{"gene":"TG_310400","gene_symbol":"GAT1","run_date":"2026-09-08T15:15:13","timeline":{"discoveries":[{"year":2020,"finding":"GAT1 is a glycosyltransferase that catalyzes addition of the terminal fifth sugar (Galα1,3Glcα linkage) to the Skp1 pentasaccharide in Toxoplasma gondii, modifying the hydroxyproline residue on Skp1. Kinetic and crystallographic experiments established that GAT1 is specific for Skp1 as its substrate. Loss of gat1 (gat1Δ) results in a slow-growth phenotype, indicating functional importance of the terminal α-galactose for glycan-mediated regulation of Skp1.","method":"Glycosyltransferase identification, kinetic assays, X-ray crystallography, gat1Δ knockout phenotype analysis, computational modeling","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure, in vitro kinetic assays, mutagenesis/knockout phenotype, and computational modeling in a single rigorous study","pmids":["32414843"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2020,"finding":"Computational analyses indicated that the Toxoplasma Skp1 pentasaccharide (including the GAT1-added terminal galactose) assumes an ordered conformation that controls Skp1 structure through nonpolar packing interactions of the fifth sugar, consistent with a conformational control model for glycoregulation of Skp1/F-box protein subcomplex assembly.","method":"Computational structural analysis, comparison with Dictyostelium glycan structure","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 4 / Moderate — computational modeling supported by biochemical and crystallographic data in the same study, but conformational control model is computationally inferred","pmids":["32414843"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2026,"finding":"GAT1 forms a homodimer that complexes with SKP1 monomers regardless of its glycosylation status, with binding affinity and stoichiometry dictated by the glycostate of SKP1. GAT1 competes with F-box proteins (FBPs) and the SKP1 homodimer for the same core hydrophobic interface on SKP1. Substoichiometric levels of GAT1 promote SKP1 monomerization in a CTR (intrinsically disordered C-terminal region)-dependent manner, indicating a non-enzymatic scaffolding role for GAT1 in controlling SKP1 monomer availability and FBP-binding preference.","method":"Sedimentation velocity analytical ultracentrifugation, computational modeling, mutational probing, gat1-knockout FBP interactome profiling","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — sedimentation velocity AUC plus mutational probing and computational modeling in a single preprint study; not yet peer-reviewed","pmids":["42327091"],"is_preprint":true,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"GAT1 is a Skp1-specific glycosyltransferase in Toxoplasma gondii that adds a terminal Galα1,3Glc sugar to the Skp1 pentasaccharide, imposing an ordered conformation on the glycan that regulates Skp1 structure, homodimerization, and F-box protein binding; beyond its enzymatic role, GAT1 also acts non-enzymatically by competitively binding the SKP1 hydrophobic interface to promote SKP1 monomerization and modulate FBP-binding preference in a glycostate- and CTR-dependent manner."},"narrative":{"mechanistic_narrative":"GAT1 is a Skp1-specific glycosyltransferase in Toxoplasma gondii that governs the assembly of Skp1/F-box protein subcomplexes through both catalytic and non-enzymatic activities [PMID:32414843, PMID:42327091]. Enzymatically, GAT1 caps the Skp1 pentasaccharide by adding a terminal fifth sugar via a Galα1,3Glcα linkage onto the hydroxyproline-linked glycan, a modification that imposes an ordered conformation on the glycan and thereby controls Skp1 structure through nonpolar packing of the terminal galactose [PMID:32414843]; loss of gat1 produces a slow-growth phenotype, marking this terminal galactose as functionally important for glycan-mediated regulation of Skp1 [PMID:32414843]. Beyond catalysis, GAT1 forms a homodimer that binds SKP1 monomers and competes with F-box proteins and the SKP1 homodimer for the same core hydrophobic interface, promoting SKP1 monomerization in a manner dependent on SKP1 glycostate and its intrinsically disordered C-terminal region, thereby biasing F-box protein binding preference [PMID:42327091].","teleology":[{"year":2020,"claim":"Establishing which enzyme completes the Skp1 glycan and whether that final sugar matters resolved the terminal step of a conserved cytoplasmic Skp1 glycosylation pathway and its physiological relevance.","evidence":"Glycosyltransferase identification with in vitro kinetic assays, X-ray crystallography, and gat1Δ knockout phenotyping in Toxoplasma gondii","pmids":["32414843"],"confidence":"High","gaps":["The mechanism linking loss of the terminal galactose to the slow-growth phenotype at the cellular level was not resolved","The full set of downstream F-box proteins affected by the modification was not defined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2020,"claim":"Modeling how the completed pentasaccharide behaves addressed why the terminal sugar matters, proposing that the glycan adopts an ordered conformation controlling Skp1 structure and subcomplex assembly.","evidence":"Computational structural analysis compared with the Dictyostelium glycan, supported by the same study's crystallographic and biochemical data","pmids":["32414843"],"confidence":"Medium","gaps":["The conformational control model is computationally inferred rather than directly observed in the assembled Skp1/F-box complex","Direct measurement of how glycan conformation alters F-box protein affinity was not performed"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2026,"claim":"Testing whether GAT1 acts only as an enzyme revealed a distinct non-enzymatic scaffolding role, in which GAT1 competitively controls SKP1 monomer availability and F-box protein binding preference.","evidence":"Sedimentation velocity analytical ultracentrifugation, mutational probing, computational modeling, and gat1-knockout F-box protein interactome profiling in Toxoplasma gondii (preprint)","pmids":["42327091"],"confidence":"Medium","gaps":["Not yet peer-reviewed","The in vivo consequences of GAT1-driven SKP1 monomerization for SCF ubiquitin ligase output were not established","How the enzymatic and scaffolding activities are coordinated on the same substrate is unresolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"How GAT1's dual glycosyltransferase and scaffolding functions are integrated to regulate SCF complex assembly and parasite growth in vivo remains open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No in vivo demonstration linking GAT1-controlled SKP1 monomerization to ubiquitin ligase function","The relationship between glycostate and scaffolding activity under physiological conditions is undefined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["GAT1 homodimer","GAT1 homodimer–SKP1 monomer complex"],"partners":["SKP1","F-BOX PROTEINS (COMPETED FOR SKP1 INTERFACE)"],"other_free_text":["Catalyzes addition of terminal fifth sugar (Galα1,3Glcα linkage) onto the hydroxyproline-linked Skp1 pentasaccharide [#0]","Terminal galactose imposes an ordered glycan conformation controlling Skp1 structure via nonpolar packing [#1]","gat1Δ knockout produces a slow-growth phenotype [#0]","Competes with F-box proteins and the SKP1 homodimer for the SKP1 core hydrophobic interface, promoting SKP1 monomerization in a glycostate- and C-terminal-region-dependent manner [#2]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"32414843","id":"PMC_32414843","title":"A terminal α3-galactose modification regulates an E3 ubiquitin ligase subunit in Toxoplasma gondii.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32414843","citation_count":16,"is_preprint":false},{"pmid":"42327091","id":"PMC_42327091","title":"Potential for the Terminal SKP1 Glycosyltransferase to Exert Non-Enzymatic Control of SKP1 in Toxoplasma gondii.","date":"2026","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/42327091","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3654,"output_tokens":1078,"usd":0.013566,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5980,"output_tokens":2287,"usd":0.043537,"stage2_stop_reason":"end_turn"},"total_usd":0.057103,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2020,\n      \"finding\": \"GAT1 is a glycosyltransferase that catalyzes addition of the terminal fifth sugar (Galα1,3Glcα linkage) to the Skp1 pentasaccharide in Toxoplasma gondii, modifying the hydroxyproline residue on Skp1. Kinetic and crystallographic experiments established that GAT1 is specific for Skp1 as its substrate. Loss of gat1 (gat1Δ) results in a slow-growth phenotype, indicating functional importance of the terminal α-galactose for glycan-mediated regulation of Skp1.\",\n      \"method\": \"Glycosyltransferase identification, kinetic assays, X-ray crystallography, gat1Δ knockout phenotype analysis, computational modeling\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure, in vitro kinetic assays, mutagenesis/knockout phenotype, and computational modeling in a single rigorous study\",\n      \"pmids\": [\"32414843\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Computational analyses indicated that the Toxoplasma Skp1 pentasaccharide (including the GAT1-added terminal galactose) assumes an ordered conformation that controls Skp1 structure through nonpolar packing interactions of the fifth sugar, consistent with a conformational control model for glycoregulation of Skp1/F-box protein subcomplex assembly.\",\n      \"method\": \"Computational structural analysis, comparison with Dictyostelium glycan structure\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 4 / Moderate — computational modeling supported by biochemical and crystallographic data in the same study, but conformational control model is computationally inferred\",\n      \"pmids\": [\"32414843\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"GAT1 forms a homodimer that complexes with SKP1 monomers regardless of its glycosylation status, with binding affinity and stoichiometry dictated by the glycostate of SKP1. GAT1 competes with F-box proteins (FBPs) and the SKP1 homodimer for the same core hydrophobic interface on SKP1. Substoichiometric levels of GAT1 promote SKP1 monomerization in a CTR (intrinsically disordered C-terminal region)-dependent manner, indicating a non-enzymatic scaffolding role for GAT1 in controlling SKP1 monomer availability and FBP-binding preference.\",\n      \"method\": \"Sedimentation velocity analytical ultracentrifugation, computational modeling, mutational probing, gat1-knockout FBP interactome profiling\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — sedimentation velocity AUC plus mutational probing and computational modeling in a single preprint study; not yet peer-reviewed\",\n      \"pmids\": [\"42327091\"],\n      \"is_preprint\": true,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"GAT1 is a Skp1-specific glycosyltransferase in Toxoplasma gondii that adds a terminal Galα1,3Glc sugar to the Skp1 pentasaccharide, imposing an ordered conformation on the glycan that regulates Skp1 structure, homodimerization, and F-box protein binding; beyond its enzymatic role, GAT1 also acts non-enzymatically by competitively binding the SKP1 hydrophobic interface to promote SKP1 monomerization and modulate FBP-binding preference in a glycostate- and CTR-dependent manner.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"GAT1 is a Skp1-specific glycosyltransferase in Toxoplasma gondii that governs the assembly of Skp1/F-box protein subcomplexes through both catalytic and non-enzymatic activities [#0, #2]. Enzymatically, GAT1 caps the Skp1 pentasaccharide by adding a terminal fifth sugar via a Galα1,3Glcα linkage onto the hydroxyproline-linked glycan, a modification that imposes an ordered conformation on the glycan and thereby controls Skp1 structure through nonpolar packing of the terminal galactose [#0, #1]; loss of gat1 produces a slow-growth phenotype, marking this terminal galactose as functionally important for glycan-mediated regulation of Skp1 [#0]. Beyond catalysis, GAT1 forms a homodimer that binds SKP1 monomers and competes with F-box proteins and the SKP1 homodimer for the same core hydrophobic interface, promoting SKP1 monomerization in a manner dependent on SKP1 glycostate and its intrinsically disordered C-terminal region, thereby biasing F-box protein binding preference [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2020,\n      \"claim\": \"Establishing which enzyme completes the Skp1 glycan and whether that final sugar matters resolved the terminal step of a conserved cytoplasmic Skp1 glycosylation pathway and its physiological relevance.\",\n      \"evidence\": \"Glycosyltransferase identification with in vitro kinetic assays, X-ray crystallography, and gat1\\u0394 knockout phenotyping in Toxoplasma gondii\",\n      \"pmids\": [\"32414843\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The mechanism linking loss of the terminal galactose to the slow-growth phenotype at the cellular level was not resolved\",\n        \"The full set of downstream F-box proteins affected by the modification was not defined\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Modeling how the completed pentasaccharide behaves addressed why the terminal sugar matters, proposing that the glycan adopts an ordered conformation controlling Skp1 structure and subcomplex assembly.\",\n      \"evidence\": \"Computational structural analysis compared with the Dictyostelium glycan, supported by the same study's crystallographic and biochemical data\",\n      \"pmids\": [\"32414843\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The conformational control model is computationally inferred rather than directly observed in the assembled Skp1/F-box complex\",\n        \"Direct measurement of how glycan conformation alters F-box protein affinity was not performed\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Testing whether GAT1 acts only as an enzyme revealed a distinct non-enzymatic scaffolding role, in which GAT1 competitively controls SKP1 monomer availability and F-box protein binding preference.\",\n      \"evidence\": \"Sedimentation velocity analytical ultracentrifugation, mutational probing, computational modeling, and gat1-knockout F-box protein interactome profiling in Toxoplasma gondii (preprint)\",\n      \"pmids\": [\"42327091\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Not yet peer-reviewed\",\n        \"The in vivo consequences of GAT1-driven SKP1 monomerization for SCF ubiquitin ligase output were not established\",\n        \"How the enzymatic and scaffolding activities are coordinated on the same substrate is unresolved\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How GAT1's dual glycosyltransferase and scaffolding functions are integrated to regulate SCF complex assembly and parasite growth in vivo remains open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No in vivo demonstration linking GAT1-controlled SKP1 monomerization to ubiquitin ligase function\",\n        \"The relationship between glycostate and scaffolding activity under physiological conditions is undefined\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008378\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0016757\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0042803\", \"supporting_discovery_ids\": [2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006486\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0043161\", \"supporting_discovery_ids\": [2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\n      \"GAT1 homodimer\",\n      \"GAT1 homodimer\\u2013SKP1 monomer complex\"\n    ],\n    \"partners\": [\n      \"SKP1\",\n      \"F-box proteins (competed for SKP1 interface)\"\n    ],\n    \"other_free_text\": [\n      \"Catalyzes addition of terminal fifth sugar (Gal\\u03b11,3Glc\\u03b1 linkage) onto the hydroxyproline-linked Skp1 pentasaccharide [#0]\",\n      \"Terminal galactose imposes an ordered glycan conformation controlling Skp1 structure via nonpolar packing [#1]\",\n      \"gat1\\u0394 knockout produces a slow-growth phenotype [#0]\",\n      \"Competes with F-box proteins and the SKP1 homodimer for the SKP1 core hydrophobic interface, promoting SKP1 monomerization in a glycostate- and C-terminal-region-dependent manner [#2]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_310400","name":"GAT1","product":"glycosyltransferase GAT1","uniprot_acc":"A0A125YHG0","chromosome":"TGME49_chrXI","start_pos":1318681},{"strain":"GT1","gene_id":"TGGT1_310400","name":null,"product":"glycosyl transferase family 8 protein","uniprot_acc":null,"chromosome":"TGGT1_chrXI","start_pos":1282502},{"strain":"RH88","gene_id":"TGRH88_049930","name":null,"product":"glycosyl transferase family 8 protein","uniprot_acc":null,"chromosome":"CM023092","start_pos":1367362},{"strain":"VEG","gene_id":"TGVEG_310400","name":null,"product":"glycosyl transferase family 8 protein","uniprot_acc":"B6KAA8","chromosome":"TGVEG_chrXI","start_pos":1329399}]}