Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004135 amylo-alpha-1,6-glucosidase activity	IBA GO_REF:0000033	ACCEPT	Summary: Amylo-alpha-1,6-glucosidase activity (EC 3.2.1.33) is one of the two core catalytic activities of AGL: it hydrolyses the alpha-1,6-glucosidic branch linkage exposed after the transferase step, releasing free glucose. This is the defining, conserved function of the debranching enzyme family and is well supported by direct enzymatic study. Reason: Correct core molecular function, matching the UniProt catalytic activity "Hydrolysis of (1->6)-alpha-D-glucosidic branch linkages in glycogen phosphorylase limit dextrin" (EC 3.2.1.33). IBA is at the appropriate level of specificity for this family. Supporting Evidence: PMID:2961257 Type III glycogen storage disease is caused by a deficiency of glycogen
GO:0005980 glycogen catabolic process	IBA GO_REF:0000033	ACCEPT	Summary: Glycogen catabolic process (glycogenolysis) is the biological process in which AGL acts; it is essential for complete degradation of glycogen branches and release of glucose, working alongside glycogen phosphorylase. Reason: Correct core biological process for the debranching enzyme. Deficiency of AGL blocks complete glycogenolysis and causes accumulation of abnormal short-outer-chain (limit-dextrin-like) glycogen (GSD III). Supporting Evidence: PMID:2961257 Type III glycogen storage disease is caused by a deficiency of glycogen
GO:0004134 4-alpha-glucanotransferase activity	IBA GO_REF:0000033	ACCEPT	Summary: 4-alpha-glucanotransferase activity (EC 2.4.1.25) is the second core catalytic activity of AGL: it transfers a maltotriose segment of a (1->4)-alpha-D-glucan from a glycogen branch to a nearby non-reducing 1,4-end, exposing the single alpha-1,6-linked glucose for subsequent hydrolysis. Reason: Correct core molecular function, matching UniProt catalytic activity "Transfers a segment of a (1->4)-alpha-D-glucan to a new position in an acceptor" (EC 2.4.1.25). IBA is appropriate for this conserved family function.
GO:0004134 4-alpha-glucanotransferase activity	IEA GO_REF:0000120	ACCEPT	Summary: Electronic assignment (ARBA/InterPro/EC 2.4.1.25) of the transferase activity, duplicating the IBA and EXP annotations for the same term. Reason: Correct core molecular function; the electronic mapping agrees with experimental and phylogenetic evidence for GO:0004134.
GO:0004135 amylo-alpha-1,6-glucosidase activity	IEA GO_REF:0000120	ACCEPT	Summary: Electronic assignment (ARBA/InterPro/EC 3.2.1.33) of the glucosidase activity, duplicating the IBA and EXP annotations for the same term. Reason: Correct core molecular function; the electronic mapping agrees with experimental and phylogenetic evidence for GO:0004135.
GO:0005737 cytoplasm	IEA GO_REF:0000120	ACCEPT	Summary: Cytoplasmic localization, consistent with AGL acting on cytosolic glycogen particles. Supported experimentally (IDA, PMID:17908927) and by UniProt subcellular location. Reason: Correct localization; AGL is a cytosolic enzyme. This term is broad but accurate; the more precise cytosol (GO:0005829) is also annotated. Supporting Evidence: PMID:17908927 Transfection studies in HepG2 cells demonstrate that AGL is
GO:0005975 carbohydrate metabolic process	IEA GO_REF:0000002	ACCEPT	Summary: Carbohydrate metabolic process is a correct, broad parent process for AGL, whose role in glycogen catabolism is a subtype of carbohydrate metabolism. Reason: Accurate though general InterPro2GO mapping. The more specific glycogen catabolic process (GO:0005980) is separately annotated and captured as core.
GO:0005978 glycogen biosynthetic process	IEA GO_REF:0000002	REMOVE	Summary: AGL is a glycogen degradation (catabolic) enzyme, not a biosynthetic enzyme. Its two activities (transferase and glucosidase) act to break down glycogen branches and release glucose; it plays no role in glycogen synthesis. Reason: Directionally incorrect electronic mapping. AGL functions in glycogen catabolism, and its loss causes accumulation (not deficiency) of glycogen; UniProt describes it as acting "in glycogen degradation." Assigning a biosynthetic process to a catabolic enzyme is a demonstrably wrong IEA (InterPro2GO/keyword artifact) and should be removed. (The "Glycogen biosynthesis" keyword likely reflects family-level signature grouping rather than AGL's actual directionality.)
GO:0005980 glycogen catabolic process	IEA GO_REF:0000120	ACCEPT	Summary: Electronic assignment of glycogen catabolic process, duplicating the IBA and Reactome-TAS annotations for the same term. Reason: Correct core biological process for AGL, in agreement with phylogenetic and pathway-based evidence.
GO:0005634 nucleus	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: AGL relocalizes partially to the nucleus specifically under glycogenolytic (glycogen-depleted) conditions, so nuclear localization is condition-dependent and not the site of its core catalytic function. Reason: Supported by experimental observation in the human/rodent system that AGL shows partial nuclear staining after glycogen depletion, but this is a regulated, condition-dependent localization rather than the constitutive cytosolic site of debranching activity. Supporting Evidence: PMID:17908927 approximately 90% of transfected cells exhibit partial
GO:0005829 cytosol	IEA GO_REF:0000107	ACCEPT	Summary: Cytosol is the site where AGL is active, acting on cytosolic glycogen particles together with glycogen phosphorylase. This is the core localization. Reason: Correct and precise localization for the core catalytic function; corroborated by IDA (HPA) and Reactome-TAS annotations to the same term.
GO:0007584 response to nutrient	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Hepatic AGL levels change with nutritional state (e.g. refeeding reduces AGL), consistent with a physiological response to nutrient availability, but this is a downstream regulatory/physiological role rather than AGL's core molecular function. Reason: Plausible orthology-transferred process annotation reflecting nutritional regulation of the debranching enzyme; retained as non-core because it describes the enzyme's regulation/physiology, not its catalytic activity. Supporting Evidence: PMID:17908927 binding to glycogen crucially
GO:0009725 response to hormone	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Glycogenolysis and AGL activity are modulated by hormonal signals (e.g. glucagon/ cAMP, glucocorticoids), so a response-to-hormone annotation is biologically plausible but peripheral to AGL's core enzymatic role. Reason: Orthology-transferred physiological process; retained as non-core rather than accepted as a core function because it captures regulation of the pathway rather than AGL's molecular activity.
GO:0016234 inclusion body	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Inclusion-body/aggresome localization is observed for the unstable GSD3 G1448R mutant of AGL upon proteasome impairment, not for the wild-type enzyme in its normal functional state. Reason: This localization reflects a disease-mutant/aggregation phenotype (the G1448R variant forms aggresomes when the proteasome is impaired) rather than a normal localization of functional AGL, so it over-states the wild-type protein's compartmentalization. Supporting Evidence: PMID:17908927 the G1448R genetic variant of AGL is unable to bind to glycogen
GO:0016529 sarcoplasmic reticulum	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Sarcoplasmic reticulum localization is transferred electronically from a rodent ortholog and is not supported for the human protein, which is a cytosolic enzyme acting on glycogen particles. Reason: Orthology-based electronic annotation lacking direct support for human AGL; AGL is established as a cytoplasmic/cytosolic enzyme (IDA), and there is no evidence it is a resident sarcoplasmic reticulum protein.
GO:0030246 carbohydrate binding	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: AGL binds glycogen (a carbohydrate) via a conserved glycogen-binding region, but "carbohydrate binding" is an uninformative molecular-function term relative to the enzyme's two catalytic activities, which already imply substrate binding. Reason: Substrate (glycogen) binding is real but is subsumed by the catalytic MF annotations (GO:0004134, GO:0004135) and the glycogen catabolic process; the generic binding term adds no functional information and is an over-annotation.
GO:0030247 polysaccharide binding	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: As with carbohydrate binding, AGL binds the polysaccharide glycogen through its glycogen-binding region, but polysaccharide binding is an uninformative generic term relative to the enzyme's catalytic activities. Reason: Glycogen (polysaccharide) binding is implicit in the debranching activities and the glycogen catabolic process; the generic binding term is an over-annotation that adds no functional specificity.
GO:0031593 polyubiquitin modification-dependent protein binding	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: AGL is itself ubiquitinated (by the E3 ligase malin/NHLRC1) and its stability is regulated by ubiquitination, but there is no evidence that AGL acts as a reader that binds polyubiquitin chains on other proteins. Reason: Likely an orthology-transfer artifact; the ubiquitin connection to AGL is that AGL is a substrate for ubiquitination, not a polyubiquitin-binding module. This generic binding term is not supported as a molecular function of AGL. Supporting Evidence: PMID:17908927 Malin interacts with and promotes the ubiquitination of AGL
GO:0051384 response to glucocorticoid	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Glucocorticoids influence hepatic glycogen metabolism, so a response-to-glucocorticoid annotation is biologically plausible for AGL but is a peripheral physiological/ regulatory role, not the core molecular function. Reason: Orthology-transferred physiological response; retained as non-core because it reflects regulation of the enzyme/pathway rather than AGL's catalytic activity.
GO:0005980 glycogen catabolic process	TAS Reactome:R-HSA-70221	ACCEPT	Summary: Reactome curates AGL as a participant in glycogen breakdown (glycogenolysis), catalysing the two debranching reactions R-HSA-71552 (transferase) and R-HSA-71593 (glucosidase). This is the core biological process. Reason: Author-curated pathway annotation consistent with the enzyme's established role in complete glycogen degradation.
GO:0004134 4-alpha-glucanotransferase activity	EXP PMID:2961257 Glycogen debranching enzyme: purification, antibody characte...	ACCEPT	Summary: Experimental annotation of the 4-alpha-glucanotransferase activity, one of the two catalytic activities of the purified debranching enzyme. Chen et al. purified the debranching enzyme and characterized it and its deficiency in GSD III. Reason: Core molecular function supported by experimental characterization of the purified enzyme; consistent with UniProt EC 2.4.1.25 and the IBA/IEA annotations. Supporting Evidence: PMID:2961257 debranching enzyme was purified 238-fold from porcine skeletal muscle
GO:0004135 amylo-alpha-1,6-glucosidase activity	EXP PMID:2961257 Glycogen debranching enzyme: purification, antibody characte...	ACCEPT	Summary: Experimental annotation of the amylo-alpha-1,6-glucosidase activity, the second catalytic activity of the purified debranching enzyme; its deficiency defines type III glycogen storage disease. Reason: Core molecular function supported by experimental characterization of the purified enzyme; consistent with UniProt EC 3.2.1.33 and the IBA/IEA annotations. Supporting Evidence: PMID:2961257 the antiserum detected no cross-reactive material in any of the liver or muscle samples from patients
GO:0005654 nucleoplasm	IDA GO_REF:0000052	KEEP AS NON CORE	Summary: HPA immunofluorescence localizes AGL to the nucleoplasm. Consistent with the condition-dependent (glycogenolytic) nuclear relocalization reported for AGL, this is a non-core localization relative to its cytosolic catalytic role. Reason: Genuine IDA localization but reflects a regulated/condition-dependent nuclear pool of AGL rather than the constitutive cytosolic site of debranching activity. Supporting Evidence: PMID:17908927 approximately 90% of transfected cells exhibit partial
GO:0005829 cytosol	IDA GO_REF:0000052	ACCEPT	Summary: HPA immunofluorescence localizes AGL to the cytosol, the core compartment where the enzyme acts on cytosolic glycogen. Reason: Direct experimental support for the core cytosolic localization, in agreement with UniProt and Reactome.
GO:0016604 nuclear body	IDA GO_REF:0000052	KEEP AS NON CORE	Summary: HPA immunofluorescence detects AGL in nuclear bodies, part of the condition-dependent nuclear pool; not the core cytosolic functional localization. Reason: Genuine IDA localization but represents a regulated nuclear sub-pool rather than the constitutive site of the debranching reaction. Supporting Evidence: PMID:17908927 approximately 90% of transfected cells exhibit partial
GO:0005515 protein binding	IPI PMID:24837458 The carbohydrate-binding domain of overexpressed STBD1 is im...	MARK AS OVER ANNOTATED	Summary: This IPI captures a physical interaction between AGL/GDE and STBD1 (starch-binding domain-containing protein 1, O95210). The interaction is real (co-IP and GST pull-down of endogenous GDE by STBD1), but "protein binding" is an uninformative molecular-function term. Reason: Per curation guidelines, bare "protein binding" is not retained as a core molecular function because it conveys no specific activity. The underlying interaction with STBD1 is documented, but the term itself is an over-annotation relative to AGL's catalytic MFs. Supporting Evidence: PMID:24837458 could bind to FLAG-tagged Laforin, GBE1 and GDE PMID:24837458 during glycogen breakdown, proteins such as GS, GDE or Laforin bind to STBD1
GO:0005576 extracellular region	TAS Reactome:R-HSA-6798748	MARK AS OVER ANNOTATED	Summary: This localization derives from AGL appearing in neutrophil-degranulation cargo datasets modeled by Reactome (secretory granule exocytosis). AGL is a cytosolic enzyme, not a bona fide secreted/extracellular protein. Reason: Artifact of the neutrophil-degranulation proteomics pathway; extracellular localization contradicts the well-established cytosolic localization of AGL and is not a functional compartment for this enzyme.
GO:0005576 extracellular region	TAS Reactome:R-HSA-6800434	MARK AS OVER ANNOTATED	Summary: Duplicate extracellular-region annotation from a second neutrophil-degranulation (ficolin-rich granule) Reactome reaction; same over-annotation rationale. Reason: Neutrophil-degranulation proteomics artifact; AGL is cytosolic, not secreted.
GO:0034774 secretory granule lumen	TAS Reactome:R-HSA-6798748	MARK AS OVER ANNOTATED	Summary: Secretory granule lumen localization arises from AGL's inclusion in neutrophil secretory-granule proteomic cargo lists modeled by Reactome, not from a functional role of AGL inside secretory granules. Reason: Artifact of the neutrophil-degranulation dataset; inconsistent with AGL's cytosolic localization and its role in cytosolic glycogen catabolism.
GO:1904813 ficolin-1-rich granule lumen	TAS Reactome:R-HSA-6800434	MARK AS OVER ANNOTATED	Summary: Ficolin-1-rich granule lumen localization is likewise derived from neutrophil granule proteomics via Reactome, not from a functional granule role of AGL. Reason: Neutrophil-degranulation proteomics artifact; AGL is a cytosolic enzyme and is not a functional resident of granule lumens.
GO:0005829 cytosol	TAS Reactome:R-HSA-71552	ACCEPT	Summary: Reactome places the AGL-catalysed transferase reaction (limit-dextrin transfer) in the cytosol, the core compartment for glycogen debranching. Reason: Author-curated pathway localization consistent with the established cytosolic site of AGL activity.
GO:0005829 cytosol	TAS Reactome:R-HSA-71593	ACCEPT	Summary: Reactome places the AGL-catalysed glucosidase reaction (release of alpha-D-glucose) in the cytosol, consistent with the core localization of the debranching reaction. Reason: Author-curated pathway localization consistent with the cytosolic site of AGL activity.
GO:0005515 protein binding	IPI PMID:17908927 A role for AGL ubiquitination in the glycogen storage disord...	MARK AS OVER ANNOTATED	Summary: This IPI captures the interaction between AGL and the E3 ubiquitin ligase malin (NHLRC1, Q6VVB1), which ubiquitinates AGL and regulates its stability. The interaction is genuine but "protein binding" is an uninformative term. Reason: Bare "protein binding" is not retained as a core molecular function per curation guidelines. The specific interaction with malin is documented and biologically important (regulation of AGL stability by ubiquitination), but the generic term adds no functional specificity. Supporting Evidence: PMID:17908927 Malin interacts with and promotes the ubiquitination of AGL
GO:0005737 cytoplasm	IDA PMID:17908927 A role for AGL ubiquitination in the glycogen storage disord...	ACCEPT	Summary: Direct experimental demonstration that AGL is cytoplasmic (transfection/localization studies in HepG2 cells), the core compartment where AGL degrades cytosolic glycogen. Reason: Strong experimental (IDA) support for the core cytoplasmic localization, matching UniProt subcellular location. Supporting Evidence: PMID:17908927 cytoplasmic whereas Malin is predominately nuclear.
GO:0043033 isoamylase complex	TAS PMID:1374391 Molecular cloning and nucleotide sequence of cDNA encoding h...	MARK AS OVER ANNOTATED	Summary: Human AGL is a single bifunctional polypeptide that acts as a monomer; it is not a subunit of a multi-protein isoamylase complex. The isoamylase complex (a bacterial/plant debranching enzyme assembly) is not the biological form of the mammalian debranching enzyme. Reason: UniProt states the subunit structure is "Monomer", and both catalytic activities reside on the single AGL polypeptide (cloned as a single multifunctional enzyme). The cited cloning paper describes the debrancher as a single multifunctional protein and does not report an isoamylase complex; the "isoamylase complex" component appears to be a legacy/mis-mapped complex annotation and over-states AGL's quaternary organization. Supporting Evidence: PMID:1374391 an important step toward defining the structure-function relationship of this

Core Functions

Removes glycogen branch points during glycogenolysis via a 4-alpha-glucanotransferase activity that relocates a maltotriose segment from the branch to a nearby alpha-1,4 chain end, exposing the single alpha-1,6-linked glucose.

Molecular Function:

4-alpha-glucanotransferase activity

Directly Involved In:

glycogen catabolic process

Cellular Locations:

cytosol

Supporting Evidence:

PMID:2961257
Type III glycogen storage disease is caused by a deficiency of glycogen

Hydrolyses the alpha-1,6-glucosidic branch linkage exposed after the transferase step, releasing free glucose and allowing complete degradation of glycogen; loss of this activity causes glycogen storage disease type III (Cori/Forbes disease).

Molecular Function:

amylo-alpha-1,6-glucosidase activity

Directly Involved In:

glycogen catabolic process

Cellular Locations:

cytosol

Supporting Evidence:

PMID:2961257
the antiserum detected no cross-reactive material in any of the liver or muscle samples from patients

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000052

Gene Ontology annotation based on curation of immunofluorescence data

GO_REF:0000107

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:1374391

Molecular cloning and nucleotide sequence of cDNA encoding human muscle glycogen debranching enzyme.

PMID:17908927

A role for AGL ubiquitination in the glycogen storage disorders of Lafora and Cori's disease.

PMID:24837458

The carbohydrate-binding domain of overexpressed STBD1 is important for its stability and protein-protein interactions.

PMID:2961257

Glycogen debranching enzyme: purification, antibody characterization, and immunoblot analyses of type III glycogen storage disease.

Reactome:R-HSA-6798748

Exocytosis of secretory granule lumen proteins

Reactome:R-HSA-6800434

Exocytosis of ficolin-rich granule lumen proteins

Reactome:R-HSA-70221

Glycogen breakdown (glycogenolysis)

Reactome:R-HSA-71552

limit dextrin-glycogenin => ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl) glycogenin

Reactome:R-HSA-71593

((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin => poly{(1,4)-alpha-glucosyl} glycogenin + alpha-D-glucose

Suggested Experiments

Experiment: Structure-guided mutagenesis of the predicted active-site residues (526, 529, 627) to dissect the contributions of the transferase versus glucosidase activities to glycogen debranching, and to model GSD III subtypes IIIc/IIId (selective loss of one activity).

Experiment: Quantitative analysis of AGL subcellular redistribution (cytosol to nucleus) as a function of glycogen depletion and hormonal stimulation, to determine whether nuclear localization is functional or a regulatory sequestration mechanism.

📚 Additional Documentation

Notes

(AGL-notes.md)

AGL (Glycogen debranching enzyme, GDE) — review notes

UniProtKB: P35573 (GDE_HUMAN); HGNC:321; gene AGL (syn. GDE); 1532 aa, ~174.8 kDa.

Core biology

AGL is the cytosolic glycogen debranching enzyme, a single ~175 kDa polypeptide that is
bifunctional / multifunctional, carrying two independent catalytic activities on one chain
(UniProt: "Multifunctional enzyme acting as 1,4-alpha-D-glucan:1,4-alpha-D-glucan 4-alpha-D-glycosyltransferase
and amylo-1,6-glucosidase in glycogen degradation"):

4-alpha-glucanotransferase (EC 2.4.1.25) = GO:0004134 — "Transfers a segment of a (1->4)-alpha-D-glucan
to a new position in an acceptor, which may be glucose or a (1->4)-alpha-D-glucan." (UniProt CATALYTIC ACTIVITY)
Amylo-alpha-1,6-glucosidase (EC 3.2.1.33) = GO:0004135 — "Hydrolysis of (1->6)-alpha-D-glucosidic branch
linkages in glycogen phosphorylase limit dextrin." (UniProt CATALYTIC ACTIVITY)

Mechanism: works with glycogen phosphorylase to fully degrade glycogen branches. Phosphorylase stalls ~4
glucose residues from an alpha-1,6 branch point (leaving a "limit dextrin"). AGL's transferase moves a
maltotriose unit (3 glucoses) to a nearby non-reducing 1,4-end, exposing the single alpha-1,6-linked glucose,
which the glucosidase then hydrolyses to release free glucose. Reactome models these as two cytoplasmic
steps: R-HSA-71552 (transferase) and R-HSA-71593 (glucosidase releasing alpha-D-glucose).

Localization: cytoplasm/cytosol (UniProt SUBCELLULAR LOCATION "Cytoplasm {ECO:0000269|PubMed:17908927}";
IDA GO:0005737 from PMID:17908927; IDA GO:0005829 cytosol from HPA). "Under glycogenolytic conditions
localizes to the nucleus" — PMID:17908927 shows ~90% of transfected cells show partial nuclear staining for
AGL after 4 h glycogen depletion. HPA also reports nucleoplasm/nuclear body IDA. Nuclear localization is
condition-dependent and not the site of the core catalytic function.

Family / domains: glycogen debranching enzyme family; CAZy GH13 + GH133; InterPro IPR006421
(Glycogen_debranch_met), IPR010401 (AGL/Gdb1). Cryo-EM structure PDB 8ZEQ (full length). Predicted active
site residues 526, 529, 627 (ECO:0000250).

Disease

Deficiency causes Glycogen storage disease type III (GSD III; Cori disease / Forbes disease), MIM:232400 —
accumulation of abnormal glycogen with short outer chains (limit-dextrin-like). Clinically: hepatomegaly,
hypoglycemia, short stature, variable myopathy, cardiomyopathy. Subtypes: IIIa (liver + muscle), IIIb (liver
only); rare IIIc/IIId reflect selective loss of glucosidase or transferase activity respectively (UniProt
DISEASE). GSD III patients often lack detectable debrancher protein (PMID:2961257 immunoblots: "the antiserum
detected no cross-reactive material in any of the liver or muscle samples from patients with Type III glycogen
storage disease").

Key references (verified against cached publications)

PMID:2961257 (Chen et al. 1987, Am J Hum Genet) — purification of debranching enzyme (single ~160 kDa
band), antibody characterization, immunoblots of GSD III. Abstract-only cache. GOA cites this (EXP, via
Reactome) for both MF activities GO:0004134 and GO:0004135. This paper is a purification/immunochemistry
study; the enzymatic activities are foundational and consistent with the assay. ACCEPT both.
PMID:1374391 (Yang et al. 1992, JBC) — cDNA cloning of human muscle debranching enzyme; "an important
step toward defining the structure-function relationship of this multifunctional enzyme." GOA cites it
(TAS, PINC) for GO:0043033 "isoamylase complex" part_of. AGL is a monomer (UniProt SUBUNIT: "Monomer.")
and the mammalian debranching enzyme is a single bifunctional polypeptide, NOT a member of the bacterial/
plant isoamylase multi-subunit complex. GO:0043033 is a legacy/dubious CC — MARK_AS_OVER_ANNOTATED
(do not REMOVE an experimental/TAS curated by a database; but flag as over-annotation; abstract does not
mention any complex).
PMID:17908927 (Cheng et al. 2007, Genes Dev) — AGL ubiquitination in Lafora/Cori disease. Verbatim:
"AGL is cytoplasmic whereas Malin is predominately nuclear"; "after depletion of glycogen stores for 4 h,
approximately 90% of transfected cells exhibit partial nuclear staining for AGL"; "the E3 ubiquitin ligase
Malin interacts with and promotes the ubiquitination of AGL"; "the G1448R genetic variant of AGL is unable
to bind to glycogen." GOA cites for GO:0005737 cytoplasm (IDA — ACCEPT) and GO:0005515 protein binding
(IPI with NHLRC1/malin Q6VVB1 — MARK_AS_OVER_ANNOTATED, bare protein binding).
PMID:24837458 (Jiang et al. 2014, Biosci Rep) — STBD1 CBM20. Full text available. Verbatim: "co-
immunoprecipitation experiments demonstrated that HA–STBD1 could bind to FLAG-tagged Laforin, GBE1 and GDE";
"STBD1 WT ... could all bind to endogenous GDE, Laforin and GS"; "co-expression of HA–STBD1 with FLAG–GDE
caused a targeting of GDE to the ER compartment as well." GOA cites for GO:0005515 protein binding
(IPI with STBD1 O95210 — MARK_AS_OVER_ANNOTATED, bare protein binding). Note: this is the STBD1 partner;
the interaction with GDE is real but "protein binding" is uninformative.

Annotation decisions summary

Core (ACCEPT): GO:0004134 (IBA, IEA, EXP), GO:0004135 (IBA, IEA, EXP), GO:0005980 glycogen catabolic process
(IBA, TAS-Reactome; IEA accepted), GO:0005829 cytosol (IDA-HPA, TAS-Reactome), GO:0005737 cytoplasm (IDA
PMID:17908927; IEA accepted).

Binding-related (MARK_AS_OVER_ANNOTATED, per policy for bare protein binding / uninformative):
GO:0005515 protein binding (both IPIs), GO:0031593 polyubiquitin modification-dependent protein binding (IEA),
GO:0030246 carbohydrate binding (IEA), GO:0030247 polysaccharide binding (IEA — glycogen-binding is real via
the CBM but these are uninformative relative to the catalytic MFs; the substrate binding is captured by the
enzymatic activities and glycogen catabolic process).

CC over-annotations from Reactome "Neutrophil degranulation" reaction propagation (AGL appears in neutrophil
degranulation cargo lists): GO:0005576 extracellular region (x2 TAS), GO:0034774 secretory granule lumen,
GO:1904813 ficolin-1-rich granule lumen — MARK_AS_OVER_ANNOTATED; AGL is a cytosolic enzyme, not a secreted/
granule-lumen protein. These are artifacts of the neutrophil-degranulation proteomics dataset.

Nuclear CC (condition-dependent, non-core): GO:0005634 nucleus (IEA), GO:0005654 nucleoplasm (IDA-HPA),
GO:0016604 nuclear body (IDA-HPA) — KEEP_AS_NON_CORE; AGL relocates to nucleus during glycogenolysis
(PMID:17908927) but core function is cytosolic.

Other CC IEA: GO:0016529 sarcoplasmic reticulum (IEA-Ensembl from rat/mouse ortholog), GO:0016234 inclusion
body (IEA-Ensembl) — MARK_AS_OVER_ANNOTATED (inclusion body relates to aggresome formation of the unstable
G1448R mutant, not WT function); sarcoplasmic reticulum is an ortholog-transfer artifact not supported for
human WT.

BP IEA: GO:0005975 carbohydrate metabolic process (IEA-InterPro) — ACCEPT (correct, broad parent).
GO:0005978 glycogen biosynthetic process (IEA-InterPro/KW) — REMOVE: AGL is a catabolic/degradation enzyme,
not biosynthetic; this is a demonstrably wrong IEA (InterPro2GO mapping of a debranching signature to
biosynthesis). Directionally contradicted by the enzyme's role in glycogen breakdown.
GO:0007584 response to nutrient, GO:0009725 response to hormone, GO:0051384 response to glucocorticoid — all
IEA-Ensembl from rat/mouse ortholog; plausible (AGL is regulated by fasting/refeeding, PMID:17908927 "Refeeding
mice ... causes a reduction in hepatic AGL levels") but not core molecular function — KEEP_AS_NON_CORE.

📄 View Raw YAML

id: P35573
gene_symbol: AGL
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  AGL (glycogen debranching enzyme, GDE) is a large (~175 kDa, 1532 aa) cytosolic,
  bifunctional enzyme that carries two independent catalytic activities on a single
  polypeptide and, working together with glycogen phosphorylase, completes the
  degradation of glycogen branch points. When phosphorylase stalls about four glucose
  residues from an alpha-1,6 branch point (leaving a phosphorylase limit dextrin),
  AGL's 4-alpha-glucanotransferase activity (EC 2.4.1.25) transfers a maltotriose
  (three-glucose) segment from the branch to a nearby non-reducing alpha-1,4 chain end,
  exposing the single glucose still attached by an alpha-1,6 linkage; AGL's
  amylo-alpha-1,6-glucosidase activity (EC 3.2.1.33) then hydrolyses that alpha-1,6 bond
  to release free glucose. AGL is a monomer and belongs to the glycogen debranching
  enzyme family (glycoside hydrolase families GH13/GH133). Loss of AGL function causes
  glycogen storage disease type III (Cori disease / Forbes disease), characterized by
  accumulation of abnormally structured glycogen with short outer chains
  (limit-dextrin-like), and clinically by hepatomegaly, fasting hypoglycemia, short
  stature, skeletal myopathy and cardiomyopathy.
alternative_products:
- name: 1 (2, 3, 4)
  id: P35573-1
- name: '5'
  id: P35573-2
  sequence_note: VSP_004270
- name: '6'
  id: P35573-3
  sequence_note: VSP_004271
existing_annotations:
- term:
    id: GO:0004135
    label: amylo-alpha-1,6-glucosidase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Amylo-alpha-1,6-glucosidase activity (EC 3.2.1.33) is one of the two core
      catalytic activities of AGL: it hydrolyses the alpha-1,6-glucosidic branch
      linkage exposed after the transferase step, releasing free glucose. This is the
      defining, conserved function of the debranching enzyme family and is well
      supported by direct enzymatic study.
    action: ACCEPT
    reason: >-
      Correct core molecular function, matching the UniProt catalytic activity
      "Hydrolysis of (1->6)-alpha-D-glucosidic branch linkages in glycogen
      phosphorylase limit dextrin" (EC 3.2.1.33). IBA is at the appropriate level of
      specificity for this family.
    supported_by:
    - reference_id: PMID:2961257
      supporting_text: Type III glycogen storage disease is caused by a deficiency of glycogen
    additional_reference_ids:
    - file:human/AGL/AGL-uniprot.txt
- term:
    id: GO:0005980
    label: glycogen catabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Glycogen catabolic process (glycogenolysis) is the biological process in which
      AGL acts; it is essential for complete degradation of glycogen branches and
      release of glucose, working alongside glycogen phosphorylase.
    action: ACCEPT
    reason: >-
      Correct core biological process for the debranching enzyme. Deficiency of AGL
      blocks complete glycogenolysis and causes accumulation of abnormal short-outer-chain
      (limit-dextrin-like) glycogen (GSD III).
    supported_by:
    - reference_id: PMID:2961257
      supporting_text: Type III glycogen storage disease is caused by a deficiency of glycogen
- term:
    id: GO:0004134
    label: 4-alpha-glucanotransferase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      4-alpha-glucanotransferase activity (EC 2.4.1.25) is the second core catalytic
      activity of AGL: it transfers a maltotriose segment of a (1->4)-alpha-D-glucan
      from a glycogen branch to a nearby non-reducing 1,4-end, exposing the single
      alpha-1,6-linked glucose for subsequent hydrolysis.
    action: ACCEPT
    reason: >-
      Correct core molecular function, matching UniProt catalytic activity "Transfers a
      segment of a (1->4)-alpha-D-glucan to a new position in an acceptor" (EC 2.4.1.25).
      IBA is appropriate for this conserved family function.
    additional_reference_ids:
    - file:human/AGL/AGL-uniprot.txt
- term:
    id: GO:0004134
    label: 4-alpha-glucanotransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic assignment (ARBA/InterPro/EC 2.4.1.25) of the transferase activity,
      duplicating the IBA and EXP annotations for the same term.
    action: ACCEPT
    reason: >-
      Correct core molecular function; the electronic mapping agrees with experimental
      and phylogenetic evidence for GO:0004134.
- term:
    id: GO:0004135
    label: amylo-alpha-1,6-glucosidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic assignment (ARBA/InterPro/EC 3.2.1.33) of the glucosidase activity,
      duplicating the IBA and EXP annotations for the same term.
    action: ACCEPT
    reason: >-
      Correct core molecular function; the electronic mapping agrees with experimental
      and phylogenetic evidence for GO:0004135.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: >-
      Cytoplasmic localization, consistent with AGL acting on cytosolic glycogen
      particles. Supported experimentally (IDA, PMID:17908927) and by UniProt
      subcellular location.
    action: ACCEPT
    reason: >-
      Correct localization; AGL is a cytosolic enzyme. This term is broad but accurate;
      the more precise cytosol (GO:0005829) is also annotated.
    supported_by:
    - reference_id: PMID:17908927
      supporting_text: Transfection studies in HepG2 cells demonstrate that AGL is
- term:
    id: GO:0005975
    label: carbohydrate metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      Carbohydrate metabolic process is a correct, broad parent process for AGL, whose
      role in glycogen catabolism is a subtype of carbohydrate metabolism.
    action: ACCEPT
    reason: >-
      Accurate though general InterPro2GO mapping. The more specific glycogen catabolic
      process (GO:0005980) is separately annotated and captured as core.
- term:
    id: GO:0005978
    label: glycogen biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      AGL is a glycogen degradation (catabolic) enzyme, not a biosynthetic enzyme. Its
      two activities (transferase and glucosidase) act to break down glycogen branches
      and release glucose; it plays no role in glycogen synthesis.
    action: REMOVE
    reason: >-
      Directionally incorrect electronic mapping. AGL functions in glycogen catabolism,
      and its loss causes accumulation (not deficiency) of glycogen; UniProt describes it
      as acting "in glycogen degradation." Assigning a biosynthetic process to a catabolic
      enzyme is a demonstrably wrong IEA (InterPro2GO/keyword artifact) and should be
      removed. (The "Glycogen biosynthesis" keyword likely reflects family-level signature
      grouping rather than AGL's actual directionality.)
    additional_reference_ids:
    - file:human/AGL/AGL-uniprot.txt
- term:
    id: GO:0005980
    label: glycogen catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: >-
      Electronic assignment of glycogen catabolic process, duplicating the IBA and
      Reactome-TAS annotations for the same term.
    action: ACCEPT
    reason: >-
      Correct core biological process for AGL, in agreement with phylogenetic and
      pathway-based evidence.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: >-
      AGL relocalizes partially to the nucleus specifically under glycogenolytic
      (glycogen-depleted) conditions, so nuclear localization is condition-dependent and
      not the site of its core catalytic function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Supported by experimental observation in the human/rodent system that AGL shows
      partial nuclear staining after glycogen depletion, but this is a regulated,
      condition-dependent localization rather than the constitutive cytosolic site of
      debranching activity.
    supported_by:
    - reference_id: PMID:17908927
      supporting_text: approximately 90% of transfected cells exhibit partial
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: is_active_in
  review:
    summary: >-
      Cytosol is the site where AGL is active, acting on cytosolic glycogen particles
      together with glycogen phosphorylase. This is the core localization.
    action: ACCEPT
    reason: >-
      Correct and precise localization for the core catalytic function; corroborated by
      IDA (HPA) and Reactome-TAS annotations to the same term.
- term:
    id: GO:0007584
    label: response to nutrient
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Hepatic AGL levels change with nutritional state (e.g. refeeding reduces AGL),
      consistent with a physiological response to nutrient availability, but this is a
      downstream regulatory/physiological role rather than AGL's core molecular function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Plausible orthology-transferred process annotation reflecting nutritional regulation
      of the debranching enzyme; retained as non-core because it describes the enzyme's
      regulation/physiology, not its catalytic activity.
    supported_by:
    - reference_id: PMID:17908927
      supporting_text: binding to glycogen crucially
- term:
    id: GO:0009725
    label: response to hormone
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Glycogenolysis and AGL activity are modulated by hormonal signals (e.g. glucagon/
      cAMP, glucocorticoids), so a response-to-hormone annotation is biologically
      plausible but peripheral to AGL's core enzymatic role.
    action: KEEP_AS_NON_CORE
    reason: >-
      Orthology-transferred physiological process; retained as non-core rather than
      accepted as a core function because it captures regulation of the pathway rather
      than AGL's molecular activity.
- term:
    id: GO:0016234
    label: inclusion body
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: >-
      Inclusion-body/aggresome localization is observed for the unstable GSD3 G1448R
      mutant of AGL upon proteasome impairment, not for the wild-type enzyme in its
      normal functional state.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      This localization reflects a disease-mutant/aggregation phenotype (the G1448R
      variant forms aggresomes when the proteasome is impaired) rather than a normal
      localization of functional AGL, so it over-states the wild-type protein's
      compartmentalization.
    supported_by:
    - reference_id: PMID:17908927
      supporting_text: the G1448R genetic variant of AGL is unable to bind to glycogen
- term:
    id: GO:0016529
    label: sarcoplasmic reticulum
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: >-
      Sarcoplasmic reticulum localization is transferred electronically from a rodent
      ortholog and is not supported for the human protein, which is a cytosolic enzyme
      acting on glycogen particles.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Orthology-based electronic annotation lacking direct support for human AGL; AGL is
      established as a cytoplasmic/cytosolic enzyme (IDA), and there is no evidence it is
      a resident sarcoplasmic reticulum protein.
- term:
    id: GO:0030246
    label: carbohydrate binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      AGL binds glycogen (a carbohydrate) via a conserved glycogen-binding region, but
      "carbohydrate binding" is an uninformative molecular-function term relative to the
      enzyme's two catalytic activities, which already imply substrate binding.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Substrate (glycogen) binding is real but is subsumed by the catalytic MF
      annotations (GO:0004134, GO:0004135) and the glycogen catabolic process; the generic
      binding term adds no functional information and is an over-annotation.
- term:
    id: GO:0030247
    label: polysaccharide binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      As with carbohydrate binding, AGL binds the polysaccharide glycogen through its
      glycogen-binding region, but polysaccharide binding is an uninformative generic
      term relative to the enzyme's catalytic activities.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Glycogen (polysaccharide) binding is implicit in the debranching activities and the
      glycogen catabolic process; the generic binding term is an over-annotation that adds
      no functional specificity.
- term:
    id: GO:0031593
    label: polyubiquitin modification-dependent protein binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      AGL is itself ubiquitinated (by the E3 ligase malin/NHLRC1) and its stability is
      regulated by ubiquitination, but there is no evidence that AGL acts as a reader that
      binds polyubiquitin chains on other proteins.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Likely an orthology-transfer artifact; the ubiquitin connection to AGL is that AGL
      is a substrate for ubiquitination, not a polyubiquitin-binding module. This generic
      binding term is not supported as a molecular function of AGL.
    supported_by:
    - reference_id: PMID:17908927
      supporting_text: Malin interacts with and promotes the ubiquitination of AGL
- term:
    id: GO:0051384
    label: response to glucocorticoid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Glucocorticoids influence hepatic glycogen metabolism, so a response-to-glucocorticoid
      annotation is biologically plausible for AGL but is a peripheral physiological/
      regulatory role, not the core molecular function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Orthology-transferred physiological response; retained as non-core because it
      reflects regulation of the enzyme/pathway rather than AGL's catalytic activity.
- term:
    id: GO:0005980
    label: glycogen catabolic process
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-70221
  qualifier: involved_in
  review:
    summary: >-
      Reactome curates AGL as a participant in glycogen breakdown (glycogenolysis),
      catalysing the two debranching reactions R-HSA-71552 (transferase) and R-HSA-71593
      (glucosidase). This is the core biological process.
    action: ACCEPT
    reason: >-
      Author-curated pathway annotation consistent with the enzyme's established role in
      complete glycogen degradation.
- term:
    id: GO:0004134
    label: 4-alpha-glucanotransferase activity
  evidence_type: EXP
  original_reference_id: PMID:2961257
  qualifier: enables
  review:
    summary: >-
      Experimental annotation of the 4-alpha-glucanotransferase activity, one of the two
      catalytic activities of the purified debranching enzyme. Chen et al. purified the
      debranching enzyme and characterized it and its deficiency in GSD III.
    action: ACCEPT
    reason: >-
      Core molecular function supported by experimental characterization of the purified
      enzyme; consistent with UniProt EC 2.4.1.25 and the IBA/IEA annotations.
    supported_by:
    - reference_id: PMID:2961257
      supporting_text: debranching enzyme was purified 238-fold from porcine skeletal muscle
- term:
    id: GO:0004135
    label: amylo-alpha-1,6-glucosidase activity
  evidence_type: EXP
  original_reference_id: PMID:2961257
  qualifier: enables
  review:
    summary: >-
      Experimental annotation of the amylo-alpha-1,6-glucosidase activity, the second
      catalytic activity of the purified debranching enzyme; its deficiency defines type
      III glycogen storage disease.
    action: ACCEPT
    reason: >-
      Core molecular function supported by experimental characterization of the purified
      enzyme; consistent with UniProt EC 3.2.1.33 and the IBA/IEA annotations.
    supported_by:
    - reference_id: PMID:2961257
      supporting_text: the antiserum detected no cross-reactive material in any of the liver or muscle samples from patients
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: >-
      HPA immunofluorescence localizes AGL to the nucleoplasm. Consistent with the
      condition-dependent (glycogenolytic) nuclear relocalization reported for AGL, this
      is a non-core localization relative to its cytosolic catalytic role.
    action: KEEP_AS_NON_CORE
    reason: >-
      Genuine IDA localization but reflects a regulated/condition-dependent nuclear pool
      of AGL rather than the constitutive cytosolic site of debranching activity.
    supported_by:
    - reference_id: PMID:17908927
      supporting_text: approximately 90% of transfected cells exhibit partial
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: >-
      HPA immunofluorescence localizes AGL to the cytosol, the core compartment where the
      enzyme acts on cytosolic glycogen.
    action: ACCEPT
    reason: >-
      Direct experimental support for the core cytosolic localization, in agreement with
      UniProt and Reactome.
- term:
    id: GO:0016604
    label: nuclear body
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: >-
      HPA immunofluorescence detects AGL in nuclear bodies, part of the condition-dependent
      nuclear pool; not the core cytosolic functional localization.
    action: KEEP_AS_NON_CORE
    reason: >-
      Genuine IDA localization but represents a regulated nuclear sub-pool rather than the
      constitutive site of the debranching reaction.
    supported_by:
    - reference_id: PMID:17908927
      supporting_text: approximately 90% of transfected cells exhibit partial
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24837458
  qualifier: enables
  review:
    summary: >-
      This IPI captures a physical interaction between AGL/GDE and STBD1 (starch-binding
      domain-containing protein 1, O95210). The interaction is real (co-IP and GST
      pull-down of endogenous GDE by STBD1), but "protein binding" is an uninformative
      molecular-function term.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Per curation guidelines, bare "protein binding" is not retained as a core molecular
      function because it conveys no specific activity. The underlying interaction with
      STBD1 is documented, but the term itself is an over-annotation relative to AGL's
      catalytic MFs.
    supported_by:
    - reference_id: PMID:24837458
      supporting_text: could bind to FLAG-tagged Laforin, GBE1 and GDE
    - reference_id: PMID:24837458
      supporting_text: during glycogen breakdown, proteins such as GS, GDE or Laforin bind to STBD1
- term:
    id: GO:0005576
    label: extracellular region
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6798748
  qualifier: located_in
  review:
    summary: >-
      This localization derives from AGL appearing in neutrophil-degranulation cargo
      datasets modeled by Reactome (secretory granule exocytosis). AGL is a cytosolic
      enzyme, not a bona fide secreted/extracellular protein.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Artifact of the neutrophil-degranulation proteomics pathway; extracellular
      localization contradicts the well-established cytosolic localization of AGL and is
      not a functional compartment for this enzyme.
- term:
    id: GO:0005576
    label: extracellular region
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6800434
  qualifier: located_in
  review:
    summary: >-
      Duplicate extracellular-region annotation from a second neutrophil-degranulation
      (ficolin-rich granule) Reactome reaction; same over-annotation rationale.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Neutrophil-degranulation proteomics artifact; AGL is cytosolic, not secreted.
- term:
    id: GO:0034774
    label: secretory granule lumen
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6798748
  qualifier: located_in
  review:
    summary: >-
      Secretory granule lumen localization arises from AGL's inclusion in neutrophil
      secretory-granule proteomic cargo lists modeled by Reactome, not from a functional
      role of AGL inside secretory granules.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Artifact of the neutrophil-degranulation dataset; inconsistent with AGL's cytosolic
      localization and its role in cytosolic glycogen catabolism.
- term:
    id: GO:1904813
    label: ficolin-1-rich granule lumen
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6800434
  qualifier: located_in
  review:
    summary: >-
      Ficolin-1-rich granule lumen localization is likewise derived from neutrophil
      granule proteomics via Reactome, not from a functional granule role of AGL.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Neutrophil-degranulation proteomics artifact; AGL is a cytosolic enzyme and is not
      a functional resident of granule lumens.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-71552
  qualifier: located_in
  review:
    summary: >-
      Reactome places the AGL-catalysed transferase reaction (limit-dextrin transfer) in
      the cytosol, the core compartment for glycogen debranching.
    action: ACCEPT
    reason: >-
      Author-curated pathway localization consistent with the established cytosolic site
      of AGL activity.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-71593
  qualifier: located_in
  review:
    summary: >-
      Reactome places the AGL-catalysed glucosidase reaction (release of alpha-D-glucose)
      in the cytosol, consistent with the core localization of the debranching reaction.
    action: ACCEPT
    reason: >-
      Author-curated pathway localization consistent with the cytosolic site of AGL
      activity.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:17908927
  qualifier: enables
  review:
    summary: >-
      This IPI captures the interaction between AGL and the E3 ubiquitin ligase malin
      (NHLRC1, Q6VVB1), which ubiquitinates AGL and regulates its stability. The
      interaction is genuine but "protein binding" is an uninformative term.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Bare "protein binding" is not retained as a core molecular function per curation
      guidelines. The specific interaction with malin is documented and biologically
      important (regulation of AGL stability by ubiquitination), but the generic term adds
      no functional specificity.
    supported_by:
    - reference_id: PMID:17908927
      supporting_text: Malin interacts with and promotes the ubiquitination of AGL
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:17908927
  qualifier: located_in
  review:
    summary: >-
      Direct experimental demonstration that AGL is cytoplasmic (transfection/localization
      studies in HepG2 cells), the core compartment where AGL degrades cytosolic glycogen.
    action: ACCEPT
    reason: >-
      Strong experimental (IDA) support for the core cytoplasmic localization, matching
      UniProt subcellular location.
    supported_by:
    - reference_id: PMID:17908927
      supporting_text: cytoplasmic whereas Malin is predominately nuclear.
- term:
    id: GO:0043033
    label: isoamylase complex
  evidence_type: TAS
  original_reference_id: PMID:1374391
  qualifier: part_of
  review:
    summary: >-
      Human AGL is a single bifunctional polypeptide that acts as a monomer; it is not a
      subunit of a multi-protein isoamylase complex. The isoamylase complex (a
      bacterial/plant debranching enzyme assembly) is not the biological form of the
      mammalian debranching enzyme.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      UniProt states the subunit structure is "Monomer", and both catalytic activities
      reside on the single AGL polypeptide (cloned as a single multifunctional enzyme).
      The cited cloning paper describes the debrancher as a single multifunctional protein
      and does not report an isoamylase complex; the "isoamylase complex" component appears
      to be a legacy/mis-mapped complex annotation and over-states AGL's quaternary
      organization.
    supported_by:
    - reference_id: PMID:1374391
      supporting_text: an important step toward defining the structure-function relationship of this
    additional_reference_ids:
    - file:human/AGL/AGL-uniprot.txt
core_functions:
- description: >-
    Removes glycogen branch points during glycogenolysis via a 4-alpha-glucanotransferase
    activity that relocates a maltotriose segment from the branch to a nearby alpha-1,4
    chain end, exposing the single alpha-1,6-linked glucose.
  molecular_function:
    id: GO:0004134
    label: 4-alpha-glucanotransferase activity
  directly_involved_in:
  - id: GO:0005980
    label: glycogen catabolic process
  locations:
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: PMID:2961257
    supporting_text: Type III glycogen storage disease is caused by a deficiency of glycogen
- description: >-
    Hydrolyses the alpha-1,6-glucosidic branch linkage exposed after the transferase step,
    releasing free glucose and allowing complete degradation of glycogen; loss of this
    activity causes glycogen storage disease type III (Cori/Forbes disease).
  molecular_function:
    id: GO:0004135
    label: amylo-alpha-1,6-glucosidase activity
  directly_involved_in:
  - id: GO:0005980
    label: glycogen catabolic process
  locations:
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: PMID:2961257
    supporting_text: the antiserum detected no cross-reactive material in any of the liver or muscle samples from patients
proposed_new_terms: []
suggested_questions:
- question: >-
    Do the two catalytic domains of AGL act processively on the same glycogen molecule, and
    what is the structural basis (from cryo-EM structure PDB 8ZEQ) for coordinating the
    transferase and glucosidase activities on a single polypeptide?
- question: >-
    What is the functional significance of AGL's condition-dependent nuclear relocalization
    during glycogenolysis, and does the nuclear pool have a distinct role?
suggested_experiments:
- description: >-
    Structure-guided mutagenesis of the predicted active-site residues (526, 529, 627) to
    dissect the contributions of the transferase versus glucosidase activities to glycogen
    debranching, and to model GSD III subtypes IIIc/IIId (selective loss of one activity).
- description: >-
    Quantitative analysis of AGL subcellular redistribution (cytosol to nucleus) as a function
    of glycogen depletion and hormonal stimulation, to determine whether nuclear localization
    is functional or a regulatory sequestration mechanism.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to
    orthologs using Ensembl Compara
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:1374391
  title: Molecular cloning and nucleotide sequence of cDNA encoding human muscle glycogen
    debranching enzyme.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified cloning of the human muscle debranching enzyme cDNA; establishes AGL
      as a single multifunctional polypeptide (~172 kDa). Cited by GOA for the
      "isoamylase complex" component, which is not supported by this paper.
- id: PMID:17908927
  title: A role for AGL ubiquitination in the glycogen storage disorders of Lafora
    and Cori's disease.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; directly about human AGL. Establishes cytoplasmic localization (IDA),
      condition-dependent nuclear relocalization during glycogenolysis, and interaction with
      malin/NHLRC1 (E3 ligase) regulating AGL stability via ubiquitination.
- id: PMID:24837458
  title: The carbohydrate-binding domain of overexpressed STBD1 is important for its
    stability and protein-protein interactions.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Full-text verified; primarily about STBD1 but documents a direct physical interaction
      between STBD1 and endogenous GDE/AGL (co-IP and GST pull-down), supporting the AGL
      protein-binding IPI to O95210.
- id: PMID:2961257
  title: 'Glycogen debranching enzyme: purification, antibody characterization, and
    immunoblot analyses of type III glycogen storage disease.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; purification and immunochemical characterization of the glycogen
      debranching enzyme and its deficiency in type III GSD, underpinning the experimental
      MF annotations (EC 2.4.1.25 and EC 3.2.1.33). Abstract-only in cache.
- id: Reactome:R-HSA-6798748
  title: Exocytosis of secretory granule lumen proteins
  findings: []
- id: Reactome:R-HSA-6800434
  title: Exocytosis of ficolin-rich granule lumen proteins
  findings: []
- id: Reactome:R-HSA-70221
  title: Glycogen breakdown (glycogenolysis)
  findings: []
- id: Reactome:R-HSA-71552
  title: limit dextrin-glycogenin => ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)
    glycogenin
  findings: []
- id: Reactome:R-HSA-71593
  title: ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin => poly{(1,4)-alpha-glucosyl}
    glycogenin + alpha-D-glucose
  findings: []

AGL

Gene Description