ALG13 encodes alternatively spliced proteins, including the short isoform 2 that supplies the catalytic subunit of the ALG13βALG14 UDP-N-acetylglucosamine transferase. At the cytoplasmic face of the endoplasmic reticulum, this complex transfers the second, beta-1,4-linked N-acetylglucosamine from UDP-GlcNAc onto GlcNAc-PP-dolichol, forming GlcNAc2-PP-dolichol during assembly of the lipid-linked glycan precursor for protein N-linked glycosylation. ALG14 anchors the soluble catalytic subunit at the membrane, and the active enzyme requires their association. Human isoform 2 is 165 amino acids long; the 1137-amino-acid isoform 1 did not bind ALG14 or display this transferase activity in comparative cellular and biochemical assays. The long protein contains an OTU domain, but its physiological molecular function remains unresolved. Pathogenic ALG13 variants cause developmental and epileptic encephalopathy; several variants reduce transferase activity even when routine transferrin glycosylation measurements are near normal.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000117 | MODIFY | Summary: The broad catalytic activity can be resolved to the specific GlcNAc transfer reaction. Reason: Human ALG13 isoform 2 in complex with ALG14 catalyzes formation of GlcNAc2-PP-dolichol (PMID:36200043). Replace the generic catalytic parent with GO:0004577 to express the measured chemistry. This does not assign the activity to every splice isoform or infer OTU catalysis from the long isoform sequence. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: ARBA:ARBA00027533 UNRESOLVED The GOA source rule is identified, but its predicates were not independently reconstructed. Human biochemical evidence resolves the broad predicted activity. Proposed replacements: N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity Supporting Evidence: PMID:36200043 This dimeric ALG13/14 catalyzes the second step of LLO synthesis, transferring a Ξ²1,4-linked N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to GlcNAc-pyrophosphate-dolichol (Gn-PDol) PMID:36200043 Unexpectedly, by this assay HA-ALG13-iso1 did not show any GnTase activity, while HA-ALG13-iso2 could catalyze the formation of Gn2-PDol under the same reaction conditions (Figure 4B). |
| GO:0004577 N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: The mapped reaction matches the experimentally characterized ALG13βALG14 enzyme. Reason: RHEA:23380 and EC:2.4.1.141 identify transfer of GlcNAc from UDP-GlcNAc onto GlcNAc-PP-dolichol. The cached UniProt reaction is assigned to isoform 2, and the purified human complex assay independently confirms the substrate/product chemistry (PMID:36200043). The seeded gene-level annotation is retained without implying that isoform 1 is active. Propagation Review Root cause: NO FAILURE CORE Sources checked: RHEA:23380 SUPPORTS TRANSFER The cached UniProt isoform-2 reaction and the live GO:0004577 RHEA cross-reference agree with the human biochemical assay. EC:2.4.1.141 SUPPORTS TRANSFER EC number identifies the specific second GlcNAc-transfer step; it does not imply all splice products catalyze it. Supporting Evidence: PMID:36200043 This dimeric ALG13/14 catalyzes the second step of LLO synthesis, transferring a Ξ²1,4-linked N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to GlcNAc-pyrophosphate-dolichol (Gn-PDol) PMID:36200043 Unexpectedly, by this assay HA-ALG13-iso1 did not show any GnTase activity, while HA-ALG13-iso2 could catalyze the formation of Gn2-PDol under the same reaction conditions (Figure 4B). |
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | ACCEPT | Summary: Cytoplasm is a valid broad location for the cytoplasm-facing ALG13 enzyme. Reason: The catalytic ALG13 pool acts on the cytoplasmic surface of the ER, a location within the cytoplasm. The broad compartment does not assert that the protein is exclusively free or soluble in the cytosol. PMID:16100110 additionally describes free cytosolic partitioning of yeast Alg13 when ALG14 recruitment is limiting; that experiment is kept distinct from a direct human localization assay. Propagation Review Root cause: NO FAILURE CORE Sources checked: ARBA:ARBA00026971 UNRESOLVED The exact rule predicates were not inspected. The broad compartment is consistent with independently supported cytoplasm-facing ER activity; no claim is made about every isoform or all cellular pools. Supporting Evidence: PMID:16100110 We show that Alg14 functions as a membrane anchor that recruits Alg13 to the cytosolic face of the ER, where catalysis of GlcNAc2-PP-dol occurs. |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: ALG13 isoform 2 associates with the ER membrane through ALG14. Reason: The UniProt subcellular-location mapping describes the peripheral membrane pool of isoform 2. The conserved ALG14-dependent recruitment mechanism and human ALG13βALG14 functional complementation support this location (PMID:16100110); later human complex biochemistry corroborates membrane-associated activity (PMID:36200043). Retain the source compartment without converting it into an integral membrane or all-isoform claim. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0097 SUPPORTS TRANSFER The cached Q9NP73 subcellular-location entry explicitly assigns ER membrane and peripheral association to isoform 2 with PMID:16100110 support. Supporting Evidence: PMID:16100110 Further evidence for the functional relevance of this interaction comes from our demonstration that the human ALG13 and ALG14 orthologues fail to pair with their yeast partners, but when co-expressed in yeast can functionally complement the loss of either ALG13 or ALG14. PMID:36200043 This experiment demonstrated that FLAG-tagged ALG14 completely failed to coprecipitate with HA-ALG13-iso1, although it efficiently interacted with HA-tagged ALG13-iso2 (Figure 4C). |
| GO:0006488 dolichol-linked oligosaccharide biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: ALG13 catalyzes a defined step of dolichol-linked oligosaccharide synthesis. Reason: The Alg13-like family assignment is consistent with direct human isoform-2 GlcNAc-transfer chemistry. ALG13 performs the second sugar addition to the lipid-linked precursor, so participation is catalytic rather than inferred solely from a glycosylation defect (PMID:36200043). Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR039042 SUPPORTS TRANSFER The cached UniProt entry identifies the Alg13-like family; human enzymology independently grounds the mapped process. The complete InterPro mapping-rule history was not reconstructed. Supporting Evidence: PMID:36200043 This dimeric ALG13/14 catalyzes the second step of LLO synthesis, transferring a Ξ²1,4-linked N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to GlcNAc-pyrophosphate-dolichol (Gn-PDol) |
| GO:0016758 hexosyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: The hexosyltransferase parent can be refined to the assayed GlcNAc-transfer activity. Reason: The glycosyltransferase-28 domain supports a sugar-transfer function, while direct human complex assays identify UDP-GlcNAc and GlcNAc-PP-dolichol as donor and acceptor (PMID:36200043). GO:0004577 captures this specific chemistry; the general domain does not establish activity of the long isoform. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: InterPro:IPR007235 SUPPORTS TRANSFER The cached entry contains Glyco_trans_28_C. It supports the generic domain assignment, while the replacement substrate specificity comes from independent human assays rather than the domain alone. Proposed replacements: N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity Supporting Evidence: PMID:36200043 This dimeric ALG13/14 catalyzes the second step of LLO synthesis, transferring a Ξ²1,4-linked N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to GlcNAc-pyrophosphate-dolichol (Gn-PDol) PMID:36200043 Unexpectedly, by this assay HA-ALG13-iso1 did not show any GnTase activity, while HA-ALG13-iso2 could catalyze the formation of Gn2-PDol under the same reaction conditions (Figure 4B). |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | REMOVE | Summary: The generic interaction annotation provides no resolved molecular function. Reason: The BioPlex IPI source associates ALG13 with SLC2A4 (UniProtKB:P14672), also listed in the cached UniProt interaction record. The accessible proteome-scale study does not establish a specific ALG13 molecular function through this pair. Remove the uninformative generic binding term without denying the reported interaction or replacing SLC2A4 binding with the independently established ALG14 enzymatic complex. The pair-level supplementary record and tested ALG13 isoform were not independently recovered. |
| GO:0005789 endoplasmic reticulum membrane | TAS Reactome:R-HSA-446207 | ACCEPT | Summary: The normal Reactome reaction places the ALG13βALG14 enzyme at the ER membrane. Reason: Reactome:R-HSA-446207 describes ALG13 as catalytic subunit and ALG14 as the membrane anchor recruiting it to the cytosolic face of the ER. This is the normal GlcNAc-addition event and agrees with the primary human complex evidence and conserved recruitment mechanism (PMID:16100110; PMID:36200043). Supporting Evidence: PMID:16100110 Further evidence for the functional relevance of this interaction comes from our demonstration that the human ALG13 and ALG14 orthologues fail to pair with their yeast partners, but when co-expressed in yeast can functionally complement the loss of either ALG13 or ALG14. PMID:36200043 This dimeric ALG13/14 catalyzes the second step of LLO synthesis, transferring a Ξ²1,4-linked N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to GlcNAc-pyrophosphate-dolichol (Gn-PDol) |
| GO:0005789 endoplasmic reticulum membrane | TAS Reactome:R-HSA-5633241 | ACCEPT | Summary: The defective-ALG14 event retains the relevant ER-membrane enzyme context. Reason: Reactome:R-HSA-5633241 concerns ALG14 variants that impair the second GlcNAc-addition step. Its background description identifies the normal ALG13 catalytic subunit and ALG14 membrane anchor. Retain the compartment, independently supported by PMID:16100110 and PMID:36200043; this event is not evidence that wild-type ALG13 lacks activity or that an ALG13 mutant was assayed. Supporting Evidence: PMID:16100110 Further evidence for the functional relevance of this interaction comes from our demonstration that the human ALG13 and ALG14 orthologues fail to pair with their yeast partners, but when co-expressed in yeast can functionally complement the loss of either ALG13 or ALG14. PMID:36200043 This experiment demonstrated that FLAG-tagged ALG14 completely failed to coprecipitate with HA-ALG13-iso1, although it efficiently interacted with HA-tagged ALG13-iso2 (Figure 4C). |
| GO:0005789 endoplasmic reticulum membrane | EXP PMID:16100110 Alg14 recruits Alg13 to the cytoplasmic face of the endoplas... | ACCEPT | Summary: Conserved recruitment and functional human complementation support ER-membrane association. Reason: The accessible PMID:16100110 abstract directly describes yeast Alg13/Alg14 interaction and membrane recruitment, then separately reports complementation by the human pair in yeast. The full 2005 article was not recovered, so the detailed yeast localization experiments are not relabeled as human-cell microscopy. The retained human location is supported by that functional conservation, the curator assessment and independent membrane-associated human complex/activity experiments in PMID:36200043. Supporting Evidence: PMID:16100110 Further evidence for the functional relevance of this interaction comes from our demonstration that the human ALG13 and ALG14 orthologues fail to pair with their yeast partners, but when co-expressed in yeast can functionally complement the loss of either ALG13 or ALG14. PMID:36200043 This experiment demonstrated that FLAG-tagged ALG14 completely failed to coprecipitate with HA-ALG13-iso1, although it efficiently interacted with HA-tagged ALG13-iso2 (Figure 4C). |
| GO:0098554 cytoplasmic side of endoplasmic reticulum membrane | IGI PMID:16100110 Alg14 recruits Alg13 to the cytoplasmic face of the endoplas... | ACCEPT | Summary: The functional ALG13 enzyme acts on the cytoplasmic face of the ER. Reason: The 2005 genetic evidence links the human ALG13βALG14 pair to the yeast pathway in which Alg14 recruits the catalytic subunit to the cytosolic ER surface (PMID:16100110). This conserved orientation agrees with the membrane-linked acceptor and human catalytic complex (PMID:36200043). The cached GO-CAM uses the same source for this compartment; no direct human microscopy is inferred from the yeast assays. Propagation Review Root cause: NO FAILURE CORE Sources checked: SGD:S000003015 SUPPORTS TRANSFER The GOA genetic-interaction partner is yeast ALG13 (YGL047W). The primary abstract reports loss of yeast ALG13 complemented only by co-expressing both human partners; this supports functional conservation, not a pairwise sequence-only transfer. Supporting Evidence: PMID:16100110 Further evidence for the functional relevance of this interaction comes from our demonstration that the human ALG13 and ALG14 orthologues fail to pair with their yeast partners, but when co-expressed in yeast can functionally complement the loss of either ALG13 or ALG14. PMID:16100110 We show that Alg14 functions as a membrane anchor that recruits Alg13 to the cytosolic face of the ER, where catalysis of GlcNAc2-PP-dol occurs. |
| GO:0004577 N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity | IDA PMID:36200043 An in vitro assay for enzymatic studies on human ALG13/14 he... | ACCEPT | Summary: Purified human ALG13-isoform-2/ALG14 catalyzes the specified reaction. Reason: PMID:36200043 uses co-expressed human proteins purified from E. coli membranes, LC-MS detection of GlcNAc2-PP-dolichol, donor-specificity assays and downstream ALG1 recognition of the product. HEK293 immunoprecipitation/activity assays independently distinguish active isoform 2 from inactive isoform 1. The enzyme is the assembled complex; merely mixing the separately expressed proteins did not yield activity under the tested conditions. Supporting Evidence: PMID:36200043 This dimeric ALG13/14 catalyzes the second step of LLO synthesis, transferring a Ξ²1,4-linked N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to GlcNAc-pyrophosphate-dolichol (Gn-PDol) PMID:36200043 Unexpectedly, by this assay HA-ALG13-iso1 did not show any GnTase activity, while HA-ALG13-iso2 could catalyze the formation of Gn2-PDol under the same reaction conditions (Figure 4B). |
| GO:0006487 protein N-linked glycosylation | IMP PMID:22492991 Gene identification in the congenital disorders of glycosyla... | ACCEPT | Summary: The ALG13-catalyzed precursor step is part of core protein N-linked glycosylation. Reason: GO:0006488 dolichol-linked oligosaccharide biosynthetic process is explicitly part_of GO:0006487 in the current ontology. ALG13 catalyzes the second sugar addition within that precursor pathway; it is not merely a required substrate. PMID:22492991 links human ALG13 deficiency to impaired enzyme activity and CDG-I, independently reinforced by direct human catalysis in PMID:36200043. Accept the broader core process without claiming that ALG13 performs the subsequent oligosaccharyltransferase reaction on proteins. The machine-supplied upstream relation is retained unchanged and is not interpreted in this term-level assessment under the explicit qualifier rule, which only interprets NOT and contributes_to. Supporting Evidence: PMID:22492991 These included the first X-linked CDG-I due to a de novo mutation in ALG13, and compound heterozygous mutations in DPAGT1, together the first two steps in dolichol-PP-glycan assembly, and mutations in PGM1 in two cases, involved in nucleotide sugar biosynthesis. PMID:22492991 The pathogenicity of the mutations was confirmed by showing the deficient activity of the corresponding enzymes in patient fibroblasts. PMID:36200043 This dimeric ALG13/14 catalyzes the second step of LLO synthesis, transferring a Ξ²1,4-linked N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to GlcNAc-pyrophosphate-dolichol (Gn-PDol) |
| GO:0004577 N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity | IMP PMID:22492991 Gene identification in the congenital disorders of glycosyla... | ACCEPT | Summary: Patient-derived deficient enzyme activity supports the specific ALG13 reaction. Reason: The PMID:22492991 abstract identifies a de novo human ALG13 defect and deficient enzyme activity in patient fibroblasts. The author-uploaded Figure 2B caption further identifies microsomal extracts, UDP-GlcNAc and radiolabeled GlcNAc1-PP-dolichol with TLC measurement of GlcNAc2-PP-dolichol. Full Methods were not recovered. Independent purified human enzyme assays in PMID:36200043 corroborate the reaction, so the IMP claim is retained without inventing uninspected assay controls. Supporting Evidence: PMID:22492991 The pathogenicity of the mutations was confirmed by showing the deficient activity of the corresponding enzymes in patient fibroblasts. PMID:36200043 This dimeric ALG13/14 catalyzes the second step of LLO synthesis, transferring a Ξ²1,4-linked N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to GlcNAc-pyrophosphate-dolichol (Gn-PDol) |
| GO:0006488 dolichol-linked oligosaccharide biosynthetic process | IMP PMID:22492991 Gene identification in the congenital disorders of glycosyla... | ACCEPT | Summary: ALG13 directly supplies a glycosyltransferase step in lipid-linked glycan synthesis. Reason: The human deficient-enzyme result and identified ALG13 defect in PMID:22492991 support this process. The substrate/product-specific Figure 2B caption and independent human enzyme assay in PMID:36200043 establish that ALG13 performs precursor synthesis, rather than merely being necessary for a downstream clinical phenotype. Supporting Evidence: PMID:22492991 These included the first X-linked CDG-I due to a de novo mutation in ALG13, and compound heterozygous mutations in DPAGT1, together the first two steps in dolichol-PP-glycan assembly, and mutations in PGM1 in two cases, involved in nucleotide sugar biosynthesis. PMID:36200043 This dimeric ALG13/14 catalyzes the second step of LLO synthesis, transferring a Ξ²1,4-linked N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to GlcNAc-pyrophosphate-dolichol (Gn-PDol) |
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Download this section (compressed HTML)Q: Does GO:0043541 intentionally include the human ALG13βALG14 dimer as used in ALG14 IDA curation and the ALG13 UniProt IDA cross-reference, despite its multienzyme definition and phosphorus-transferase-complex ancestry, or should the DPAGT1-containing assembly and the dimer be distinguished?
Q: What physiological molecular activity is performed by human ALG13 isoform 1, and how do isoforms 3 and 4 contribute to ALG13 biology?
Q: Which cell-specific glycosylation substrates or additional molecular activities connect ALG13 variants to neuronal dysfunction when routine transferrin glycosylation is near normal?
Experiment: Use isoform-specific endogenous tagging, quantitative complex purification and targeted glycosyltransferase assays in human cells to resolve ALG13 isoform composition, ALG14 recruitment and possible DPAGT1 association.
Experiment: Compare isogenic human neural cells bearing disease variants with isoform-specific rescue, measuring lipid-linked glycans and glycoprotein occupancy alongside neuronal phenotypes to distinguish catalytic defects from other isoform functions.
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