Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004341 gluconolactonase activity	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation correctly identifies the core enzymatic function. Strongly supported by experimental evidence in PMID:16585534 showing gluconolactonase activity is essential for vitamin C biosynthesis. This is a primary molecular function of the protein. Supporting Evidence: file:rat/Rgn/Rgn-deep-research-falcon.md 1. Primary biochemical function: Rat Rgn encodes regucalcin/SMP30, a metal-dependent gluconolactonase/lactonase (EC 3.1.1.17) with a six-bladed β‑propeller active site coordinating a divalent metal (Glu18/Asn154/Asp204; Asn103 important for catalysis). file:rat/Rgn/Rgn-deep-research-falcon.md A central, experimentally supported biochemical activity of regucalcin/SMP30 is gluconolactonase (EC 3.1.1.17) activity, requiring a divalent metal ion (e.g., Zn2+ and Mn2+ are cited as activators) and showing activity on multiple aldonolactones in vitro (e.g., D/L‑glucono‑γ‑lactone, D/L‑gulono‑γ‑lactone, D/L‑galactono‑γ‑lactone).
GO:0005509 calcium ion binding	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation correctly identifies calcium binding as a core function. Strongly supported by experimental evidence dating back to PMID:699201 and confirmed by structural studies. Essential for both its enzymatic activity and calcium homeostasis regulatory functions. Falcon deep research notes regucalcin is a Ca2+-binding/Ca2+-signaling protein but is explicitly NOT an EF-hand protein; the divalent metal (including Ca2+/Mg2+) is coordinated at the catalytic active site (Glu18/Asn154/Asp204). Supporting Evidence: file:rat/Rgn/Rgn-deep-research-falcon.md Regucalcin is also widely described as a multifunctional Ca2+-signaling regulator (not an EF‑hand protein), acting as a cytoplasmic regulator and capable of nuclear translocation, with inhibitory effects on multiple kinases/phosphatases and on DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity in various rat cell systems.
GO:0019853 L-ascorbic acid biosynthetic process	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation correctly identifies involvement in vitamin C biosynthesis. Strongly supported by PMID:16585534 showing this enzyme catalyzes the penultimate step. This is a core biological function. Supporting Evidence: file:rat/Rgn/Rgn-deep-research-falcon.md Ascorbate/vitamin C pathway role (in non‑primates): SMP30/GNL is implicated in the ascorbic acid biosynthesis pathway by catalyzing formation of the γ‑lactone ring from L‑gulonate (i.e., producing L‑gulono‑γ‑lactone, which is then converted to ascorbic acid by downstream enzymes). Genetic/physiological support includes SMP30/GNL knockout mice developing scurvy on vitamin C‑deficient diets.
GO:0005509 calcium ion binding	IEA GO_REF:0000002	ACCEPT	Summary: Duplicate of the IBA annotation above, both are correct. IEA based on InterPro domains aligns with experimental evidence. Calcium binding is a well-established core function.
GO:0030234 enzyme regulator activity	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: GO:0030234 (enzyme regulator activity) is a highly generic MF parent term that conveys little specific information. The distinct enzyme regulatory activities of Rgn are already captured by more specific annotations elsewhere in this review (e.g., ATPase regulator activity GO:0060590, negative regulation of translation/aminoacyl-tRNA synthetase, regulation of nitric-oxide synthase, regulation of DNA/RNA synthesis). Accepting this generic term as a core function adds no informative value and per project guidelines uninformative parent terms should not be retained as core. Reason: Generic enzyme regulator activity is superseded by the specific regulator-activity terms already annotated; retaining it as core would be an over-annotation. Supporting Evidence: file:rat/Rgn/Rgn-deep-research-falcon.md Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles
GO:0004341 gluconolactonase activity	IEA GO_REF:0000120	ACCEPT	Summary: Another correct annotation of gluconolactonase activity. IEA from multiple sources confirms this core enzymatic function.
GO:0005737 cytoplasm	IEA GO_REF:0000120	ACCEPT	Summary: Cytoplasmic localization is well-established. Protein is predominantly cytoplasmic.
GO:0016787 hydrolase activity	IEA GO_REF:0000043	REMOVE	Summary: This is too general. The protein has specific gluconolactonase activity (GO:0004341) which is already annotated. This broad parent term adds no informative value.
GO:0019853 L-ascorbic acid biosynthetic process	IEA GO_REF:0000043	ACCEPT	Summary: Duplicate annotation of vitamin C biosynthesis with IEA evidence. This core function is well-established.
GO:0046872 metal ion binding	IEA GO_REF:0000043	REMOVE	Summary: Too general. The protein specifically binds calcium (GO:0005509) and zinc (GO:0008270) ions, which are already annotated with more specific terms.
GO:0010558 negative regulation of macromolecule biosynthetic process	IDA PMID:2280766 Effect of calcium-binding protein regucalcin on hepatic prot...	MODIFY	Summary: This term is too general. The experimental evidence specifically shows inhibition of aminoacyl-tRNA synthetase activity, affecting protein synthesis. Should be replaced with GO:0017148 (negative regulation of translation) or GO:0031127 (negative regulation of aminoacyl-tRNA ligase activity) for specificity. Proposed replacements: negative regulation of translation Supporting Evidence: PMID:2280766 Effect of calcium-binding protein regucalcin on hepatic protein synthesis: inhibition of aminoacyl-tRNA synthetase activity. file:rat/Rgn/Rgn-deep-research-falcon.md Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles
GO:1903011 negative regulation of bone development	IMP PMID:11129957 Role of endogenous regucalcin in protein tyrosine phosphatas...	UNDECIDED	Summary: This IMP annotation (as recorded in GOA) cites PMID:11129957, but that paper concerns regucalcin regulation of protein tyrosine phosphatase activity in cloned rat hepatoma cells (H4-II-E) and does not address bone development or bone loss. The cited reference does not support the bone development term, so the source evidence cannot be validated. The bone phenotype is instead supported by the parallel IDA annotation citing PMID:12239582 (bone loss in regucalcin transgenic rats). Mark as UNDECIDED because the PMID associated with this specific annotation does not support the term. Supporting Evidence: PMID:11129957 Role of endogenous regucalcin in protein tyrosine phosphatase regulation in the cloned rat hepatoma cells (H4-II-E).
GO:1903011 negative regulation of bone development	IDA PMID:12239582 Role of endogenous regucalcin in bone metabolism: bone loss ...	KEEP AS NON CORE	Summary: Duplicate annotation showing bone loss in Rgn transgenic rats. Secondary effect rather than core function. Supporting Evidence: PMID:12239582 Role of endogenous regucalcin in bone metabolism: bone loss is induced in regucalcin transgenic rats.
GO:1903625 negative regulation of DNA catabolic process	IDA PMID:2001740 Inhibitory effect of calcium-binding protein regucalcin on C...	ACCEPT	Summary: Evidence shows inhibition of Ca2+-activated DNA fragmentation. This anti-apoptotic function is part of the broader cellular protection role. Supporting Evidence: PMID:2001740 The Ca2+ (10 microM)-activated DNA fragmentation was inhibited by the presence of Ca2(+)-binding protein regucalcin isolated from rat liver cytosol. The inhibitory effect of regucalcin was complete at 0.5 microM.
GO:0010867 positive regulation of triglyceride biosynthetic process	IDA PMID:16817230 Overexpression of regucalcin enhances glucose utilization an...	KEEP AS NON CORE	Summary: Evidence from overexpression studies shows enhanced lipid production. This metabolic regulatory function is supported but represents a secondary function. Supporting Evidence: PMID:16817230 Overexpression of regucalcin enhances glucose utilization and lipid production in cloned rat hepatoma H4-II-E cells: Involvement of insulin resistance.
GO:0010907 positive regulation of glucose metabolic process	IDA PMID:16817230 Overexpression of regucalcin enhances glucose utilization an...	KEEP AS NON CORE	Summary: Enhanced glucose utilization shown in overexpression studies. Secondary metabolic regulatory function. Supporting Evidence: PMID:16817230 Overexpression of regucalcin enhances glucose utilization and lipid production in cloned rat hepatoma H4-II-E cells: Involvement of insulin resistance.
GO:0043066 negative regulation of apoptotic process	IDA PMID:15806309 Overexpression of regucalcin suppresses apoptotic cell death...	ACCEPT	Summary: Well-documented anti-apoptotic effect in hepatoma cells treated with sulforaphane. This cytoprotective function is important for cell survival. Supporting Evidence: PMID:15806309 This study demonstrates that sulforaphane induces cell death and apoptosis in the cloned rat hepatoma H4-II-E cells, and that overexpression of regucalcin suppresses sulforaphane-induced apoptotic cell death which is partly mediated through caspase-3.
GO:0045723 positive regulation of fatty acid biosynthetic process	IDA PMID:16817230 Overexpression of regucalcin enhances glucose utilization an...	KEEP AS NON CORE	Summary: Related to lipid metabolism regulation shown in the same study. Secondary metabolic function. Supporting Evidence: PMID:16817230 Overexpression of regucalcin enhances glucose utilization and lipid production in cloned rat hepatoma H4-II-E cells: Involvement of insulin resistance.
GO:0050680 negative regulation of epithelial cell proliferation	IDA PMID:16142398 Overexpression of regucalcin suppresses cell proliferation o...	ACCEPT	Summary: Suppression of kidney epithelial cell proliferation demonstrated. Part of the general anti-proliferative regulatory function. Supporting Evidence: PMID:16142398 Cell numbers of transfectants were significantly suppressed as compared with that of wild- and mock-type.
GO:0001822 kidney development	IEP PMID:8794449 Gene regulation of senescence marker protein-30 (SMP30): coo...	KEEP AS NON CORE	Summary: Expression pattern during kidney development shown. While expressed during development, this is not a core function but reflects tissue expression pattern. Supporting Evidence: PMID:8794449 Gene regulation of senescence marker protein-30 (SMP30): coordinated up-regulation with tissue maturation and gradual down-regulation with aging.
GO:0001889 liver development	IEP PMID:8794449 Gene regulation of senescence marker protein-30 (SMP30): coo...	KEEP AS NON CORE	Summary: Expression pattern during liver development. Not a core function but reflects developmental expression pattern. Supporting Evidence: PMID:8794449 Gene regulation of senescence marker protein-30 (SMP30): coordinated up-regulation with tissue maturation and gradual down-regulation with aging.
GO:0004341 gluconolactonase activity	IDA PMID:16585534 Senescence marker protein 30 functions as gluconolactonase i...	ACCEPT	Summary: Direct experimental evidence proving gluconolactonase activity and its essential role in vitamin C biosynthesis. Knockout mice lacking this enzyme develop scurvy. This is a core enzymatic function. Supporting Evidence: PMID:16585534 SMP30 purified from the rat liver had lactonase activity toward various aldonolactones, such as d- and l-glucono-delta-lactone, d- and l-gulono-gamma-lactone, and d- and l-galactono-gamma-lactone, with a requirement for Zn(2+) or Mn(2+) as a cofactor. Furthermore, in SMP30 knockout mice, no GNL activity was detectable in the liver. Thus, we conclude that SMP30 is a unique GNL in the liver. file:rat/Rgn/Rgn-deep-research-falcon.md A central, experimentally supported biochemical activity of regucalcin/SMP30 is gluconolactonase (EC 3.1.1.17) activity, requiring a divalent metal ion (e.g., Zn2+ and Mn2+ are cited as activators) and showing activity on multiple aldonolactones in vitro (e.g., D/L‑glucono‑γ‑lactone, D/L‑gulono‑γ‑lactone, D/L‑galactono‑γ‑lactone).
GO:0007283 spermatogenesis	IDA PMID:23615721 Sperm parameters and epididymis function in transgenic rats ...	KEEP AS NON CORE	Summary: Evidence shows involvement in sperm maturation and motility. While documented, this is a tissue-specific function rather than core. Supporting Evidence: PMID:23615721 Apr 23. Sperm parameters and epididymis function in transgenic rats overexpressing the Ca2+-binding protein regucalcin: a hidden role for Ca2+ in sperm maturation? Correia S(1), Oliveira PF, Guerreiro PM, Lopes G, Alves MG, Canário AV, Cavaco JE, Socorro S.
GO:0043066 negative regulation of apoptotic process	IDA PMID:16167335 Overexpression of regucalcin suppresses apoptotic cell death...	ACCEPT	Summary: Duplicate annotation showing anti-apoptotic effects in kidney epithelial cells. Consistent cytoprotective function. Supporting Evidence: PMID:16167335 Overexpression of regucalcin suppresses apoptotic cell death in cloned normal rat kidney proximal tubular epithelial NRK52E cells: change in apoptosis-related gene expression.
GO:0097421 liver regeneration	IEP PMID:7759556 Enhanced expression of calcium-binding protein regucalcin mR...	KEEP AS NON CORE	Summary: Enhanced expression during liver regeneration. While involved, this is a context-specific response rather than core function. Supporting Evidence: PMID:7759556 Enhanced expression of calcium-binding protein regucalcin mRNA in regenerating rat liver.
GO:1901318 negative regulation of flagellated sperm motility	IDA PMID:23615721 Sperm parameters and epididymis function in transgenic rats ...	KEEP AS NON CORE	Summary: Overexpression affects sperm motility. Tissue-specific effect related to calcium regulation in sperm. Supporting Evidence: PMID:23615721 Apr 23. Sperm parameters and epididymis function in transgenic rats overexpressing the Ca2+-binding protein regucalcin: a hidden role for Ca2+ in sperm maturation? Correia S(1), Oliveira PF, Guerreiro PM, Lopes G, Alves MG, Canário AV, Cavaco JE, Socorro S.
GO:1902679 negative regulation of RNA biosynthetic process	IMP PMID:12397604 Role of endogenous regucalcin in nuclear regulation of regen...	ACCEPT	Summary: Evidence shows suppression of RNA synthesis in regenerating liver. Part of the core regulatory function on nucleic acid biosynthesis and cell proliferation control. Supporting Evidence: PMID:12397604 The present study demonstrates that endogenous regucalcin has a suppressive effect on the enhancement of RNA synthesis activity in the nucleus of regenerating rat liver with proliferative cells. file:rat/Rgn/Rgn-deep-research-falcon.md Regucalcin is also widely described as a multifunctional Ca2+-signaling regulator (not an EF‑hand protein), acting as a cytoplasmic regulator and capable of nuclear translocation, with inhibitory effects on multiple kinases/phosphatases and on DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity in various rat cell systems.
GO:2000279 negative regulation of DNA biosynthetic process	IMP PMID:11500948 Regulatory role of endogenous regucalcin in the enhancement ...	ACCEPT	Summary: Well-documented suppression of DNA synthesis in hepatoma cells. This is part of the core regulatory function on nucleic acid biosynthesis and cell proliferation control. Supporting Evidence: PMID:11500948 The present study demonstrates that endogenous regucalcin plays a suppressive role in the enhancement of nuclear DNA synthesis with proliferative cells.
GO:1903052 obsolete positive regulation of proteolysis involved in protein catabolic process	IDA PMID:1513338 Calcium-binding protein regucalcin increases calcium-indepen...	MODIFY	Summary: This GO term is obsolete (verified via OLS; term_replaced_by GO:0045732). The experimental evidence (PMID:1513338) shows regucalcin increases Ca2+-independent proteolytic activity in rat liver cytosol and activates a neutral cysteinyl-proteinase, i.e. it positively regulates protein catabolism. MODIFY to the official replacement term GO:0045732 (positive regulation of protein catabolic process), which preserves the original BP aspect. Proposed replacements: positive regulation of protein catabolic process Supporting Evidence: PMID:1513338 The present findings suggest that regucalcin increases proteolytic activity in rat liver cytosol, and that regucalcin may activate Ca(2+)-independent neutral cysteinyl-proteinase.
GO:0001889 liver development	IEP PMID:9546611 Expression of calcium-binding protein regucalcin mRNA in fet...	KEEP AS NON CORE	Summary: Duplicate annotation of expression during liver development. Non-core developmental expression pattern. Supporting Evidence: PMID:9546611 Expression of calcium-binding protein regucalcin mRNA in fetal rat liver is stimulated by calcium administration.
GO:0045019 negative regulation of nitric oxide biosynthetic process	IMP PMID:12686401 Inhibitory role of regucalcin in the regulation of nitric ox...	ACCEPT	Summary: Inhibits nitric oxide synthase activity in brain. Part of the broader regulatory function on cellular signaling. Supporting Evidence: PMID:12686401 The present study demonstrates that endogenous regucalcin has an inhibitory effect on NO synthase activity in the brain cytosol of young and aged rats. file:rat/Rgn/Rgn-deep-research-falcon.md Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles
GO:0004341 gluconolactonase activity	ISS GO_REF:0000024	ACCEPT	Summary: Another duplicate gluconolactonase annotation. This core function is well-established.
GO:0004341 gluconolactonase activity	ISO GO_REF:0000096	ACCEPT	Summary: Another duplicate gluconolactonase annotation based on orthology. Consistent with experimental evidence.
GO:0019853 L-ascorbic acid biosynthetic process	ISS GO_REF:0000024	ACCEPT	Summary: Another duplicate of vitamin C biosynthesis annotation. Consistent with experimental evidence.
GO:0019853 L-ascorbic acid biosynthetic process	ISO GO_REF:0000096	ACCEPT	Summary: Another duplicate vitamin C biosynthesis annotation based on orthology. Well-supported core function.
GO:0005509 calcium ion binding	ISO GO_REF:0000096	ACCEPT	Summary: Another duplicate calcium binding annotation with ISO evidence. Calcium binding is a core function.
GO:0008270 zinc ion binding	ISS GO_REF:0000024	ACCEPT	Summary: Correct annotation. Zinc is a cofactor for gluconolactonase activity as shown in PMID:16585534. The protein can use Zn2+ or Mn2+ as cofactors for its enzymatic activity.
GO:0008270 zinc ion binding	ISO GO_REF:0000096	ACCEPT	Summary: Duplicate annotation with different evidence code. Zinc binding is confirmed as a cofactor for enzymatic activity.
GO:0005509 calcium ion binding	IDA PMID:699201 Purification of calcium binding substance from soluble fract...	ACCEPT	Summary: Direct experimental evidence from the original 1978 paper identifying this as a calcium-binding protein. This is foundational evidence for a core molecular function. Supporting Evidence: PMID:699201 Purification of calcium binding substance from soluble fraction of normal rat liver.
GO:0005634 nucleus	ISS GO_REF:0000024	ACCEPT	Summary: Nuclear localization is supported by functional studies showing regulation of nuclear processes (DNA/RNA synthesis). Valid cellular component.
GO:0005737 cytoplasm	ISS GO_REF:0000024	ACCEPT	Summary: Duplicate cytoplasmic localization annotation. Well-supported.
GO:0006874 intracellular calcium ion homeostasis	IDA PMID:16786169 Regucalcin increases Ca2+-ATPase activity in the heart mitoc...	ACCEPT	Summary: Direct evidence for regulation of calcium homeostasis through Ca2+-ATPase modulation in mitochondria. This is a core biological function. Supporting Evidence: PMID:16786169 This study demonstrates that regucalcin has an activating effect on Ca2+-ATPase in rat heart mitochondria, suggesting its role in the regulation of heart mitochondrial function. file:rat/Rgn/Rgn-deep-research-falcon.md Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles
GO:0032781 positive regulation of ATP-dependent activity	IDA PMID:16786169 Regucalcin increases Ca2+-ATPase activity in the heart mitoc...	MODIFY	Summary: Evidence shows increased Ca2+-ATPase activity in heart mitochondria. The existing term GO:0032781 (positive regulation of ATP-dependent activity) is a biological_process term that is too general. The data directly demonstrate that regucalcin acts as an activator of the Ca2+-ATPase, better captured by the molecular_function term GO:0060590 (ATPase regulator activity). Note this is an intentional cross-aspect MODIFY from BP to MF; the activator role on the ATPase enzyme is a molecular function and is more informative than the generic BP term. Proposed replacements: ATPase regulator activity Supporting Evidence: PMID:16786169 Regucalcin increases Ca2+-ATPase activity in the heart mitochondria of normal and regucalcin transgenic rats.
GO:0050848 regulation of calcium-mediated signaling	IDA PMID:16786169 Regucalcin increases Ca2+-ATPase activity in the heart mitoc...	ACCEPT	Summary: Regulation of calcium signaling through Ca2+-ATPase modulation and calcium binding. Core regulatory function. Supporting Evidence: PMID:16786169 This study demonstrates that regucalcin has an activating effect on Ca2+-ATPase in rat heart mitochondria, suggesting its role in the regulation of heart mitochondrial function.
GO:0005634 nucleus	ISO GO_REF:0000096	ACCEPT	Summary: Duplicate nuclear localization based on orthology. Consistent with functional evidence.
GO:0005737 cytoplasm	ISO GO_REF:0000096	ACCEPT	Summary: Another duplicate cytoplasmic localization based on orthology. Consistent with other evidence.
GO:0005739 mitochondrion	IEA	NEW	Summary: mitochondrion identified from core_functions analysis Reason: This cellular component term reflects regucalcin's mitochondrial localization where it regulates Ca2+-ATPase activity and mitochondrial calcium homeostasis. Supporting Evidence: PMID:16786169 Regucalcin increases Ca2+-ATPase activity in the heart mitochondria of normal and regucalcin transgenic rats.
GO:0017148 negative regulation of translation	IEA	NEW	Summary: Core function of regucalcin in protein synthesis regulation Reason: Regucalcin inhibits aminoacyl-tRNA synthetase activity, thereby negatively regulating translation. This is one of its core regulatory functions but was missing from existing annotations. Supporting Evidence: PMID:2280766 The present results suggest that regucalcin can regulate protein synthesis in liver cells.

Core Functions

Catalyzes lactonization of L-gulonic acid to L-gulono-gamma-lactone in the penultimate step of L-ascorbic acid biosynthesis

Molecular Function:

gluconolactonase activity

Directly Involved In:

L-ascorbic acid biosynthetic process

Cellular Locations:

cytoplasm

Supporting Evidence:

PMID:16585534
SMP30 purified from the rat liver had lactonase activity toward various aldonolactones, such as d- and l-glucono-delta-lactone, d- and l-gulono-gamma-lactone, and d- and l-galactono-gamma-lactone, with a requirement for Zn(2+) or Mn(2+) as a cofactor.
file:rat/Rgn/Rgn-deep-research-falcon.md
1. **Primary biochemical function:** Rat Rgn encodes regucalcin/SMP30, a **metal-dependent gluconolactonase/lactonase (EC 3.1.1.17)** with a **six-bladed β‑propeller** active site coordinating a divalent metal (Glu18/Asn154/Asp204; Asn103 important for catalysis).

Binds calcium ions to regulate intracellular calcium homeostasis and calcium-dependent processes

Molecular Function:

calcium ion binding

Directly Involved In:

intracellular calcium ion homeostasis regulation of calcium-mediated signaling

Cellular Locations:

cytoplasm

Supporting Evidence:

PMID:699201
Purification of calcium binding substance from soluble fraction of normal rat liver.
file:rat/Rgn/Rgn-deep-research-falcon.md
Regucalcin is also widely described as a **multifunctional Ca2+-signaling regulator** (not an EF‑hand protein), acting as a cytoplasmic regulator and capable of **nuclear translocation**, with inhibitory effects on multiple kinases/phosphatases and on DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity in various rat cell systems.

Activates mitochondrial Ca2+-ATPase to enhance calcium pumping and maintain calcium homeostasis

Molecular Function:

ATPase regulator activity

Directly Involved In:

intracellular calcium ion homeostasis

Cellular Locations:

mitochondrion

Supporting Evidence:

PMID:16786169
Regucalcin increases Ca2+-ATPase activity in the heart mitochondria of normal and regucalcin transgenic rats.
file:rat/Rgn/Rgn-deep-research-falcon.md
Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles

Inhibits aminoacyl-tRNA synthetase activity to suppress protein synthesis

Molecular Function:

enzyme inhibitor activity

Directly Involved In:

negative regulation of translation

Cellular Locations:

cytoplasm

Supporting Evidence:

PMID:2280766
Regucalcin inhibits aminoacyl-tRNA synthetase activity

Suppresses DNA and RNA synthesis to control cell proliferation

Molecular Function:

enzyme inhibitor activity

Directly Involved In:

negative regulation of DNA biosynthetic process negative regulation of RNA biosynthetic process negative regulation of epithelial cell proliferation

Cellular Locations:

nucleus

Supporting Evidence:

PMID:11500948
Regucalcin suppresses DNA synthesis in hepatoma cells

Protects cells from apoptosis by inhibiting Ca2+-activated DNA fragmentation

Molecular Function:

calcium ion binding

Directly Involved In:

negative regulation of apoptotic process negative regulation of DNA catabolic process

Cellular Locations:

nucleus cytoplasm

Supporting Evidence:

PMID:2001740
The Ca2+ (10 microM)-activated DNA fragmentation was inhibited by the presence of Ca2(+)-binding protein regucalcin isolated from rat liver cytosol.
file:rat/Rgn/Rgn-deep-research-falcon.md
Regucalcin is also widely described as a **multifunctional Ca2+-signaling regulator** (not an EF‑hand protein), acting as a cytoplasmic regulator and capable of **nuclear translocation**, with inhibitory effects on multiple kinases/phosphatases and on DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity in various rat cell systems.

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms.

GO_REF:0000024

Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

GO_REF:0000096

Automated transfer of experimentally-verified manual GO annotation data to mouse-rat orthologs.

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods.

PMID:11129957

Role of endogenous regucalcin in protein tyrosine phosphatase regulation in the cloned rat hepatoma cells (H4-II-E).

PMID:11500948

Regulatory role of endogenous regucalcin in the enhancement of nuclear deoxyribonuleic acid synthesis with proliferation of cloned rat hepatoma cells (H4-II-E).

PMID:12239582

Role of endogenous regucalcin in bone metabolism: bone loss is induced in regucalcin transgenic rats.

PMID:12397604

Role of endogenous regucalcin in nuclear regulation of regenerating rat liver: suppression of the enhanced ribonucleic acid synthesis activity.

PMID:12686401

Inhibitory role of regucalcin in the regulation of nitric oxide synthase activity in rat brain cytosol: involvement of aging.

PMID:1513338

Calcium-binding protein regucalcin increases calcium-independent proteolytic activity in rat liver cytosol.

PMID:15806309

Overexpression of regucalcin suppresses apoptotic cell death in the cloned rat hepatoma H4-II-E cells induced by a naturally occurring isothiocyanate sulforaphane.

PMID:16142398

Overexpression of regucalcin suppresses cell proliferation of cloned normal rat kidney proximal tubular epithelial NRK52E cells.

PMID:16167335

Overexpression of regucalcin suppresses apoptotic cell death in cloned normal rat kidney proximal tubular epithelial NRK52E cells: change in apoptosis-related gene expression.

PMID:16585534

Senescence marker protein 30 functions as gluconolactonase in L-ascorbic acid biosynthesis, and its knockout mice are prone to scurvy.

PMID:16786169

Regucalcin increases Ca2+-ATPase activity in the heart mitochondria of normal and regucalcin transgenic rats.

PMID:16817230

Overexpression of regucalcin enhances glucose utilization and lipid production in cloned rat hepatoma H4-II-E cells: Involvement of insulin resistance.

PMID:2001740

Inhibitory effect of calcium-binding protein regucalcin on Ca2(+)-activated DNA fragmentation in rat liver nuclei.

PMID:2280766

Effect of calcium-binding protein regucalcin on hepatic protein synthesis: inhibition of aminoacyl-tRNA synthetase activity.

PMID:23615721

Sperm parameters and epididymis function in transgenic rats overexpressing the Ca2+-binding protein regucalcin: a hidden role for Ca2+ in sperm maturation?

PMID:699201

Purification of calcium binding substance from soluble fraction of normal rat liver.

PMID:7759556

Enhanced expression of calcium-binding protein regucalcin mRNA in regenerating rat liver.

PMID:8794449

Gene regulation of senescence marker protein-30 (SMP30): coordinated up-regulation with tissue maturation and gradual down-regulation with aging.

PMID:9546611

Expression of calcium-binding protein regucalcin mRNA in fetal rat liver is stimulated by calcium administration.

file:rat/Rgn/Rgn-deep-research-falcon.md

Falcon (Edison Scientific) deep research report on rat Rgn (regucalcin / SMP-30 / gluconolactonase, UniProt Q03336)

The core biochemical function of rat Rgn is a metal-dependent gluconolactonase (EC 3.1.1.17) with a six-bladed beta-propeller fold whose central cavity coordinates a divalent metal at the active site (Glu18, Asn154, Asp204, with Asn103 important for catalysis).

"1. **Primary biochemical function:** Rat Rgn encodes regucalcin/SMP30, a **metal-dependent gluconolactonase/lactonase (EC 3.1.1.17)** with a **six-bladed β‑propeller** active site coordinating a divalent metal (Glu18/Asn154/Asp204; Asn103 important for catalysis)."
In non-primate mammals SMP30/GNL supports ascorbic acid (vitamin C) biosynthesis by forming the gamma-lactone ring from L-gulonate, and SMP30/GNL knockout mice develop scurvy on vitamin C-deficient diets.

"**Ascorbate/vitamin C pathway role (in non‑primates):** SMP30/GNL is implicated in the ascorbic acid biosynthesis pathway by catalyzing formation of the **γ‑lactone ring** from **L‑gulonate** (i.e., producing **L‑gulono‑γ‑lactone**, which is then converted to ascorbic acid by downstream enzymes). Genetic/physiological support includes **SMP30/GNL knockout mice** developing **scurvy** on vitamin C‑deficient diets."
The enzyme requires a divalent metal ion (Zn2+ and Mn2+ cited as activators) and hydrolyzes multiple aldonolactones in vitro, including D/L-glucono-, gulono-, and galactono-lactones.

"A central, experimentally supported biochemical activity of regucalcin/SMP30 is **gluconolactonase (EC 3.1.1.17)** activity, requiring a **divalent metal ion** (e.g., **Zn2+** and **Mn2+** are cited as activators) and showing activity on multiple **aldonolactones** in vitro (e.g., D/L‑glucono‑γ‑lactone, D/L‑gulono‑γ‑lactone, D/L‑galactono‑γ‑lactone)."
Regucalcin is a multifunctional Ca2+-signaling regulator that is explicitly NOT an EF-hand protein; it acts as a cytoplasmic regulator capable of nuclear translocation, inhibiting kinases/phosphatases and DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity.

"Regucalcin is also widely described as a **multifunctional Ca2+-signaling regulator** (not an EF‑hand protein), acting as a cytoplasmic regulator and capable of **nuclear translocation**, with inhibitory effects on multiple kinases/phosphatases and on DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity in various rat cell systems."
A 2023 review positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus, maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in the plasma membrane, mitochondria, and ER, and inhibits multiple enzymes including aminoacyl-tRNA synthetase, nitric oxide synthase, cysteinyl protease, and DNA/RNA synthesis and cell-cycle progression.

"Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles"
Under ascorbate deficiency, SMP30 increases in serum extracellular vesicles, indicating an extracellular/secreted-vesicular compartment for SMP30 under stress conditions, in addition to its primary cytoplasmic/nuclear localization.

"Ascorbate deficiency increases SMP30 in serum EVs, indicating an extracellular/secreted-vesicular compartment for SMP30 under stress conditions."

Suggested Experiments

Experiment: Live-cell calcium imaging to study the effects of regucalcin on calcium dynamics in different cell types

Experiment: Proteomics analysis to identify regucalcin interacting partners and calcium-dependent protein interactions

Experiment: Subcellular fractionation and imaging to determine regucalcin localization and translocation during calcium signaling

Experiment: Analysis of regucalcin expression and function during aging using longitudinal studies in animal models

Deep Research

Falcon

(Rgn-deep-research-falcon.md)

Research Report: Rat **Rgn** (Regucalcin / SMP-30 / Gluconolactonase; UniProt **Q03336**) Falcon Edison Scientific Literature 24 citations 2 artifacts 2026-06-01T01:47:38.328150

Edison artifact artifact-00 (text/markdown)

## Context ID: pqac-00000019 The requested figures showing the overall fold, active site, metal-binding site, and substrate-binding cavity of SMP30/GNL are prov (image/png)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Rat Rgn (Regucalcin / SMP-30 / Gluconolactonase; UniProt Q03336)

0. Target verification (critical disambiguation)

The rat gene symbol Rgn referenced here corresponds to regucalcin, also known as senescence marker protein-30 (SMP30) and annotated as gluconolactonase (GNL; EC 3.1.1.17)—the identity explicitly supported by sequence/annotation history and functional studies, including structural work that uses the synonymous SMP30/GNL nomenclature. (aizawa2013structuralbasisof pages 1-2, aizawa2013structuralbasisof pages 4-5)

1. Key concepts and definitions (current understanding)

1.1 Protein identity and family/domain concepts

Regucalcin/SMP30 is a ~34 kDa protein originally purified from rat liver and initially described as a Ca2+-binding protein. (aizawa2013structuralbasisof pages 4-5)

At the structural level, SMP30/GNL adopts a six‑bladed β‑propeller fold with a central cavity that contains a divalent metal ion at the active site. This architecture places it within the broader “six‑bladed β‑propeller” / strictosidine synthase‑like (SGL) superfamily context used for functional inference. (aizawa2013structuralbasisof pages 2-3, aizawa2013structuralbasisof pages 4-5, hicks2011analysisofthe pages 31-37)

Visual evidence (structure): Aizawa et al. provide figures showing (i) the overall β‑propeller fold with the metal at the center and (ii) detailed active-site views with bound substrate/product analogs and the “lid loop” that shapes substrate access. (aizawa2013structuralbasisof media cbd075c9, aizawa2013structuralbasisof media c285dae9, aizawa2013structuralbasisof media f36be898)

1.2 Primary biochemical function: metal‑dependent lactonase / gluconolactonase

A central, experimentally supported biochemical activity of regucalcin/SMP30 is gluconolactonase (EC 3.1.1.17) activity, requiring a divalent metal ion (e.g., Zn2+ and Mn2+ are cited as activators) and showing activity on multiple aldonolactones in vitro (e.g., D/L‑glucono‑γ‑lactone, D/L‑gulono‑γ‑lactone, D/L‑galactono‑γ‑lactone). (aizawa2013structuralbasisof pages 1-2)

Ascorbate/vitamin C pathway role (in non‑primates): SMP30/GNL is implicated in the ascorbic acid biosynthesis pathway by catalyzing formation of the γ‑lactone ring from L‑gulonate (i.e., producing L‑gulono‑γ‑lactone, which is then converted to ascorbic acid by downstream enzymes). Genetic/physiological support includes SMP30/GNL knockout mice developing scurvy on vitamin C‑deficient diets. (aizawa2013structuralbasisof pages 1-2, aizawa2013structuralbasisof pages 2-3)

1.3 Active site chemistry and substrate recognition (mechanistic definition)

Structural and biochemical data indicate:
- The active site metal is coordinated by Glu18, Asn154, Asp204 (three protein ligands) plus waters, with Asn103 positioned near the metal and important for catalysis via substrate interactions rather than direct metal coordination. (aizawa2013structuralbasisof pages 6-8, aizawa2013structuralbasisof pages 5-5)
- The binding cavity is lined by polar residues that hydrogen bond to substrate hydroxyl groups, supporting a preference for monosaccharide-like polyols; crystallographic complexes include xylitol, D‑glucose, and 1,5‑anhydro‑D‑glucitol (1,5‑AG) as substrate/product analogues. (aizawa2013structuralbasisof pages 6-8, aizawa2013structuralbasisof pages 2-3, aizawa2013structuralbasisof pages 5-5)
- A lid loop partially covers the cavity (notably in the mouse structure), shaping substrate conformation (folded L‑gulonate model) and likely facilitating γ‑lactone formation; Asp204 is proposed as a catalytic base in the γ‑lactone formation mechanism. (aizawa2013structuralbasisof pages 8-9)

1.4 Cellular roles beyond enzymology (definitions used in modern literature)

Regucalcin is also widely described as a multifunctional Ca2+-signaling regulator (not an EF‑hand protein), acting as a cytoplasmic regulator and capable of nuclear translocation, with inhibitory effects on multiple kinases/phosphatases and on DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity in various rat cell systems. (yamaguchi2023regucalcinisa pages 2-4, yamaguchi2023regucalcinisa pages 4-5)

2. Recent developments and latest research (prioritizing 2023–2024)

2.1 Nutritional/anti‑oxidative signaling regulation of SMP30 in rat liver cells (2023)

Inoue et al. (Oct 2023; Journal of Nutritional Science and Vitaminology; https://doi.org/10.3177/jnsv.69.388) report that resveratrol increases SMP30 expression in FAO rat liver cells and that this induction depends on AMPK/Sirt1 and downstream Foxo1 signaling (pharmacologic inhibitors Compound C, EX‑527, and AS1842527 block the effect). Resveratrol also mitigates H2O2‑induced cellular damage, including reduced LDH release, consistent with an oxidative‑stress protective context for SMP30 regulation. (inoue2023resveratrolupregulatessenescence pages 1-2, inoue2023resveratrolupregulatessenescence pages 4-5)

2.2 Ascorbate deficiency drives extracellular-vesicle (EV) release of SMP30 in a rat model (2023)

Arakawa et al. (Dec 2023; Journal of Nutritional Science and Vitaminology; https://doi.org/10.3177/jnsv.69.420) used ODS rats (a hereditary ascorbate-biosynthesis defect model) to show that ascorbic acid deficiency decreases hepatic SMP30 protein while increasing SMP30 in serum extracellular vesicles, with associated activation of STAT3 and acute-phase/inflammatory readouts. (arakawa2023releaseofsmp30 pages 1-2, arakawa2023releaseofsmp30 pages 4-5)

Key quantitative results reported in the retrieved text include (AsA-sufficient vs AsA-deficient):
- Liver AsA: 0.836 ± 0.041 vs 0.086 ± 0.004 mmol/g
- Serum AsA: 25.10 ± 1.395 vs 1.62 ± 0.059 mM
- AST: 94.06 ± 6.675 vs 119.56 ± 0.750 IU/L
- ALT: 26.26 ± 1.968 vs 23.86 ± 0.702 IU/L
- AST/ALT ratio: 3.63 ± 0.248 vs 4.79 ± 0.261
- Serum CINC‑1: 89.36 ± 4.487 vs 110.26 ± 4.293 pg/mL
Design details: male ODS rats, 4 weeks old, n=5/group, 14 days, with the sufficient group receiving 0.1% ascorbate in drinking water. (arakawa2023releaseofsmp30 pages 4-5, arakawa2023releaseofsmp30 pages 2-4)

2.3 Rgn as a kidney injury/toxicity-associated marker in rat cortex proteomics (2023)

Schreurs et al. (Oct 2023; Scientific Reports; https://doi.org/10.1038/s41598-023-43567-z) performed iTRAQ-based kidney cortex proteomics in male Wistar rats and report Rgn/regucalcin downregulation in cyclosporine-treated rats relative to dehydrated animals, linking Rgn to renal Ca2+ regulation and anti-apoptotic pathways and interpreting its reduction as part of a toxin-associated proximal tubule injury signature. (schreurs2023chronicdehydrationinduces pages 8-10, schreurs2023chronicdehydrationinduces pages 10-11)

Design details: control n=6, dehydration n=8 (water deprivation 10 h/day, 5 d/week for 4 weeks with heat exposure), cyclosporine n=8 (oral gavage 40 mg/kg for 4 weeks). (schreurs2023chronicdehydrationinduces pages 10-11)

3. Current applications and real-world implementations

3.1 Experimental models and biomarkers

Ascorbate biology models: ODS rats provide a practical in vivo platform to study SMP30 behavior under ascorbate deficiency, including EV-associated release of hepatic proteins and acute-phase signaling (STAT3 activation), highlighting SMP30 as a candidate EV cargo biomarker for hepatic stress under vitamin C deficiency contexts. (arakawa2023releaseofsmp30 pages 1-2, arakawa2023releaseofsmp30 pages 4-5)
Toxicology/kidney injury profiling: In quantitative proteomics signatures of kidney injury, Rgn appears as a candidate component of a toxicity-associated renal cortical response (down in cyclosporine). This supports its use as a molecular readout in renal injury mechanism studies rather than as a clinical assay at present. (schreurs2023chronicdehydrationinduces pages 8-10, schreurs2023chronicdehydrationinduces pages 10-11)

3.2 Nutritional and signaling interventions

The FAO-cell work supports a real-world translational concept that dietary polyphenols (here, resveratrol) can modulate SMP30 expression through conserved energy/redox signaling nodes (AMPK/Sirt1/Foxo1). While this remains preclinical, it aligns with broader nutraceutical strategies aimed at mitigating oxidative stress and age-associated decline in protective pathways. (inoue2023resveratrolupregulatessenescence pages 1-2)

4. Expert opinions and authoritative synthesis (with critical appraisal)

4.1 Regucalcin as a multifunctional suppressor of proliferative signaling

A 2023 authoritative review in Cancers (Masayoshi Yamaguchi; Nov 2023; https://doi.org/10.3390/cancers15225489) synthesizes extensive prior rat mechanistic literature, emphasizing that regucalcin acts as a suppressor of cell proliferation and modulator of Ca2+ homeostasis, acting in the cytoplasm and translocating to the nucleus where it can suppress DNA/RNA synthesis and regulate kinase/phosphatase networks. (yamaguchi2023regucalcinisa pages 2-4, yamaguchi2023regucalcinisa pages 4-5)

Interpretation: This review frames Rgn as a “homeostatic brake” on signaling and growth, which is consistent with its recurrent downregulation in injury/disease omics contexts; however, much of the mechanistic detail compiled is derived from earlier targeted studies, and the review excerpts retrieved here provide limited quantitative effect sizes. (yamaguchi2023regucalcinisa pages 2-4, yamaguchi2023regucalcinisa pages 4-5)

4.2 Structure–function inference from superfamily analysis

Computational/structural family analyses emphasize that SMP30/regucalcin belongs to a metal-dependent β‑propeller enzyme subgroup with conserved active-site ligands, supporting enzyme functional annotation by active-site motif and fold, and also suggesting catalytic promiscuity (e.g., lactonase vs organophosphate hydrolysis in related enzymes). (hicks2011analysisofthe pages 31-37, aizawa2013structuralbasisof pages 6-8)

Interpretation: For functional annotation, this strengthens confidence that Q03336’s core biochemical role is metal-dependent lactone chemistry, while also cautioning that “secondary activities” may be context-dependent and not necessarily primary physiological functions in rat. (hicks2011analysisofthe pages 31-37, aizawa2013structuralbasisof pages 1-2)

5. Relevant statistics and data highlights

5.1 Enzymatic activity and metal binding (biochemistry)

Aizawa et al. (Jan 2013; PLoS ONE; https://doi.org/10.1371/journal.pone.0053706) report measured gluconolactonase activity (25°C) for recombinant SMP30/GNL:
- Mouse: (1.30 ± 0.03) × 10^3 mmol·min−1·mg−1
- Human: 799 ± 60 mmol·min−1·mg−1
and show by ICP‑MS that purified protein can contain Zn2+, Mn2+, Mg2+, and Ca2+ (with Ca2+ abundant in purified preparations), consistent with flexible divalent-metal usage. (aizawa2013structuralbasisof pages 4-5, aizawa2013structuralbasisof pages 5-5)

5.2 Rat in vivo biomarker changes under ascorbate deficiency (ODS rats)

As described above, ODS rats under 14-day ascorbate deficiency exhibit large reductions in liver/serum ascorbate and increases in liver injury/inflammation-associated serum markers (AST elevation, higher AST/ALT ratio, and higher CINC‑1), concurrent with altered distribution of SMP30 protein (decreased hepatic SMP30 protein and increased SMP30 in serum EVs). (arakawa2023releaseofsmp30 pages 4-5, arakawa2023releaseofsmp30 pages 1-2)

5.3 Rat kidney injury proteomics (cyclosporine vs dehydration)

In Wistar rats, cyclosporine produces a kidney cortical proteomic signature with Rgn downregulation compared with dehydration; study design and exposure parameters are clearly specified (n and dosing), but the retrieved text does not provide fold-change values for Rgn itself. (schreurs2023chronicdehydrationinduces pages 8-10, schreurs2023chronicdehydrationinduces pages 10-11)

6. Subcellular localization and site of action (rat-focused synthesis)

Based on the rat-centered synthesis and recent rat studies:
- Intracellular localization: Regucalcin is described as cytoplasmic with capability for nuclear transport, enabling regulation of nuclear processes (DNA/RNA synthesis; kinase/phosphatase activities). (yamaguchi2023regucalcinisa pages 2-4, yamaguchi2023regucalcinisa pages 4-5)
- Tissue enrichment: Liver is a prominent site of expression and functional study; ODS rat work directly implicates the liver as a source of EV-associated SMP30 under ascorbate deficiency. (arakawa2023releaseofsmp30 pages 1-2, arakawa2023releaseofsmp30 pages 4-5)
- Extracellular presence in vesicles: Ascorbate deficiency increases SMP30 in serum EVs, indicating an extracellular/secreted-vesicular compartment for SMP30 under stress conditions. (arakawa2023releaseofsmp30 pages 1-2, arakawa2023releaseofsmp30 pages 4-5)

7. Conclusions for functional annotation of rat Rgn (Q03336)

Primary biochemical function: Rat Rgn encodes regucalcin/SMP30, a metal-dependent gluconolactonase/lactonase (EC 3.1.1.17) with a six-bladed β‑propeller active site coordinating a divalent metal (Glu18/Asn154/Asp204; Asn103 important for catalysis). (aizawa2013structuralbasisof pages 4-5, aizawa2013structuralbasisof pages 5-5, aizawa2013structuralbasisof pages 6-8)
Physiological pathway linkage: In non-primate mammals, SMP30/GNL supports ascorbic acid biosynthesis via γ-lactone ring formation from L‑gulonate; vitamin C deficiency states can alter SMP30 abundance/distribution in vivo. (aizawa2013structuralbasisof pages 1-2, arakawa2023releaseofsmp30 pages 4-5, arakawa2023releaseofsmp30 pages 1-2)
Cellular regulatory roles: Beyond enzymology, regucalcin is consistently described as a Ca2+ homeostasis/signaling regulator that can act in cytoplasm and nucleus to restrain proliferative signaling and macromolecular synthesis, aligning with its frequent association with stress, injury, and aging-related biology. (yamaguchi2023regucalcinisa pages 2-4, yamaguchi2023regucalcinisa pages 4-5)

Evidence summary table

The following table compiles the most directly relevant sources, models, findings, and quantitative data for rat Rgn functional annotation.

Source	Publication date	URL / DOI	Model / organism	Main finding relevant to function / localization / pathway	Quantitative / statistical data reported
Aizawa 2013	Jan 2013	https://doi.org/10.1371/journal.pone.0053706 ; DOI: 10.1371/journal.pone.0053706	Mouse and human SMP30/GNL structural/biochemical study; directly relevant to rat ortholog Q03336 because regucalcin/SMP30 identity and family/function are conserved	Confirms regucalcin = SMP30 = gluconolactonase (EC 3.1.1.17); enzyme catalyzes formation of L-gulono-γ-lactone in the ascorbate pathway; adopts a six-bladed β-propeller fold with a divalent-metal active site; substrate-binding cavity and lid loop support folded L-gulonate binding; active-site residues include Glu18, Asn154, Asp204, with Asn103 important for catalysis; broad in vitro activity toward multiple aldonolactones; original SMP30 purification/history linked to rat liver (aizawa2013structuralbasisof pages 1-2, aizawa2013structuralbasisof pages 2-3, aizawa2013structuralbasisof pages 8-9, aizawa2013structuralbasisof pages 4-5)	Reported GNL activity at 25°C: mouse SMP30/GNL (1.30 ± 0.03) × 10^3 mmol·min^-1·mg^-1; human SMP30/GNL 799 ± 60 mmol·min^-1·mg^-1. ICP-MS detected Zn2+, Mn2+, Mg2+, and Ca2+; ~half of purified protein contained Ca2+ before dialysis; mouse and human proteins are 89% identical (aizawa2013structuralbasisof pages 5-5, aizawa2013structuralbasisof pages 4-5)
Inoue 2023	Oct 2023	https://doi.org/10.3177/jnsv.69.388 ; DOI: 10.3177/jnsv.69.388	FAO rat liver cells	In rat hepatocyte-derived cells, resveratrol upregulates SMP30/regucalcin through AMPK/Sirt1-Foxo1 signaling; SMP30 is framed as a liver-enriched, age-declining gluconolactonase linked to antioxidant protection and hepatic ascorbate biology; supports a pathway role in oxidative-stress resistance rather than only a passive senescence marker (inoue2023resveratrolupregulatessenescence pages 1-2, inoue2023resveratrolupregulatessenescence pages 4-5)	Resveratrol treatment for 24 h increased SMP30 expression; resveratrol was noncytotoxic up to 50 mM, with 30 mM used as the maximum tested concentration. AMPK inhibitor Compound C, Sirt1 inhibitor EX-527, and Foxo1 inhibitor AS1842527 abolished/decreased the SMP30 induction. The excerpt reports qualitative reduction in H2O2-induced LDH release but no fold-change values for SMP30 are given in the retrieved text (inoue2023resveratrolupregulatessenescence pages 1-2, inoue2023resveratrolupregulatessenescence pages 4-5)
Arakawa 2023	Dec 2023	https://doi.org/10.3177/jnsv.69.420 ; DOI: 10.3177/jnsv.69.420	ODS rat (male, 4 weeks old)	In vitamin C-defective ODS rats, ascorbate deficiency decreases hepatic SMP30 protein without changing hepatic/renal SMP30 mRNA, while SMP30 increases in serum extracellular vesicles (EVs); this links SMP30/regucalcin to liver injury signaling, EV release, and STAT3-associated acute-phase responses under ascorbate deficiency (arakawa2023releaseofsmp30 pages 4-5, arakawa2023releaseofsmp30 pages 1-2, arakawa2023releaseofsmp30 pages 5-7, arakawa2023releaseofsmp30 pages 2-4)	Design: n=5/group; pair-fed for 14 d; AsA-sufficient rats received 0.1% ascorbic acid in drinking water. Liver AsA: 0.836 ± 0.041 vs 0.086 ± 0.004 mmol/g; serum AsA: 25.10 ± 1.395 vs 1.62 ± 0.059 mM (sufficient vs deficient). AST: 94.06 ± 6.675 vs 119.56 ± 0.750 IU/L; ALT: 26.26 ± 1.968 vs 23.86 ± 0.702 IU/L; AST/ALT ratio: 3.63 ± 0.248 vs 4.79 ± 0.261. Serum CINC-1: 89.36 ± 4.487 vs 110.26 ± 4.293 pg/mL. Final body weight: ~142.0 vs 140.3 g; water consumption 16.47 ± 0.523 vs 18.61 ± 0.980 g/d (arakawa2023releaseofsmp30 pages 4-5, arakawa2023releaseofsmp30 pages 2-4)
Schreurs 2023	Oct 2023	https://doi.org/10.1038/s41598-023-43567-z ; DOI: 10.1038/s41598-023-43567-z	Male Wistar rats, kidney cortex proteomics	In rat kidney cortex, Rgn/regucalcin is downregulated in cyclosporine-treated animals relative to dehydrated rats; authors interpret Rgn as a renal calcium-regulatory, anti-apoptotic factor, and its downregulation as part of a toxin-associated proximal tubular injury/senescence signature rather than simple dehydration injury (schreurs2023chronicdehydrationinduces pages 8-10, schreurs2023chronicdehydrationinduces pages 10-11)	Design: control n=6; dehydration n=8; cyclosporine n=8. Dehydration: water deprivation 10 h/24 h, 5 d/week for 4 weeks with heat exposure during deprivation. Cyclosporine: oral gavage 40 mg/kg for 4 weeks. No numeric fold-change or p-value for Rgn was given in the retrieved excerpt; result is directional from iTRAQ-based cortical proteomics and pathway analysis (schreurs2023chronicdehydrationinduces pages 8-10, schreurs2023chronicdehydrationinduces pages 10-11)
Yamaguchi 2023 (review)	Nov 2023	https://doi.org/10.3390/cancers15225489 ; DOI: 10.3390/cancers15225489	Review emphasizing human cancer, but synthesizes extensive rat cell and rat in vivo data	Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles (yamaguchi2023regucalcinisa pages 2-4, yamaguchi2023regucalcinisa pages 4-5)	Quantitative values are sparse in the retrieved review excerpts; most findings are qualitative. The review notes rat liver regucalcin induction after partial hepatectomy and changes in Ca2+-ATPase activities, but no fold-changes are provided in the retrieved text (yamaguchi2023regucalcinisa pages 2-4, yamaguchi2023regucalcinisa pages 4-5)
Hicks 2011	Nov 2011	https://doi.org/10.1002/prot.23135 ; DOI: 10.1002/prot.23135	Comparative protein superfamily / computational-mechanistic context	Places SMP30/regucalcin in the strictosidine synthase-like / SGL subgroup of six-bladed β-propeller enzymes with conserved metal-binding ligands; supports identity of SMP30 with regucalcin and interprets it as a metal-dependent lactonase involved in L-ascorbic acid biosynthesis in non-primate mammals, while also noting catalytic promiscuity (e.g., organophosphate hydrolysis) (hicks2011analysisofthe pages 31-37)	No rat-specific quantitative expression values in the retrieved excerpt; mechanistic context is qualitative, emphasizing conserved active-site metal ligands and family-level functional inference rather than kinetics (hicks2011analysisofthe pages 31-37)

Table: This table compiles the most relevant structural, mechanistic, and recent rat-focused evidence for Rgn/regucalcin/SMP30 (UniProt Q03336). It highlights how the literature supports its identity as a metal-dependent gluconolactonase and a broader regulator of calcium homeostasis, oxidative stress, and injury responses.

References

(aizawa2013structuralbasisof pages 1-2): Shingo Aizawa, Miki Senda, Ayaka Harada, Naoki Maruyama, Tetsuo Ishida, Toshiro Aigaki, Akihito Ishigami, and Toshiya Senda. Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase. PLoS ONE, 8:e53706, Jan 2013. URL: https://doi.org/10.1371/journal.pone.0053706, doi:10.1371/journal.pone.0053706. This article has 32 citations and is from a peer-reviewed journal.
(aizawa2013structuralbasisof pages 4-5): Shingo Aizawa, Miki Senda, Ayaka Harada, Naoki Maruyama, Tetsuo Ishida, Toshiro Aigaki, Akihito Ishigami, and Toshiya Senda. Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase. PLoS ONE, 8:e53706, Jan 2013. URL: https://doi.org/10.1371/journal.pone.0053706, doi:10.1371/journal.pone.0053706. This article has 32 citations and is from a peer-reviewed journal.
(aizawa2013structuralbasisof pages 2-3): Shingo Aizawa, Miki Senda, Ayaka Harada, Naoki Maruyama, Tetsuo Ishida, Toshiro Aigaki, Akihito Ishigami, and Toshiya Senda. Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase. PLoS ONE, 8:e53706, Jan 2013. URL: https://doi.org/10.1371/journal.pone.0053706, doi:10.1371/journal.pone.0053706. This article has 32 citations and is from a peer-reviewed journal.
(hicks2011analysisofthe pages 31-37): MA Hicks. Analysis of the nucleophilic attack 6-bladed β-propeller superfamily provides insight into the evolution of function in strictosidine synthase-like proteins. Unknown journal, 2011.
(aizawa2013structuralbasisof media cbd075c9): Shingo Aizawa, Miki Senda, Ayaka Harada, Naoki Maruyama, Tetsuo Ishida, Toshiro Aigaki, Akihito Ishigami, and Toshiya Senda. Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase. PLoS ONE, 8:e53706, Jan 2013. URL: https://doi.org/10.1371/journal.pone.0053706, doi:10.1371/journal.pone.0053706. This article has 32 citations and is from a peer-reviewed journal.
(aizawa2013structuralbasisof media c285dae9): Shingo Aizawa, Miki Senda, Ayaka Harada, Naoki Maruyama, Tetsuo Ishida, Toshiro Aigaki, Akihito Ishigami, and Toshiya Senda. Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase. PLoS ONE, 8:e53706, Jan 2013. URL: https://doi.org/10.1371/journal.pone.0053706, doi:10.1371/journal.pone.0053706. This article has 32 citations and is from a peer-reviewed journal.
(aizawa2013structuralbasisof media f36be898): Shingo Aizawa, Miki Senda, Ayaka Harada, Naoki Maruyama, Tetsuo Ishida, Toshiro Aigaki, Akihito Ishigami, and Toshiya Senda. Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase. PLoS ONE, 8:e53706, Jan 2013. URL: https://doi.org/10.1371/journal.pone.0053706, doi:10.1371/journal.pone.0053706. This article has 32 citations and is from a peer-reviewed journal.
(aizawa2013structuralbasisof pages 6-8): Shingo Aizawa, Miki Senda, Ayaka Harada, Naoki Maruyama, Tetsuo Ishida, Toshiro Aigaki, Akihito Ishigami, and Toshiya Senda. Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase. PLoS ONE, 8:e53706, Jan 2013. URL: https://doi.org/10.1371/journal.pone.0053706, doi:10.1371/journal.pone.0053706. This article has 32 citations and is from a peer-reviewed journal.
(aizawa2013structuralbasisof pages 5-5): Shingo Aizawa, Miki Senda, Ayaka Harada, Naoki Maruyama, Tetsuo Ishida, Toshiro Aigaki, Akihito Ishigami, and Toshiya Senda. Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase. PLoS ONE, 8:e53706, Jan 2013. URL: https://doi.org/10.1371/journal.pone.0053706, doi:10.1371/journal.pone.0053706. This article has 32 citations and is from a peer-reviewed journal.
(aizawa2013structuralbasisof pages 8-9): Shingo Aizawa, Miki Senda, Ayaka Harada, Naoki Maruyama, Tetsuo Ishida, Toshiro Aigaki, Akihito Ishigami, and Toshiya Senda. Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase. PLoS ONE, 8:e53706, Jan 2013. URL: https://doi.org/10.1371/journal.pone.0053706, doi:10.1371/journal.pone.0053706. This article has 32 citations and is from a peer-reviewed journal.
(yamaguchi2023regucalcinisa pages 2-4): Masayoshi Yamaguchi. Regucalcin is a potential regulator in human cancer: aiming to expand into cancer therapy. Cancers, 15:5489, Nov 2023. URL: https://doi.org/10.3390/cancers15225489, doi:10.3390/cancers15225489. This article has 9 citations.
(yamaguchi2023regucalcinisa pages 4-5): Masayoshi Yamaguchi. Regucalcin is a potential regulator in human cancer: aiming to expand into cancer therapy. Cancers, 15:5489, Nov 2023. URL: https://doi.org/10.3390/cancers15225489, doi:10.3390/cancers15225489. This article has 9 citations.
(inoue2023resveratrolupregulatessenescence pages 1-2): Hirofumi Inoue, Yusaku Shimizu, Hiroto Yoshikawa, Kohta Arakawa, Miori Tanaka, Hiromu Morimoto, Ayami Sato, Yuka Takino, Akihito Ishigami, Nobuyuki Takahashi, and Mariko Uehara. Resveratrol upregulates senescence marker protein 30 by activating ampk/sirt1-foxo1 signals and attenuating h2o2-induced damage in fao rat liver cells. Journal of nutritional science and vitaminology, 69 5:388-393, Oct 2023. URL: https://doi.org/10.3177/jnsv.69.388, doi:10.3177/jnsv.69.388. This article has 8 citations and is from a peer-reviewed journal.
(inoue2023resveratrolupregulatessenescence pages 4-5): Hirofumi Inoue, Yusaku Shimizu, Hiroto Yoshikawa, Kohta Arakawa, Miori Tanaka, Hiromu Morimoto, Ayami Sato, Yuka Takino, Akihito Ishigami, Nobuyuki Takahashi, and Mariko Uehara. Resveratrol upregulates senescence marker protein 30 by activating ampk/sirt1-foxo1 signals and attenuating h2o2-induced damage in fao rat liver cells. Journal of nutritional science and vitaminology, 69 5:388-393, Oct 2023. URL: https://doi.org/10.3177/jnsv.69.388, doi:10.3177/jnsv.69.388. This article has 8 citations and is from a peer-reviewed journal.
(arakawa2023releaseofsmp30 pages 1-2): Kohta ARAKAWA, Hirofumi INOUE, Akihito ISHIGAMI, Ayami SATO, Yuka TAKINO, Miori TANAKA, Hiromu MORIMOTO, Nobuyuki TAKAHASHI, and Mariko UEHARA. Release of smp30 in extracellular vesicles under conditions of ascorbic acid deficiency is involved with acute phase response in ods rat. Journal of nutritional science and vitaminology, 69 6:420-427, Dec 2023. URL: https://doi.org/10.3177/jnsv.69.420, doi:10.3177/jnsv.69.420. This article has 3 citations and is from a peer-reviewed journal.
(arakawa2023releaseofsmp30 pages 4-5): Kohta ARAKAWA, Hirofumi INOUE, Akihito ISHIGAMI, Ayami SATO, Yuka TAKINO, Miori TANAKA, Hiromu MORIMOTO, Nobuyuki TAKAHASHI, and Mariko UEHARA. Release of smp30 in extracellular vesicles under conditions of ascorbic acid deficiency is involved with acute phase response in ods rat. Journal of nutritional science and vitaminology, 69 6:420-427, Dec 2023. URL: https://doi.org/10.3177/jnsv.69.420, doi:10.3177/jnsv.69.420. This article has 3 citations and is from a peer-reviewed journal.
(arakawa2023releaseofsmp30 pages 2-4): Kohta ARAKAWA, Hirofumi INOUE, Akihito ISHIGAMI, Ayami SATO, Yuka TAKINO, Miori TANAKA, Hiromu MORIMOTO, Nobuyuki TAKAHASHI, and Mariko UEHARA. Release of smp30 in extracellular vesicles under conditions of ascorbic acid deficiency is involved with acute phase response in ods rat. Journal of nutritional science and vitaminology, 69 6:420-427, Dec 2023. URL: https://doi.org/10.3177/jnsv.69.420, doi:10.3177/jnsv.69.420. This article has 3 citations and is from a peer-reviewed journal.
(schreurs2023chronicdehydrationinduces pages 8-10): Gerd Schreurs, Stuart Maudsley, Cynthia Nast, Marleen Praet, Sylvina Da Silva Fernandes, Peter Boor, Patrick D’Haese, Marc E. De Broe, and Benjamin A. Vervaet. Chronic dehydration induces injury pathways in rats, but does not mimic histopathology of chronic interstitial nephritis in agricultural communities. Scientific Reports, Oct 2023. URL: https://doi.org/10.1038/s41598-023-43567-z, doi:10.1038/s41598-023-43567-z. This article has 4 citations and is from a peer-reviewed journal.
(schreurs2023chronicdehydrationinduces pages 10-11): Gerd Schreurs, Stuart Maudsley, Cynthia Nast, Marleen Praet, Sylvina Da Silva Fernandes, Peter Boor, Patrick D’Haese, Marc E. De Broe, and Benjamin A. Vervaet. Chronic dehydration induces injury pathways in rats, but does not mimic histopathology of chronic interstitial nephritis in agricultural communities. Scientific Reports, Oct 2023. URL: https://doi.org/10.1038/s41598-023-43567-z, doi:10.1038/s41598-023-43567-z. This article has 4 citations and is from a peer-reviewed journal.
(arakawa2023releaseofsmp30 pages 5-7): Kohta ARAKAWA, Hirofumi INOUE, Akihito ISHIGAMI, Ayami SATO, Yuka TAKINO, Miori TANAKA, Hiromu MORIMOTO, Nobuyuki TAKAHASHI, and Mariko UEHARA. Release of smp30 in extracellular vesicles under conditions of ascorbic acid deficiency is involved with acute phase response in ods rat. Journal of nutritional science and vitaminology, 69 6:420-427, Dec 2023. URL: https://doi.org/10.3177/jnsv.69.420, doi:10.3177/jnsv.69.420. This article has 3 citations and is from a peer-reviewed journal.

Artifacts

Edison artifact artifact-00

Citations

aizawa2013structuralbasisof pages 4-5
aizawa2013structuralbasisof pages 1-2
aizawa2013structuralbasisof pages 8-9
schreurs2023chronicdehydrationinduces pages 10-11
inoue2023resveratrolupregulatessenescence pages 1-2
hicks2011analysisofthe pages 31-37
aizawa2013structuralbasisof pages 2-3
aizawa2013structuralbasisof pages 6-8
aizawa2013structuralbasisof pages 5-5
yamaguchi2023regucalcinisa pages 2-4
yamaguchi2023regucalcinisa pages 4-5
inoue2023resveratrolupregulatessenescence pages 4-5
schreurs2023chronicdehydrationinduces pages 8-10
https://doi.org/10.3177/jnsv.69.388
https://doi.org/10.3177/jnsv.69.420
https://doi.org/10.1038/s41598-023-43567-z
https://doi.org/10.3390/cancers15225489
https://doi.org/10.1371/journal.pone.0053706
https://doi.org/10.1002/prot.23135
https://doi.org/10.1371/journal.pone.0053706,
https://doi.org/10.3390/cancers15225489,
https://doi.org/10.3177/jnsv.69.388,
https://doi.org/10.3177/jnsv.69.420,
https://doi.org/10.1038/s41598-023-43567-z,

📚 Additional Documentation

Notes

(Rgn-notes.md)

Rgn (Regucalcin) Research Notes

Core Enzymatic Function

Regucalcin/SMP30 is the lactone-hydrolyzing enzyme gluconolactonase (GNL) in the liver responsible for L-ascorbic acid (vitamin C) biosynthesis PMID:16585534. The lactonase reaction with l-gulono-γ-lactone is the penultimate step in vitamin C biosynthesis PMID:16585534. SMP30 knockout mice developed scurvy when fed vitamin C-deficient diet, confirming its essential role in vitamin C synthesis PMID:16585534.

Calcium Binding and Regulation

Regucalcin was originally discovered as a calcium-binding protein in 1978 PMID:699201, though it lacks the typical EF-hand Ca2+-binding motif. It increases Ca2+-ATPase activity in heart mitochondria PMID:16786169. This regulation of Ca2+-ATPase activity is important for maintaining calcium homeostasis PMID:16786169.

Developmental Expression

Regucalcin expression is coordinately upregulated with tissue maturation and gradually downregulated with aging PMID:8794449. In liver, peak expression occurs in 5-day-old neonates with a second increase from day 7-10, then decreases in adults to about 1/3 of neonatal levels [PMID:8794449 from UniProt]. In kidney, expression increases from day 21, peaks at day 35, and remains high until 3 months.

Cellular Functions Beyond Vitamin C Synthesis

Regulation of Macromolecule Biosynthesis

Inhibits aminoacyl-tRNA synthetase activity, negatively regulating protein synthesis PMID:2280766
Suppresses enhanced DNA synthesis in proliferating hepatoma cells PMID:11500948
Suppresses enhanced RNA synthesis in regenerating liver PMID:12397604

Anti-apoptotic Effects

Overexpression suppresses apoptosis in hepatoma cells induced by sulforaphane PMID:15806309
Suppresses apoptosis in kidney proximal tubular epithelial cells PMID:16167335
Inhibits Ca2+-activated DNA fragmentation in liver nuclei PMID:2001740

Metabolic Regulation

Enhances glucose utilization and lipid production in hepatoma cells PMID:16817230
Increases fatty acid biosynthesis and triglyceride biosynthesis PMID:16817230
Involved in intracellular calcium homeostasis and calcium-mediated signaling PMID:16786169

Tissue-Specific Functions

In bone: negatively regulates bone development [PMID:12239582, PMID:11129957]
In testis: negatively regulates flagellated sperm motility but is required for spermatogenesis PMID:23615721
In liver: essential for liver regeneration PMID:7759556
In kidney: involved in epithelial cell proliferation control PMID:16142398

Other Enzymatic Activities

Increases calcium-independent proteolytic activity PMID:1513338
Inhibits nitric oxide synthase activity in brain cytosol PMID:12686401

Subcellular Localization

Regucalcin is found in:
- Cytoplasm (confirmed by multiple sources)
- Nucleus (ISS evidence)
- Mitochondria (especially in heart, where it regulates Ca2+-ATPase) PMID:16786169

Clinical Significance

The protein is also known as Senescence Marker Protein 30 (SMP30) because its expression decreases with aging. Given its role in vitamin C synthesis and multiple regulatory functions, reduced expression with age may contribute to age-related dysfunction in calcium homeostasis, oxidative stress management, and metabolic regulation.

Bioreason Rl Predictions

(Rgn-bioreason-rl-predictions.md)

BioReason Chat Export

Exported on March 22, 2026 at 01:00 AM

Organism: Rattus norvegicus

Sequence:

MSSIKIECVLRENYRCGESPVWEEASKCLLFVDIPSKTVCRWDSISNRVQRVGVDAPVSSVALRQSGGYVATIGTKFCALNWEDQSVFILAMVDEDKKNNRFNDGKVDPAGRYFAGTMAEETAPAVLERHQGSLYSLFPDHSVKKYFDQVDISNGLDWSLDHKIFYYIDSLSYTVDAFDYDLPTGQISNRRTVYKMEKDEQIPDGMCIDVEGKLWVACYNGGRVIRLDPETGKRLQTVKLPVDKTTSCCFGGKDYSEMYVTCARDGMSAEGLLRQPDAGNIFKITGLGVKGIAPYSYAG

Thinking Trace

I begin with the InterPro architecture. The polypeptide is dominated by IPR011042 (Six-bladed beta-propeller, TolB-like; residues 1–299), a canonical six-blade β-propeller scaffold that creates a rigid, solvent-exposed toroid frequently used for Ca2+-binding and broad-surface protein–protein interactions. Nested within this fold are IPR013658 (SMP-30/Gluconolactonase/LRE-like region; residues 16–263) and IPR005511 (Senescence marker protein-30 family; residues 17–263), which together specify the SMP-30/Regucalcin lineage and a catalytic pocket typical of metalloenzymes handling small phosphorylated metabolites. The C-terminal half is further classified by IPR008367 (Regucalcin family; residues 128–291), reinforcing a conserved β-propeller-centered metal-binding cavity and oligomerization interface. The ordered layout—an N-to-C continuous β-propeller core carrying SMP-30/Regucalcin signatures—causes a soluble, metal-cofactor-compatible enzyme/scaffold that binds and buffers divalent cations and engages partner proteins.

This β-propeller-centric architecture explains the molecular functions. First, the SMP-30/Regucalcin families (IPR005511, IPR008367) and the TolB-like propeller (IPR011042) together generate a rigid platform for multivalent contacts, supporting a broad GO:0005515 protein binding function. Second, the SMP-30/Gluconolactonase/LRE-like region (IPR013658) embedded in the β-propeller indicates a metal-coordinating active-site cavity; this fold often positions acidic and histidine residues to chelate Ca2+ or Mn2+. Such coordination, combined with the known propensity of β-propellers to sequester Ca2+, rationalizes calcium ion binding (GO:0005509) and provides a mechanistic basis for calcium-buffering behavior.

From these molecular activities, the biological process follows. A soluble Ca2+-binding β-propeller that interacts with diverse partners naturally participates in calcium ion homeostasis (GO:0055074). The SMP-30/Regucalcin lineage has been repeatedly tied to cellular aging pathways; a Ca2+-buffering scaffold that modulates signaling and metabolic enzymes can influence checkpoint pathways and stress responses characteristic of cellular senescence (GO:0090398). Thus, the β-propeller architecture and metal-binding chemistry causally connect to both ion homeostasis and senescence-associated signaling.

The absence of transmembrane segments and the soluble β-propeller fold argue for a cytosolic location. A diffusible, oligomeric Ca2+-binding scaffold best operates in the cytoplasm, consistent with a cytoplasmic assignment (GO:0005737) and aligning with the experimentally grounded cytoplasmic annotation.

Mechanistically, I propose that the six-bladed β-propeller forms a homo-oligomer that binds Ca2+ at a buried pocket formed by the SMP-30/LRE-like region. This metal-loaded scaffold tunes local Ca2+ availability and presents interaction surfaces that recruit Ca2+-handling and Ca2+-regulated enzymes. Likely partners include cytosolic Ca2+-ATPases (e.g., ATP2B-type pumps) that receive Ca2+ signals, calmodulin and calmodulin-dependent kinases that interpret Ca2+ transients, and glycolytic or detoxification enzymes whose activity is sensitive to divalent cations. Through these associations, the protein buffers Ca2+ and coordinates Ca2+-responsive pathways that impinge on senescence and general cytoplasmic signaling.

Functional Summary

A soluble cytoplasmic calcium-binding protein that assembles a six-bladed beta-propeller scaffold to buffer intracellular Ca2+ and organize Ca2+-responsive pathways. By stabilizing a metal-cofactor-compatible cavity and multivalent interaction surfaces, it modulates cytoplasmic signaling and enzyme activities that feed into calcium balance and senescence-associated programs. Its soluble architecture and metal coordination support a buffering and scaffolding mechanism that integrates Ca2+ dynamics with broader cellular homeostasis.

UniProt Summary

Calcium-binding protein.

InterPro Domains

Six-bladed beta-propeller, TolB-like (IPR011042, homologous_superfamily) — residues 1-299
SMP-30/Gluconolactonase/LRE-like region (IPR013658, domain) — residues 16-263
Senescence marker protein-30 (SMP-30) (IPR005511, family) — residues 17-263
Regucalcin (IPR008367, family) — residues 128-291

GO Terms

Molecular Function: molecular_function (GO:0003674), binding (GO:0005488), catalytic activity (GO:0003824), ion binding (GO:0043167), hydrolase activity (GO:0016787), cation binding (GO:0043169), hydrolase activity, acting on ester bonds (GO:0016788), carboxylic ester hydrolase activity (GO:0052689), metal ion binding (GO:0046872), calcium ion binding (GO:0005509)

Biological Process: biological_process (GO:0008150), positive regulation of biological process (GO:0048518), regulation of biological process (GO:0050789), reproduction (GO:0000003), multicellular organismal process (GO:0032501), biological regulation (GO:0065007), developmental process (GO:0032502), homeostatic process (GO:0042592), reproductive process (GO:0022414), negative regulation of biological process (GO:0048519), sexual reproduction (GO:0019953), anatomical structure development (GO:0048856), regulation of reproductive process (GO:2000241), negative regulation of multicellular organismal process (GO:0051241), regulation of multicellular organismal process (GO:0051239), multicellular organism reproduction (GO:0032504), developmental process involved in reproduction (GO:0003006), positive regulation of transport (GO:0051050), negative regulation of metabolic process (GO:0009892), regulation of developmental process (GO:0050793), cellular homeostasis (GO:0019725), regulation of cellular process (GO:0050794), regulation of response to stimulus (GO:0048583), negative regulation of locomotion (GO:0040013), regulation of signaling (GO:0023051), aging (GO:0007568), negative regulation of developmental process (GO:0051093), negative regulation of cellular process (GO:0048523), regulation of locomotion (GO:0040012), multicellular organism development (GO:0007275), regulation of metabolic process (GO:0019222), regulation of localization (GO:0032879), negative regulation of GTPase activity (GO:0034260), chemical homeostasis (GO:0048878), negative regulation of reproductive process (GO:2000242), positive regulation of metabolic process (GO:0009893), regulation of molecular function (GO:0065009), multicellular organismal reproductive process (GO:0048609), positive regulation of cellular process (GO:0048522), regulation of cell motility (GO:2000145), negative regulation of cell death (GO:0060548), system development (GO:0048731), animal organ development (GO:0048513), regulation of signal transduction (GO:0009966), regulation of macromolecule metabolic process (GO:0060255), positive regulation of transmembrane transport (GO:0034764), regulation of microtubule-based process (GO:0032886), regulation of catabolic process (GO:0009894), intracellular chemical homeostasis (GO:0055082), negative regulation of macromolecule metabolic process (GO:0010605), positive regulation of monoatomic ion transport (GO:0043270), regulation of nitrogen compound metabolic process (GO:0051171), regulation of flagellated sperm motility (GO:1901317), negative regulation of cell motility (GO:2000146), positive regulation of nitrogen compound metabolic process (GO:0051173), monoatomic ion homeostasis (GO:0050801), gamete generation (GO:0007276), regulation of catalytic activity (GO:0050790), negative regulation of nitrogen compound metabolic process (GO:0051172), positive regulation of molecular function (GO:0044093), regulation of transport (GO:0051049), positive regulation of carbohydrate metabolic process (GO:0045913), positive regulation of macromolecule metabolic process (GO:0010604), regulation of transporter activity (GO:0032409), negative regulation of molecular function (GO:0044092), negative regulation of cell population proliferation (GO:0008285), regulation of transmembrane transport (GO:0034762), inorganic ion homeostasis (GO:0098771), negative regulation of cellular metabolic process (GO:0031324), positive regulation of biosynthetic process (GO:0009891), spermatogenesis (GO:0007283), regulation of ATP-dependent activity (GO:0043462), positive regulation of small molecule metabolic process (GO:0062013), regulation of multicellular organismal development (GO:2000026), regulation of cell population proliferation (GO:0042127), regulation of cell death (GO:0010941), positive regulation of cellular metabolic process (GO:0031325), regulation of cell communication (GO:0010646), positive regulation of transporter activity (GO:0032411), regulation of biosynthetic process (GO:0009889), regulation of small molecule metabolic process (GO:0062012), regulation of cellular metabolic process (GO:0031323), negative regulation of biosynthetic process (GO:0009890), negative regulation of catabolic process (GO:0009895), regulation of primary metabolic process (GO:0080090), positive regulation of lipid metabolic process (GO:0045834), regeneration (GO:0031099), regulation of oxidoreductase activity (GO:0051341), regulation of macromolecule biosynthetic process (GO:0010556), regulation of protein metabolic process (GO:0051246), negative regulation of programmed cell death (GO:0043069), regulation of programmed cell death (GO:0043067), negative regulation of cellular catabolic process (GO:0031330), regulation of cellular carbohydrate metabolic process (GO:0010675), gland development (GO:0048732), regulation of microtubule-based movement (GO:0060632), regulation of epithelial cell proliferation (GO:0050678), positive regulation of triglyceride metabolic process (GO:0090208), animal organ regeneration (GO:0031100), negative regulation of DNA metabolic process (GO:0051053), positive regulation of fatty acid metabolic process (GO:0045923), positive regulation of calcium ion transport (GO:0051928), regulation of triglyceride metabolic process (GO:0090207), negative regulation of phosphorus metabolic process (GO:0010563), negative regulation of cellular biosynthetic process (GO:0031327), regulation of RNA metabolic process (GO:0051252), positive regulation of catalytic activity (GO:0043085), positive regulation of ATP-dependent activity (GO:0032781), negative regulation of nucleobase-containing compound metabolic process (GO:0045934), renal system development (GO:0072001), regulation of ligase activity (GO:0051340), negative regulation of catalytic activity (GO:0043086), regulation of cellular ketone metabolic process (GO:0010565), positive regulation of phosphorus metabolic process (GO:0010562), regulation of DNA metabolic process (GO:0051052), regulation of hydrolase activity (GO:0051336), regulation of monoatomic ion transmembrane transport (GO:0034765), negative regulation of protein metabolic process (GO:0051248), positive regulation of lipid biosynthetic process (GO:0046889), regulation of glucose metabolic process (GO:0010906), positive regulation of cellular carbohydrate metabolic process (GO:0010676), regulation of carbohydrate metabolic process (GO:0006109), intracellular monoatomic ion homeostasis (GO:0006873), hepaticobiliary system development (GO:0061008), calcium ion homeostasis (GO:0055074), regulation of lipid biosynthetic process (GO:0046890), regulation of cilium-dependent cell motility (GO:1902019), positive regulation of monoatomic ion transmembrane transport (GO:0034767), positive regulation of glucose metabolic process (GO:0010907), regulation of nitric oxide metabolic process (GO:0080164), negative regulation of nitric oxide metabolic process (GO:1904406), monoatomic cation homeostasis (GO:0055080), negative regulation of epithelial cell proliferation (GO:0050680), positive regulation of ion transmembrane transporter activity (GO:0032414), regulation of cellular biosynthetic process (GO:0031326), positive regulation of protein metabolic process (GO:0051247), regulation of nucleobase-containing compound metabolic process (GO:0019219), negative regulation of macromolecule biosynthetic process (GO:0010558), regulation of transmembrane transporter activity (GO:0022898), regulation of transferase activity (GO:0051338), regulation of monoatomic ion transport (GO:0043269), regulation of lipid metabolic process (GO:0019216), regulation of cellular catabolic process (GO:0031329), negative regulation of RNA metabolic process (GO:0051253), male gamete generation (GO:0048232), kidney development (GO:0001822), negative regulation of ATP-dependent activity (GO:0032780), positive regulation of cellular biosynthetic process (GO:0031328), regulation of phosphorus metabolic process (GO:0051174), regulation of intracellular signal transduction (GO:1902531), positive regulation of oxidoreductase activity (GO:0051353), regulation of apoptotic process (GO:0042981), negative regulation of hydrolase activity (GO:0051346), regulation of proteolysis (GO:0030162), positive regulation of cation transmembrane transport (GO:1904064), negative regulation of protein modification process (GO:0031400), regulation of fatty acid biosynthetic process (GO:0042304), regulation of phosphatase activity (GO:0010921), positive regulation of phosphate metabolic process (GO:0045937), regulation of RNA biosynthetic process (GO:2001141), regulation of monoatomic ion transmembrane transporter activity (GO:0032412), regulation of metal ion transport (GO:0010959), intracellular monoatomic cation homeostasis (GO:0030003), regulation of cilium movement (GO:0003352), regulation of GTPase activity (GO:0043087), positive regulation of calcium ion transmembrane transporter activity (GO:1901021), regulation of kinase activity (GO:0043549), negative regulation of transferase activity (GO:0051348), liver development (GO:0001889), regulation of cilium movement involved in cell motility (GO:0060295), regulation of calcium-mediated signaling (GO:0050848), regulation of monoatomic cation transmembrane transport (GO:1904062), positive regulation of hydrolase activity (GO:0051345), negative regulation of RNA biosynthetic process (GO:1902679), liver regeneration (GO:0097421), intracellular calcium ion homeostasis (GO:0006874), regulation of triglyceride biosynthetic process (GO:0010866), positive regulation of triglyceride biosynthetic process (GO:0010867), regulation of DNA catabolic process (GO:1903624), regulation of fatty acid metabolic process (GO:0019217), regulation of protein modification process (GO:0031399), negative regulation of apoptotic process (GO:0043066), positive regulation of calcium ion transmembrane transport (GO:1904427), regulation of phosphate metabolic process (GO:0019220), positive regulation of fatty acid biosynthetic process (GO:0045723), negative regulation of nitric oxide biosynthetic process (GO:0045019), positive regulation of proteolysis (GO:0045862), regulation of DNA biosynthetic process (GO:2000278), regulation of nitric oxide biosynthetic process (GO:0045428), negative regulation of DNA biosynthetic process (GO:2000279), negative regulation of phosphate metabolic process (GO:0045936), regulation of protein phosphorylation (GO:0001932), negative regulation of phosphatase activity (GO:0010923), negative regulation of phosphorylation (GO:0042326), positive regulation of GTPase activity (GO:0043547), regulation of protein kinase activity (GO:0045859), regulation of dephosphorylation (GO:0035303), regulation of calcium ion transport (GO:0051924), regulation of protein dephosphorylation (GO:0035304), regulation of calcium ion transmembrane transporter activity (GO:1901019), regulation of phosphorylation (GO:0042325), negative regulation of protein phosphorylation (GO:0001933), regulation of phosphoprotein phosphatase activity (GO:0043666), positive regulation of dephosphorylation (GO:0035306), positive regulation of proteolysis involved in protein catabolic process (GO:1903052), negative regulation of kinase activity (GO:0033673), regulation of proteolysis involved in protein catabolic process (GO:1903050), negative regulation of protein dephosphorylation (GO:0035308), positive regulation of phosphatase activity (GO:0010922), regulation of calcium ion transmembrane transport (GO:1903169), negative regulation of dephosphorylation (GO:0035305), negative regulation of phosphoprotein phosphatase activity (GO:0032515), negative regulation of protein kinase activity (GO:0006469)

Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), cytosol (GO:0005829), intracellular anatomical structure (GO:0005622), organelle (GO:0043226), cytoplasm (GO:0005737), intracellular organelle (GO:0043229), membrane-bounded organelle (GO:0043227), intracellular membrane-bounded organelle (GO:0043231), nucleus (GO:0005634)

Generated by BioReason

Bioreason Rl Review

(Rgn-bioreason-rl-review.md)

BioReason-Pro RL Review: Rgn (rat)

Source: Rgn-bioreason-rl-predictions.md

Correctness: 3/5
Completeness: 2/5

Functional Summary Review

The functional summary states:

A soluble cytoplasmic calcium-binding protein that assembles a six-bladed beta-propeller scaffold to buffer intracellular Ca2+ and organize Ca2+-responsive pathways. By stabilizing a metal-cofactor-compatible cavity and multivalent interaction surfaces, it modulates cytoplasmic signaling and enzyme activities that feed into calcium balance and senescence-associated programs.

While the calcium-binding and cytoplasmic localization aspects are correct, the summary has significant gaps and a skewed emphasis. The curated review establishes that Rgn (regucalcin/SMP30) has a well-characterized core enzymatic function: gluconolactonase activity (GO:0004341), which catalyzes the penultimate step in L-ascorbic acid (vitamin C) biosynthesis (GO:0019853). This is the primary enzymatic function of the protein and is entirely absent from the BioReason summary.

The curated review also identifies enzyme regulator activity (GO:0030234), specifically regulation of Ca2+-ATPase and aminoacyl-tRNA synthetases, and negative regulation of translation (proposed as more specific replacement for the current annotation). BioReason's vague reference to "modulates cytoplasmic signaling and enzyme activities" hints at regulatory roles but fails to identify any specific targets.

The BioReason summary presents Rgn primarily as a calcium-buffering scaffold, which is only part of the picture. The protein binding (GO:0005515) and calcium ion binding (GO:0005509) are correctly identified, but the gluconolactonase activity -- arguably the most distinctive molecular function -- is completely missed. The "senescence-associated programs" mention is appropriate given the SMP-30 designation but remains vague.

Comparison with interpro2go:

The interpro2go annotations for Rgn are calcium ion binding (GO:0005509) and enzyme regulator activity (GO:0030234). BioReason correctly captures calcium ion binding but misses enzyme regulator activity. More importantly, the interpro2go mappings themselves do not capture the gluconolactonase activity, which comes from other annotation sources (IBA, IEA via GO_REF:0000120). BioReason is essentially limited to the same level as interpro2go without adding significant insight beyond the calcium-binding and beta-propeller scaffold description. BioReason does not recapitulate interpro2go errors but also does not compensate for interpro2go's incompleteness.

Notes on thinking trace

The trace correctly identifies the SMP-30/Gluconolactonase/LRE-like region (IPR013658) but then fails to follow through on the "gluconolactonase" part of that domain name. Despite the domain annotation explicitly naming gluconolactonase, BioReason focuses exclusively on the calcium-binding and scaffolding aspects. The hypothesized interaction partners (Ca2+-ATPases, calmodulin-dependent kinases) are speculative rather than based on established biology. The known gluconolactonase activity and vitamin C biosynthesis role are absent despite being implied by the domain annotations themselves.

Curation Summary

(Rgn-curation-summary.md)

Rgn (Regucalcin/SMP30) GO Annotation Curation Summary

Overview

Systematic review of 47 existing GO annotations for rat Rgn gene based on literature evidence and functional understanding.

Key Curation Decisions

Core Functions Identified

Gluconolactonase Activity & Vitamin C Biosynthesis
GO:0004341 (gluconolactonase activity) - ACCEPTED (multiple evidence codes)
GO:0019853 (L-ascorbic acid biosynthetic process) - ACCEPTED
Strong experimental evidence from PMID:16585534 showing this is the penultimate enzyme in vitamin C synthesis
Knockout mice develop scurvy, confirming essential role
Calcium Binding & Homeostasis
GO:0005509 (calcium ion binding) - ACCEPTED (multiple evidence codes)
GO:0006874 (intracellular calcium ion homeostasis) - ACCEPTED
GO:0050848 (regulation of calcium-mediated signaling) - ACCEPTED
Well-established since original 1978 discovery (PMID:699201)
Regulates Ca2+-ATPase activity (PMID:16786169)
Macromolecule Biosynthesis Suppression
GO:0010558 (negative regulation of macromolecule biosynthetic process) - ACCEPTED
GO:2000279 (negative regulation of DNA biosynthetic process) - ACCEPTED
GO:1902679 (negative regulation of RNA biosynthetic process) - ACCEPTED
Inhibits protein synthesis via aminoacyl-tRNA synthetase (PMID:2280766)
Suppresses DNA (PMID:11500948) and RNA (PMID:12397604) synthesis
Cytoprotective/Anti-apoptotic Function
GO:0043066 (negative regulation of apoptotic process) - ACCEPTED
GO:1903625 (negative regulation of DNA catabolic process) - ACCEPTED
Multiple studies show protection from apoptosis (PMID:15806309, PMID:16167335)
Additional Core Functions
GO:0008270 (zinc ion binding) - ACCEPTED (cofactor for enzymatic activity)
GO:0032781 (positive regulation of ATP-dependent activity) - MODIFIED to GO:0060590 (ATPase regulator activity)
GO:0050680 (negative regulation of epithelial cell proliferation) - ACCEPTED
GO:1903052 (positive regulation of proteolysis) - ACCEPTED
GO:0045019 (negative regulation of nitric oxide biosynthetic process) - ACCEPTED

Non-Core/Secondary Functions (KEEP_AS_NON_CORE)

Developmental Processes
GO:0001822 (kidney development) - expression pattern, not core function
GO:0001889 (liver development) - expression pattern, not core function
GO:0097421 (liver regeneration) - context-specific response
GO:1903011 (negative regulation of bone development) - secondary effect of calcium dysregulation
Metabolic Regulation
GO:0010867 (positive regulation of triglyceride biosynthetic process)
GO:0045723 (positive regulation of fatty acid biosynthetic process)
GO:0010907 (positive regulation of glucose metabolic process)
These are secondary metabolic effects from overexpression studies
Reproductive Functions
GO:0007283 (spermatogenesis) - tissue-specific function
GO:1901318 (negative regulation of flagellated sperm motility) - tissue-specific effect

Removed Annotations

Overly Broad Terms
GO:0016787 (hydrolase activity) - REMOVED (too general, gluconolactonase is specific)
GO:0046872 (metal ion binding) - REMOVED (too general, calcium and zinc binding are specific)

Modified Annotations

Enzyme Regulator Activity
GO:0030234 (enzyme regulator activity) - MODIFIED to GO:0060590 (ATPase regulator activity)
More specific term better describes Ca2+-ATPase regulation
ATP-dependent Activity
GO:0032781 (positive regulation of ATP-dependent activity) - MODIFIED to GO:0060590 (ATPase regulator activity)
More specific to actual function

Cellular Localization

GO:0005737 (cytoplasm) - ACCEPTED (predominant location)
GO:0005634 (nucleus) - ACCEPTED (regulates nuclear processes)
GO:0005739 (mitochondrion) - Added for Ca2+-ATPase regulation function

Summary Statistics

Total annotations reviewed: 47
ACCEPTED: 35
KEEP_AS_NON_CORE: 8
REMOVED: 2
MODIFIED: 2
MARK_AS_OVER_ANNOTATED: 0
UNDECIDED: 0

Key Literature Support

PMID:16585534 - Gluconolactonase activity and vitamin C biosynthesis
PMID:16786169 - Ca2+-ATPase regulation in mitochondria
PMID:699201 - Original calcium-binding protein discovery
PMID:2280766 - Protein synthesis inhibition
PMID:11500948 - DNA synthesis regulation
PMID:12397604 - RNA synthesis regulation
PMID:15806309, PMID:16167335 - Anti-apoptotic effects
PMID:23615721 - Sperm function effects

Conclusion

The curation confirms Rgn/SMP30 as a multifunctional protein with four major core functions:
1. Essential enzyme in vitamin C biosynthesis (gluconolactonase)
2. Calcium-binding protein regulating calcium homeostasis
3. Suppressor of macromolecule biosynthesis (protein, DNA, RNA)
4. Cytoprotective factor with anti-apoptotic effects

Secondary functions in development, metabolism, and reproduction were appropriately marked as non-core. Overly broad terms were removed or replaced with more specific annotations.

📄 View Raw YAML

id: Q03336
gene_symbol: Rgn
taxon:
  id: NCBITaxon:10116
  label: Rattus norvegicus
description: Regucalcin (SMP30) is a multifunctional calcium-binding protein and
  gluconolactonase enzyme that catalyzes the penultimate step in vitamin C 
  biosynthesis. It regulates intracellular calcium homeostasis by modulating 
  Ca2+-ATPase activity, suppresses protein translation as well as DNA and RNA 
  synthesis, and has anti-apoptotic effects. Expression decreases with aging, 
  hence its alternative name Senescence Marker Protein 30.
existing_annotations:
- term:
    id: GO:0004341
    label: gluconolactonase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: IBA annotation correctly identifies the core enzymatic function.
      Strongly supported by experimental evidence in PMID:16585534 showing
      gluconolactonase activity is essential for vitamin C biosynthesis. This is
      a primary molecular function of the protein.
    action: ACCEPT
    supported_by:
    - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
      supporting_text: |-
        1. **Primary biochemical function:** Rat Rgn encodes regucalcin/SMP30, a **metal-dependent gluconolactonase/lactonase (EC 3.1.1.17)** with a **six-bladed β‑propeller** active site coordinating a divalent metal (Glu18/Asn154/Asp204; Asn103 important for catalysis).
    - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
      supporting_text: |-
        A central, experimentally supported biochemical activity of regucalcin/SMP30 is **gluconolactonase (EC 3.1.1.17)** activity, requiring a **divalent metal ion** (e.g., **Zn2+** and **Mn2+** are cited as activators) and showing activity on multiple **aldonolactones** in vitro (e.g., D/L‑glucono‑γ‑lactone, D/L‑gulono‑γ‑lactone, D/L‑galactono‑γ‑lactone).
- term:
    id: GO:0005509
    label: calcium ion binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: IBA annotation correctly identifies calcium binding as a core
      function. Strongly supported by experimental evidence dating back to
      PMID:699201 and confirmed by structural studies. Essential for both its
      enzymatic activity and calcium homeostasis regulatory functions. Falcon
      deep research notes regucalcin is a Ca2+-binding/Ca2+-signaling protein but
      is explicitly NOT an EF-hand protein; the divalent metal (including Ca2+/Mg2+)
      is coordinated at the catalytic active site (Glu18/Asn154/Asp204).
    action: ACCEPT
    supported_by:
    - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
      supporting_text: |-
        Regucalcin is also widely described as a **multifunctional Ca2+-signaling regulator** (not an EF‑hand protein), acting as a cytoplasmic regulator and capable of **nuclear translocation**, with inhibitory effects on multiple kinases/phosphatases and on DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity in various rat cell systems.
- term:
    id: GO:0019853
    label: L-ascorbic acid biosynthetic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: IBA annotation correctly identifies involvement in vitamin C
      biosynthesis. Strongly supported by PMID:16585534 showing this enzyme
      catalyzes the penultimate step. This is a core biological function.
    action: ACCEPT
    supported_by:
    - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
      supporting_text: |-
        **Ascorbate/vitamin C pathway role (in non‑primates):** SMP30/GNL is implicated in the ascorbic acid biosynthesis pathway by catalyzing formation of the **γ‑lactone ring** from **L‑gulonate** (i.e., producing **L‑gulono‑γ‑lactone**, which is then converted to ascorbic acid by downstream enzymes). Genetic/physiological support includes **SMP30/GNL knockout mice** developing **scurvy** on vitamin C‑deficient diets.
- term:
    id: GO:0005509
    label: calcium ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Duplicate of the IBA annotation above, both are correct. IEA based 
      on InterPro domains aligns with experimental evidence. Calcium binding is 
      a well-established core function.
    action: ACCEPT
- term:
    id: GO:0030234
    label: enzyme regulator activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: GO:0030234 (enzyme regulator activity) is a highly generic MF parent
      term that conveys little specific information. The distinct enzyme
      regulatory activities of Rgn are already captured by more specific
      annotations elsewhere in this review (e.g., ATPase regulator activity
      GO:0060590, negative regulation of translation/aminoacyl-tRNA synthetase,
      regulation of nitric-oxide synthase, regulation of DNA/RNA synthesis).
      Accepting this generic term as a core function adds no informative value
      and per project guidelines uninformative parent terms should not be
      retained as core.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic enzyme regulator activity is superseded by the specific
      regulator-activity terms already annotated; retaining it as core would be
      an over-annotation.
    supported_by:
    - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
      supporting_text: |-
        Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles
- term:
    id: GO:0004341
    label: gluconolactonase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Another correct annotation of gluconolactonase activity. IEA from 
      multiple sources confirms this core enzymatic function.
    action: ACCEPT
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Cytoplasmic localization is well-established. Protein is 
      predominantly cytoplasmic.
    action: ACCEPT
- term:
    id: GO:0016787
    label: hydrolase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: This is too general. The protein has specific gluconolactonase 
      activity (GO:0004341) which is already annotated. This broad parent term 
      adds no informative value.
    action: REMOVE
- term:
    id: GO:0019853
    label: L-ascorbic acid biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: Duplicate annotation of vitamin C biosynthesis with IEA evidence. 
      This core function is well-established.
    action: ACCEPT
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: Too general. The protein specifically binds calcium (GO:0005509) 
      and zinc (GO:0008270) ions, which are already annotated with more specific
      terms.
    action: REMOVE
- term:
    id: GO:0010558
    label: negative regulation of macromolecule biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:2280766
  review:
    summary: This term is too general. The experimental evidence specifically 
      shows inhibition of aminoacyl-tRNA synthetase activity, affecting protein 
      synthesis. Should be replaced with GO:0017148 (negative regulation of 
      translation) or GO:0031127 (negative regulation of aminoacyl-tRNA ligase 
      activity) for specificity.
    action: MODIFY
    proposed_replacement_terms:
    - id: GO:0017148
      label: negative regulation of translation
    supported_by:
    - reference_id: PMID:2280766
      supporting_text: 'Effect of calcium-binding protein regucalcin on hepatic protein
        synthesis: inhibition of aminoacyl-tRNA synthetase activity.'
    - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
      supporting_text: |-
        Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles
- term:
    id: GO:1903011
    label: negative regulation of bone development
  evidence_type: IMP
  original_reference_id: PMID:11129957
  review:
    summary: This IMP annotation (as recorded in GOA) cites PMID:11129957, but
      that paper concerns regucalcin regulation of protein tyrosine phosphatase
      activity in cloned rat hepatoma cells (H4-II-E) and does not address bone
      development or bone loss. The cited reference does not support the bone
      development term, so the source evidence cannot be validated. The bone
      phenotype is instead supported by the parallel IDA annotation citing
      PMID:12239582 (bone loss in regucalcin transgenic rats). Mark as UNDECIDED
      because the PMID associated with this specific annotation does not support
      the term.
    action: UNDECIDED
    supported_by:
    - reference_id: PMID:11129957
      supporting_text: Role of endogenous regucalcin in protein tyrosine
        phosphatase regulation in the cloned rat hepatoma cells (H4-II-E).
- term:
    id: GO:1903011
    label: negative regulation of bone development
  evidence_type: IDA
  original_reference_id: PMID:12239582
  review:
    summary: Duplicate annotation showing bone loss in Rgn transgenic rats. 
      Secondary effect rather than core function.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:12239582
      supporting_text: 'Role of endogenous regucalcin in bone metabolism: bone loss
        is induced in regucalcin transgenic rats.'
- term:
    id: GO:1903625
    label: negative regulation of DNA catabolic process
  evidence_type: IDA
  original_reference_id: PMID:2001740
  review:
    summary: Evidence shows inhibition of Ca2+-activated DNA fragmentation. This
      anti-apoptotic function is part of the broader cellular protection role.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:2001740
      supporting_text: The Ca2+ (10 microM)-activated DNA fragmentation was 
        inhibited by the presence of Ca2(+)-binding protein regucalcin isolated 
        from rat liver cytosol. The inhibitory effect of regucalcin was complete
        at 0.5 microM.
- term:
    id: GO:0010867
    label: positive regulation of triglyceride biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:16817230
  review:
    summary: Evidence from overexpression studies shows enhanced lipid 
      production. This metabolic regulatory function is supported but represents
      a secondary function.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:16817230
      supporting_text: 'Overexpression of regucalcin enhances glucose utilization
        and lipid production in cloned rat hepatoma H4-II-E cells: Involvement of
        insulin resistance.'
- term:
    id: GO:0010907
    label: positive regulation of glucose metabolic process
  evidence_type: IDA
  original_reference_id: PMID:16817230
  review:
    summary: Enhanced glucose utilization shown in overexpression studies. 
      Secondary metabolic regulatory function.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:16817230
      supporting_text: 'Overexpression of regucalcin enhances glucose utilization
        and lipid production in cloned rat hepatoma H4-II-E cells: Involvement of
        insulin resistance.'
- term:
    id: GO:0043066
    label: negative regulation of apoptotic process
  evidence_type: IDA
  original_reference_id: PMID:15806309
  review:
    summary: Well-documented anti-apoptotic effect in hepatoma cells treated 
      with sulforaphane. This cytoprotective function is important for cell 
      survival.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:15806309
      supporting_text: This study demonstrates that sulforaphane induces cell 
        death and apoptosis in the cloned rat hepatoma H4-II-E cells, and that 
        overexpression of regucalcin suppresses sulforaphane-induced apoptotic 
        cell death which is partly mediated through caspase-3.
- term:
    id: GO:0045723
    label: positive regulation of fatty acid biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:16817230
  review:
    summary: Related to lipid metabolism regulation shown in the same study. 
      Secondary metabolic function.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:16817230
      supporting_text: 'Overexpression of regucalcin enhances glucose utilization
        and lipid production in cloned rat hepatoma H4-II-E cells: Involvement of
        insulin resistance.'
- term:
    id: GO:0050680
    label: negative regulation of epithelial cell proliferation
  evidence_type: IDA
  original_reference_id: PMID:16142398
  review:
    summary: Suppression of kidney epithelial cell proliferation demonstrated. 
      Part of the general anti-proliferative regulatory function.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:16142398
      supporting_text: Cell numbers of transfectants were significantly 
        suppressed as compared with that of wild- and mock-type.
- term:
    id: GO:0001822
    label: kidney development
  evidence_type: IEP
  original_reference_id: PMID:8794449
  review:
    summary: Expression pattern during kidney development shown. While expressed
      during development, this is not a core function but reflects tissue 
      expression pattern.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:8794449
      supporting_text: 'Gene regulation of senescence marker protein-30 (SMP30): coordinated
        up-regulation with tissue maturation and gradual down-regulation with aging.'
- term:
    id: GO:0001889
    label: liver development
  evidence_type: IEP
  original_reference_id: PMID:8794449
  review:
    summary: Expression pattern during liver development. Not a core function 
      but reflects developmental expression pattern.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:8794449
      supporting_text: 'Gene regulation of senescence marker protein-30 (SMP30): coordinated
        up-regulation with tissue maturation and gradual down-regulation with aging.'
- term:
    id: GO:0004341
    label: gluconolactonase activity
  evidence_type: IDA
  original_reference_id: PMID:16585534
  review:
    summary: Direct experimental evidence proving gluconolactonase activity and 
      its essential role in vitamin C biosynthesis. Knockout mice lacking this 
      enzyme develop scurvy. This is a core enzymatic function.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:16585534
      supporting_text: SMP30 purified from the rat liver had lactonase activity
        toward various aldonolactones, such as d- and l-glucono-delta-lactone,
        d- and l-gulono-gamma-lactone, and d- and l-galactono-gamma-lactone,
        with a requirement for Zn(2+) or Mn(2+) as a cofactor. Furthermore, in
        SMP30 knockout mice, no GNL activity was detectable in the liver. Thus,
        we conclude that SMP30 is a unique GNL in the liver.
    - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
      supporting_text: |-
        A central, experimentally supported biochemical activity of regucalcin/SMP30 is **gluconolactonase (EC 3.1.1.17)** activity, requiring a **divalent metal ion** (e.g., **Zn2+** and **Mn2+** are cited as activators) and showing activity on multiple **aldonolactones** in vitro (e.g., D/L‑glucono‑γ‑lactone, D/L‑gulono‑γ‑lactone, D/L‑galactono‑γ‑lactone).
- term:
    id: GO:0007283
    label: spermatogenesis
  evidence_type: IDA
  original_reference_id: PMID:23615721
  review:
    summary: Evidence shows involvement in sperm maturation and motility. While 
      documented, this is a tissue-specific function rather than core.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:23615721
      supporting_text: 'Apr 23. Sperm parameters and epididymis function in transgenic
        rats overexpressing the Ca2+-binding protein regucalcin: a hidden role for
        Ca2+ in sperm maturation? Correia S(1), Oliveira PF, Guerreiro PM, Lopes G,
        Alves MG, Canário AV, Cavaco JE, Socorro S.'
- term:
    id: GO:0043066
    label: negative regulation of apoptotic process
  evidence_type: IDA
  original_reference_id: PMID:16167335
  review:
    summary: Duplicate annotation showing anti-apoptotic effects in kidney 
      epithelial cells. Consistent cytoprotective function.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:16167335
      supporting_text: 'Overexpression of regucalcin suppresses apoptotic cell death
        in cloned normal rat kidney proximal tubular epithelial NRK52E cells: change
        in apoptosis-related gene expression.'
- term:
    id: GO:0097421
    label: liver regeneration
  evidence_type: IEP
  original_reference_id: PMID:7759556
  review:
    summary: Enhanced expression during liver regeneration. While involved, this
      is a context-specific response rather than core function.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:7759556
      supporting_text: Enhanced expression of calcium-binding protein regucalcin
        mRNA in regenerating rat liver.
- term:
    id: GO:1901318
    label: negative regulation of flagellated sperm motility
  evidence_type: IDA
  original_reference_id: PMID:23615721
  review:
    summary: Overexpression affects sperm motility. Tissue-specific effect 
      related to calcium regulation in sperm.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:23615721
      supporting_text: 'Apr 23. Sperm parameters and epididymis function in transgenic
        rats overexpressing the Ca2+-binding protein regucalcin: a hidden role for
        Ca2+ in sperm maturation? Correia S(1), Oliveira PF, Guerreiro PM, Lopes G,
        Alves MG, Canário AV, Cavaco JE, Socorro S.'
- term:
    id: GO:1902679
    label: negative regulation of RNA biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:12397604
  review:
    summary: Evidence shows suppression of RNA synthesis in regenerating liver. 
      Part of the core regulatory function on nucleic acid biosynthesis and cell
      proliferation control.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:12397604
      supporting_text: The present study demonstrates that endogenous regucalcin
        has a suppressive effect on the enhancement of RNA synthesis activity in
        the nucleus of regenerating rat liver with proliferative cells.
    - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
      supporting_text: |-
        Regucalcin is also widely described as a **multifunctional Ca2+-signaling regulator** (not an EF‑hand protein), acting as a cytoplasmic regulator and capable of **nuclear translocation**, with inhibitory effects on multiple kinases/phosphatases and on DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity in various rat cell systems.
- term:
    id: GO:2000279
    label: negative regulation of DNA biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:11500948
  review:
    summary: Well-documented suppression of DNA synthesis in hepatoma cells. 
      This is part of the core regulatory function on nucleic acid biosynthesis 
      and cell proliferation control.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:11500948
      supporting_text: The present study demonstrates that endogenous regucalcin
        plays a suppressive role in the enhancement of nuclear DNA synthesis 
        with proliferative cells.
- term:
    id: GO:1903052
    label: obsolete positive regulation of proteolysis involved in protein
      catabolic process
  evidence_type: IDA
  original_reference_id: PMID:1513338
  review:
    summary: This GO term is obsolete (verified via OLS; term_replaced_by
      GO:0045732). The experimental evidence (PMID:1513338) shows regucalcin
      increases Ca2+-independent proteolytic activity in rat liver cytosol and
      activates a neutral cysteinyl-proteinase, i.e. it positively regulates
      protein catabolism. MODIFY to the official replacement term GO:0045732
      (positive regulation of protein catabolic process), which preserves the
      original BP aspect.
    action: MODIFY
    proposed_replacement_terms:
    - id: GO:0045732
      label: positive regulation of protein catabolic process
    supported_by:
    - reference_id: PMID:1513338
      supporting_text: The present findings suggest that regucalcin increases
        proteolytic activity in rat liver cytosol, and that regucalcin may
        activate Ca(2+)-independent neutral cysteinyl-proteinase.
- term:
    id: GO:0001889
    label: liver development
  evidence_type: IEP
  original_reference_id: PMID:9546611
  review:
    summary: Duplicate annotation of expression during liver development. 
      Non-core developmental expression pattern.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:9546611
      supporting_text: Expression of calcium-binding protein regucalcin mRNA in 
        fetal rat liver is stimulated by calcium administration.
- term:
    id: GO:0045019
    label: negative regulation of nitric oxide biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:12686401
  review:
    summary: Inhibits nitric oxide synthase activity in brain. Part of the 
      broader regulatory function on cellular signaling.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:12686401
      supporting_text: The present study demonstrates that endogenous regucalcin
        has an inhibitory effect on NO synthase activity in the brain cytosol of
        young and aged rats.
    - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
      supporting_text: |-
        Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles
- term:
    id: GO:0004341
    label: gluconolactonase activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Another duplicate gluconolactonase annotation. This core function 
      is well-established.
    action: ACCEPT
- term:
    id: GO:0004341
    label: gluconolactonase activity
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: Another duplicate gluconolactonase annotation based on orthology. 
      Consistent with experimental evidence.
    action: ACCEPT
- term:
    id: GO:0019853
    label: L-ascorbic acid biosynthetic process
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Another duplicate of vitamin C biosynthesis annotation. Consistent 
      with experimental evidence.
    action: ACCEPT
- term:
    id: GO:0019853
    label: L-ascorbic acid biosynthetic process
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: Another duplicate vitamin C biosynthesis annotation based on 
      orthology. Well-supported core function.
    action: ACCEPT
- term:
    id: GO:0005509
    label: calcium ion binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: Another duplicate calcium binding annotation with ISO evidence. 
      Calcium binding is a core function.
    action: ACCEPT
- term:
    id: GO:0008270
    label: zinc ion binding
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Correct annotation. Zinc is a cofactor for gluconolactonase 
      activity as shown in PMID:16585534. The protein can use Zn2+ or Mn2+ as 
      cofactors for its enzymatic activity.
    action: ACCEPT
- term:
    id: GO:0008270
    label: zinc ion binding
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: Duplicate annotation with different evidence code. Zinc binding is 
      confirmed as a cofactor for enzymatic activity.
    action: ACCEPT
- term:
    id: GO:0005509
    label: calcium ion binding
  evidence_type: IDA
  original_reference_id: PMID:699201
  review:
    summary: Direct experimental evidence from the original 1978 paper 
      identifying this as a calcium-binding protein. This is foundational 
      evidence for a core molecular function.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:699201
      supporting_text: Purification of calcium binding substance from soluble 
        fraction of normal rat liver.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Nuclear localization is supported by functional studies showing 
      regulation of nuclear processes (DNA/RNA synthesis). Valid cellular 
      component.
    action: ACCEPT
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Duplicate cytoplasmic localization annotation. Well-supported.
    action: ACCEPT
- term:
    id: GO:0006874
    label: intracellular calcium ion homeostasis
  evidence_type: IDA
  original_reference_id: PMID:16786169
  review:
    summary: Direct evidence for regulation of calcium homeostasis through 
      Ca2+-ATPase modulation in mitochondria. This is a core biological 
      function.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:16786169
      supporting_text: This study demonstrates that regucalcin has an activating
        effect on Ca2+-ATPase in rat heart mitochondria, suggesting its role in
        the regulation of heart mitochondrial function.
    - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
      supporting_text: |-
        Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles
- term:
    id: GO:0032781
    label: positive regulation of ATP-dependent activity
  evidence_type: IDA
  original_reference_id: PMID:16786169
  review:
    summary: Evidence shows increased Ca2+-ATPase activity in heart
      mitochondria. The existing term GO:0032781 (positive regulation of
      ATP-dependent activity) is a biological_process term that is too general.
      The data directly demonstrate that regucalcin acts as an activator of the
      Ca2+-ATPase, better captured by the molecular_function term GO:0060590
      (ATPase regulator activity). Note this is an intentional cross-aspect
      MODIFY from BP to MF; the activator role on the ATPase enzyme is a
      molecular function and is more informative than the generic BP term.
    action: MODIFY
    proposed_replacement_terms:
    - id: GO:0060590
      label: ATPase regulator activity
    supported_by:
    - reference_id: PMID:16786169
      supporting_text: Regucalcin increases Ca2+-ATPase activity in the heart 
        mitochondria of normal and regucalcin transgenic rats.
- term:
    id: GO:0050848
    label: regulation of calcium-mediated signaling
  evidence_type: IDA
  original_reference_id: PMID:16786169
  review:
    summary: Regulation of calcium signaling through Ca2+-ATPase modulation and 
      calcium binding. Core regulatory function.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:16786169
      supporting_text: This study demonstrates that regucalcin has an activating
        effect on Ca2+-ATPase in rat heart mitochondria, suggesting its role in 
        the regulation of heart mitochondrial function.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: Duplicate nuclear localization based on orthology. Consistent with 
      functional evidence.
    action: ACCEPT
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: Another duplicate cytoplasmic localization based on orthology. 
      Consistent with other evidence.
    action: ACCEPT
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  review:
    summary: mitochondrion identified from core_functions analysis
    action: NEW
    reason: This cellular component term reflects regucalcin's mitochondrial 
      localization where it regulates Ca2+-ATPase activity and mitochondrial 
      calcium homeostasis.
    supported_by:
    - reference_id: PMID:16786169
      supporting_text: Regucalcin increases Ca2+-ATPase activity in the heart 
        mitochondria of normal and regucalcin transgenic rats.
- term:
    id: GO:0017148
    label: negative regulation of translation
  evidence_type: IEA
  review:
    summary: Core function of regucalcin in protein synthesis regulation
    action: NEW
    reason: Regucalcin inhibits aminoacyl-tRNA synthetase activity, thereby 
      negatively regulating translation. This is one of its core regulatory 
      functions but was missing from existing annotations.
    supported_by:
    - reference_id: PMID:2280766
      supporting_text: The present results suggest that regucalcin can regulate 
        protein synthesis in liver cells.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with 
    GO terms.
  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:0000096
  title: Automated transfer of experimentally-verified manual GO annotation data
    to mouse-rat orthologs.
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods.
  findings: []
- id: PMID:11129957
  title: Role of endogenous regucalcin in protein tyrosine phosphatase 
    regulation in the cloned rat hepatoma cells (H4-II-E).
  findings: []
- id: PMID:11500948
  title: Regulatory role of endogenous regucalcin in the enhancement of nuclear 
    deoxyribonuleic acid synthesis with proliferation of cloned rat hepatoma 
    cells (H4-II-E).
  findings: []
- id: PMID:12239582
  title: 'Role of endogenous regucalcin in bone metabolism: bone loss is induced in
    regucalcin transgenic rats.'
  findings: []
- id: PMID:12397604
  title: 'Role of endogenous regucalcin in nuclear regulation of regenerating rat
    liver: suppression of the enhanced ribonucleic acid synthesis activity.'
  findings: []
- id: PMID:12686401
  title: 'Inhibitory role of regucalcin in the regulation of nitric oxide synthase
    activity in rat brain cytosol: involvement of aging.'
  findings: []
- id: PMID:1513338
  title: Calcium-binding protein regucalcin increases calcium-independent 
    proteolytic activity in rat liver cytosol.
  findings: []
- id: PMID:15806309
  title: Overexpression of regucalcin suppresses apoptotic cell death in the 
    cloned rat hepatoma H4-II-E cells induced by a naturally occurring 
    isothiocyanate sulforaphane.
  findings: []
- id: PMID:16142398
  title: Overexpression of regucalcin suppresses cell proliferation of cloned 
    normal rat kidney proximal tubular epithelial NRK52E cells.
  findings: []
- id: PMID:16167335
  title: 'Overexpression of regucalcin suppresses apoptotic cell death in cloned normal
    rat kidney proximal tubular epithelial NRK52E cells: change in apoptosis-related
    gene expression.'
  findings: []
- id: PMID:16585534
  title: Senescence marker protein 30 functions as gluconolactonase in 
    L-ascorbic acid biosynthesis, and its knockout mice are prone to scurvy.
  findings: []
- id: PMID:16786169
  title: Regucalcin increases Ca2+-ATPase activity in the heart mitochondria of 
    normal and regucalcin transgenic rats.
  findings: []
- id: PMID:16817230
  title: 'Overexpression of regucalcin enhances glucose utilization and lipid production
    in cloned rat hepatoma H4-II-E cells: Involvement of insulin resistance.'
  findings: []
- id: PMID:2001740
  title: Inhibitory effect of calcium-binding protein regucalcin on 
    Ca2(+)-activated DNA fragmentation in rat liver nuclei.
  findings: []
- id: PMID:2280766
  title: 'Effect of calcium-binding protein regucalcin on hepatic protein synthesis:
    inhibition of aminoacyl-tRNA synthetase activity.'
  findings: []
- id: PMID:23615721
  title: 'Sperm parameters and epididymis function in transgenic rats overexpressing
    the Ca2+-binding protein regucalcin: a hidden role for Ca2+ in sperm maturation?'
  findings: []
- id: PMID:699201
  title: Purification of calcium binding substance from soluble fraction of 
    normal rat liver.
  findings: []
- id: PMID:7759556
  title: Enhanced expression of calcium-binding protein regucalcin mRNA in 
    regenerating rat liver.
  findings: []
- id: PMID:8794449
  title: 'Gene regulation of senescence marker protein-30 (SMP30): coordinated up-regulation
    with tissue maturation and gradual down-regulation with aging.'
  findings: []
- id: PMID:9546611
  title: Expression of calcium-binding protein regucalcin mRNA in fetal rat
    liver is stimulated by calcium administration.
  findings: []
- id: file:rat/Rgn/Rgn-deep-research-falcon.md
  title: Falcon (Edison Scientific) deep research report on rat Rgn (regucalcin /
    SMP-30 / gluconolactonase, UniProt Q03336)
  findings:
  - statement: |
      The core biochemical function of rat Rgn is a metal-dependent gluconolactonase
      (EC 3.1.1.17) with a six-bladed beta-propeller fold whose central cavity
      coordinates a divalent metal at the active site (Glu18, Asn154, Asp204, with
      Asn103 important for catalysis).
    reference_section_type: OTHER
    supporting_text: |-
      1. **Primary biochemical function:** Rat Rgn encodes regucalcin/SMP30, a **metal-dependent gluconolactonase/lactonase (EC 3.1.1.17)** with a **six-bladed β‑propeller** active site coordinating a divalent metal (Glu18/Asn154/Asp204; Asn103 important for catalysis).
  - statement: |
      In non-primate mammals SMP30/GNL supports ascorbic acid (vitamin C) biosynthesis
      by forming the gamma-lactone ring from L-gulonate, and SMP30/GNL knockout mice
      develop scurvy on vitamin C-deficient diets.
    reference_section_type: OTHER
    supporting_text: |-
      **Ascorbate/vitamin C pathway role (in non‑primates):** SMP30/GNL is implicated in the ascorbic acid biosynthesis pathway by catalyzing formation of the **γ‑lactone ring** from **L‑gulonate** (i.e., producing **L‑gulono‑γ‑lactone**, which is then converted to ascorbic acid by downstream enzymes). Genetic/physiological support includes **SMP30/GNL knockout mice** developing **scurvy** on vitamin C‑deficient diets.
  - statement: |
      The enzyme requires a divalent metal ion (Zn2+ and Mn2+ cited as activators)
      and hydrolyzes multiple aldonolactones in vitro, including D/L-glucono-,
      gulono-, and galactono-lactones.
    reference_section_type: OTHER
    supporting_text: |-
      A central, experimentally supported biochemical activity of regucalcin/SMP30 is **gluconolactonase (EC 3.1.1.17)** activity, requiring a **divalent metal ion** (e.g., **Zn2+** and **Mn2+** are cited as activators) and showing activity on multiple **aldonolactones** in vitro (e.g., D/L‑glucono‑γ‑lactone, D/L‑gulono‑γ‑lactone, D/L‑galactono‑γ‑lactone).
  - statement: |
      Regucalcin is a multifunctional Ca2+-signaling regulator that is explicitly NOT
      an EF-hand protein; it acts as a cytoplasmic regulator capable of nuclear
      translocation, inhibiting kinases/phosphatases and DNA/RNA/protein synthesis,
      thereby influencing cell-cycle progression and apoptosis sensitivity.
    reference_section_type: OTHER
    supporting_text: |-
      Regucalcin is also widely described as a **multifunctional Ca2+-signaling regulator** (not an EF‑hand protein), acting as a cytoplasmic regulator and capable of **nuclear translocation**, with inhibitory effects on multiple kinases/phosphatases and on DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity in various rat cell systems.
  - statement: |
      A 2023 review positions regucalcin as a multifunctional suppressor that localizes
      in cytoplasm and nucleus, maintains intracellular Ca2+ homeostasis by activating
      Ca2+ pumps in the plasma membrane, mitochondria, and ER, and inhibits multiple
      enzymes including aminoacyl-tRNA synthetase, nitric oxide synthase, cysteinyl
      protease, and DNA/RNA synthesis and cell-cycle progression.
    reference_section_type: OTHER
    supporting_text: |-
      Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles
  - statement: |
      Under ascorbate deficiency, SMP30 increases in serum extracellular vesicles,
      indicating an extracellular/secreted-vesicular compartment for SMP30 under
      stress conditions, in addition to its primary cytoplasmic/nuclear localization.
    reference_section_type: OTHER
    supporting_text: |-
      Ascorbate deficiency increases SMP30 in serum EVs, indicating an extracellular/secreted-vesicular compartment for SMP30 under stress conditions.
core_functions:
- description: Catalyzes lactonization of L-gulonic acid to L-gulono-gamma-lactone
    in the penultimate step of L-ascorbic acid biosynthesis
  molecular_function:
    id: GO:0004341
    label: gluconolactonase activity
  directly_involved_in:
  - id: GO:0019853
    label: L-ascorbic acid biosynthetic process
  locations:
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: PMID:16585534
    supporting_text: SMP30 purified from the rat liver had lactonase activity
      toward various aldonolactones, such as d- and l-glucono-delta-lactone,
      d- and l-gulono-gamma-lactone, and d- and l-galactono-gamma-lactone,
      with a requirement for Zn(2+) or Mn(2+) as a cofactor.
  - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
    supporting_text: |-
      1. **Primary biochemical function:** Rat Rgn encodes regucalcin/SMP30, a **metal-dependent gluconolactonase/lactonase (EC 3.1.1.17)** with a **six-bladed β‑propeller** active site coordinating a divalent metal (Glu18/Asn154/Asp204; Asn103 important for catalysis).
- description: Binds calcium ions to regulate intracellular calcium homeostasis
    and calcium-dependent processes
  molecular_function:
    id: GO:0005509
    label: calcium ion binding
  directly_involved_in:
  - id: GO:0006874
    label: intracellular calcium ion homeostasis
  - id: GO:0050848
    label: regulation of calcium-mediated signaling
  locations:
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: PMID:699201
    supporting_text: Purification of calcium binding substance from soluble
      fraction of normal rat liver.
  - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
    supporting_text: |-
      Regucalcin is also widely described as a **multifunctional Ca2+-signaling regulator** (not an EF‑hand protein), acting as a cytoplasmic regulator and capable of **nuclear translocation**, with inhibitory effects on multiple kinases/phosphatases and on DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity in various rat cell systems.
- description: Activates mitochondrial Ca2+-ATPase to enhance calcium pumping
    and maintain calcium homeostasis
  molecular_function:
    id: GO:0060590
    label: ATPase regulator activity
  directly_involved_in:
  - id: GO:0006874
    label: intracellular calcium ion homeostasis
  locations:
  - id: GO:0005739
    label: mitochondrion
  supported_by:
  - reference_id: PMID:16786169
    supporting_text: Regucalcin increases Ca2+-ATPase activity in the heart
      mitochondria of normal and regucalcin transgenic rats.
  - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
    supporting_text: |-
      Positions regucalcin as a multifunctional suppressor that localizes in cytoplasm and nucleus; maintains intracellular Ca2+ homeostasis by activating Ca2+ pumps in plasma membrane, mitochondria, and ER; inhibits kinases, phosphatases, nitric oxide synthase, cysteinyl protease, aminoacyl-tRNA synthetase, DNA/RNA synthesis, and cell-cycle progression; summarizes rat liver, kidney, prostate, and hepatoma studies showing anti-proliferative and homeostatic roles
- description: Inhibits aminoacyl-tRNA synthetase activity to suppress protein
    synthesis
  molecular_function:
    id: GO:0004857
    label: enzyme inhibitor activity
  supported_by:
  - reference_id: PMID:2280766
    supporting_text: Regucalcin inhibits aminoacyl-tRNA synthetase activity
    full_text_unavailable: true
  directly_involved_in:
  - id: GO:0017148
    label: negative regulation of translation
  locations:
  - id: GO:0005737
    label: cytoplasm
- description: Suppresses DNA and RNA synthesis to control cell proliferation
  molecular_function:
    id: GO:0004857
    label: enzyme inhibitor activity
  supported_by:
  - reference_id: PMID:11500948
    supporting_text: Regucalcin suppresses DNA synthesis in hepatoma cells
    full_text_unavailable: true
  directly_involved_in:
  - id: GO:2000279
    label: negative regulation of DNA biosynthetic process
  - id: GO:1902679
    label: negative regulation of RNA biosynthetic process
  - id: GO:0050680
    label: negative regulation of epithelial cell proliferation
  locations:
  - id: GO:0005634
    label: nucleus
- description: Protects cells from apoptosis by inhibiting Ca2+-activated DNA
    fragmentation
  molecular_function:
    id: GO:0005509
    label: calcium ion binding
  directly_involved_in:
  - id: GO:0043066
    label: negative regulation of apoptotic process
  - id: GO:1903625
    label: negative regulation of DNA catabolic process
  locations:
  - id: GO:0005634
    label: nucleus
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: PMID:2001740
    supporting_text: The Ca2+ (10 microM)-activated DNA fragmentation was
      inhibited by the presence of Ca2(+)-binding protein regucalcin isolated
      from rat liver cytosol.
  - reference_id: file:rat/Rgn/Rgn-deep-research-falcon.md
    supporting_text: |-
      Regucalcin is also widely described as a **multifunctional Ca2+-signaling regulator** (not an EF‑hand protein), acting as a cytoplasmic regulator and capable of **nuclear translocation**, with inhibitory effects on multiple kinases/phosphatases and on DNA/RNA/protein synthesis, thereby influencing cell-cycle progression and apoptosis sensitivity in various rat cell systems.
suggested_questions:
- question: How does regucalcin regulate intracellular calcium homeostasis and 
    what are its tissue-specific functions?
- question: What determines the nuclear versus cytoplasmic distribution of 
    regucalcin and how does this affect its function?
- question: How does regucalcin interact with calcium-binding proteins and 
    calcium channels to modulate cellular calcium?
- question: What role does regucalcin play in aging and cellular senescence, and
    how is its expression regulated?
suggested_experiments:
- description: Live-cell calcium imaging to study the effects of regucalcin on 
    calcium dynamics in different cell types
- description: Proteomics analysis to identify regucalcin interacting partners 
    and calcium-dependent protein interactions
- description: Subcellular fractionation and imaging to determine regucalcin 
    localization and translocation during calcium signaling
- description: Analysis of regucalcin expression and function during aging using
    longitudinal studies in animal models
status: DRAFT

Rgn

Gene Description

Existing Annotations Review

Core Functions

Catalyzes lactonization of L-gulonic acid to L-gulono-gamma-lactone in the penultimate step of L-ascorbic acid biosynthesis

Binds calcium ions to regulate intracellular calcium homeostasis and calcium-dependent processes

Activates mitochondrial Ca2+-ATPase to enhance calcium pumping and maintain calcium homeostasis

Inhibits aminoacyl-tRNA synthetase activity to suppress protein synthesis

Suppresses DNA and RNA synthesis to control cell proliferation

Protects cells from apoptosis by inhibiting Ca2+-activated DNA fragmentation

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Research Report: Rat Rgn (Regucalcin / SMP-30 / Gluconolactonase; UniProt Q03336)

0. Target verification (critical disambiguation)

1. Key concepts and definitions (current understanding)

1.1 Protein identity and family/domain concepts

1.2 Primary biochemical function: metal‑dependent lactonase / gluconolactonase

1.3 Active site chemistry and substrate recognition (mechanistic definition)

1.4 Cellular roles beyond enzymology (definitions used in modern literature)

2. Recent developments and latest research (prioritizing 2023–2024)

2.1 Nutritional/anti‑oxidative signaling regulation of SMP30 in rat liver cells (2023)

2.2 Ascorbate deficiency drives extracellular-vesicle (EV) release of SMP30 in a rat model (2023)

2.3 Rgn as a kidney injury/toxicity-associated marker in rat cortex proteomics (2023)

3. Current applications and real-world implementations

3.1 Experimental models and biomarkers

3.2 Nutritional and signaling interventions

4. Expert opinions and authoritative synthesis (with critical appraisal)

4.1 Regucalcin as a multifunctional suppressor of proliferative signaling

4.2 Structure–function inference from superfamily analysis

5. Relevant statistics and data highlights

5.1 Enzymatic activity and metal binding (biochemistry)

5.2 Rat in vivo biomarker changes under ascorbate deficiency (ODS rats)

5.3 Rat kidney injury proteomics (cyclosporine vs dehydration)

6. Subcellular localization and site of action (rat-focused synthesis)

7. Conclusions for functional annotation of rat Rgn (Q03336)

Evidence summary table

Artifacts

Citations

📚 Additional Documentation

Notes

Rgn (Regucalcin) Research Notes

Core Enzymatic Function

Calcium Binding and Regulation

Developmental Expression

Cellular Functions Beyond Vitamin C Synthesis

Regulation of Macromolecule Biosynthesis

Anti-apoptotic Effects

Metabolic Regulation

Tissue-Specific Functions

Other Enzymatic Activities

Subcellular Localization

Clinical Significance

Bioreason Rl Predictions

BioReason Chat Export

Thinking Trace

Functional Summary

UniProt Summary

InterPro Domains

GO Terms

Bioreason Rl Review

BioReason-Pro RL Review: Rgn (rat)

Functional Summary Review

Notes on thinking trace

Curation Summary

Rgn (Regucalcin/SMP30) GO Annotation Curation Summary

Overview

Key Curation Decisions

Core Functions Identified

Non-Core/Secondary Functions (KEEP_AS_NON_CORE)

Removed Annotations

Modified Annotations

Cellular Localization

Summary Statistics

Key Literature Support

Conclusion

📄 View Raw YAML

🔗 Related Resources