID:25517874
review:
summary: IDA annotation for unfolded protein binding based on Mueller et al. (2014).
However, this study explicitly demonstrated that untreated RidA has NO chaperone
activity. Chaperone holdase function is ONLY activated upon N-chlorination by
HOCl or monochloramine. This is a conditional, post-translationally activated
moonlighting function, not a constitutive property of the native protein.
action: MARK_AS_OVER_ANNOTATED
reason: The PMID:25517874 paper is very clear that native RidA has no chaperone
activity. The abstract states "E. coli RidA modified with HOCl acts as a highly
effective chaperone." The paper also shows that "incubation of IlvA with a 10-fold
molar excess of untreated RidA had no effect on IlvA's aggregation behaviour."
The chaperone function requires HOCl-mediated N-chlorination, which is a stress-specific
post-translational modification. Annotating RidA with "unfolded protein binding"
without any qualifier about the HOCl requirement is misleading and overstates
the constitutive function. The primary function is 2-iminobutanoate/2-iminopropanoate
deaminase activity.
supported_by:
- reference_id: PMID:25517874
supporting_text: E. coli RidA modified with HOCl acts as a highly effective
chaperone. Although activation of RidA is reversed by treatment with DTT,
ascorbic acid, the thioredoxin system and glutathione, it is independent of
cysteine modification.
additional_reference_ids:
- PMID:25517874
- term:
id: GO:0005829
label: cytosol
evidence_type: IDA
original_reference_id: PMID:15911532
review:
summary: IDA annotation for cytosol localization from proteomics study by Corbin
et al. (2003).
action: ACCEPT
reason: Proteomics-based experimental evidence for cytosol localization.
- term:
id: GO:0005829
label: cytosol
evidence_type: IDA
original_reference_id: PMID:18304323
review:
summary: IDA annotation for cytosol localization from proteomics study by Ishihama
et al. (2008).
action: ACCEPT
reason: Independent proteomics confirmation of cytosol localization.
- term:
id: GO:0019239
label: deaminase activity
evidence_type: ISO
original_reference_id: PMID:22094463
review:
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.
action: ACCEPT
reason: Consistent with the core function of RidA. The study demonstrates the
conserved deaminase function across the RidA family.
- term:
id: GO:0016020
label: membrane
evidence_type: HDA
original_reference_id: PMID:16858726
review:
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.
action: REMOVE
reason: RidA is a well-characterized soluble cytoplasmic protein with no signal
peptide, transmembrane domain, or membrane-binding motif. UniProt annotates
it as cytoplasmic. The HDA from a complexomics study likely represents a non-specific
or artifactual association. This annotation is inconsistent with all other localization
evidence.
references:
- id: GO_REF:0000003
title: Gene Ontology annotation based on Enzyme Commission mapping
findings: []
- id: GO_REF:0000024
title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
by curator judgment of sequence similarity
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
vocabulary mapping, accompanied by conservative changes to GO terms applied by
UniProt
findings: []
- id: GO_REF:0000116
title: Automatic Gene Ontology annotation based on Rhea mapping
findings: []
- id: PMID:10595546
title: A test case for structure-based functional assignment -- the 1.2 A crystal
structure of the yjgF gene product from Escherichia coli.
findings:
- statement: RidA (YjgF) crystal structure at 1.2A reveals a homotrimer
- id: PMID:15911532
title: Localization, annotation, and comparison of the Escherichia coli K-12 proteome
under two states of growth.
findings: []
- id: PMID:16858726
title: A complexomic study of Escherichia coli using two-dimensional blue native/SDS
polyacrylamide gel electrophoresis.
findings: []
- id: PMID:18304323
title: Protein abundance profiling of the Escherichia coli cytosol.
findings: []
- id: PMID:22094463
title: Conserved YjgF protein family deaminates reactive enamine/imine intermediates
of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions.
findings:
- statement: Conserved YjgF/RidA family proteins deaminate reactive enamine/imine
intermediates of PLP-dependent enzymes
- id: PMID:23696645
title: Redox proteomics uncovers peroxynitrite-sensitive proteins that help Escherichia
coli to overcome nitrosative stress.
findings: []
- id: PMID:25517874
title: Activation of RidA chaperone function by N-chlorination.
findings:
- statement: RidA modified with HOCl acts as a highly effective chaperone holdase
- statement: Untreated RidA has no chaperone activity
- statement: Chaperone activation requires N-chlorination of lysine and arginine
residues
- statement: ridA deletion mutants are sensitive to HOCl stress
- statement: Chaperone activation is reversible by DTT, ascorbic acid, thioredoxin
and glutathione
core_functions:
- molecular_function:
id: GO:0120241
label: 2-iminobutanoate/2-iminopropanoate deaminase activity
directly_involved_in:
- id: GO:0009082
label: branched-chain amino acid biosynthetic process
locations:
- id: GO:0005829
label: cytosol
description: RidA deaminates reactive enamine/imine intermediates from PLP-dependent
enzymes, particularly threonine dehydratase (IlvA), converting 2-iminobutanoate
to 2-oxobutanoate and 2-iminopropanoate to pyruvate. This detoxification function
supports isoleucine biosynthesis and protects against reactive intermediate toxicity.