{"uniprot":"U3KPV4","gene":"A3GALT2","name":"Alpha-1,3-galactosyltransferase 2","organism":"Homo sapiens (Human)","status":"dark","length":340,"sequence":"MALKEGLRAWKRIFWRQILLTLGLLGLFLYGLPKFRHLEALIPMGVCPSATMSQLRDNFTGALRPWARPEVLTCTPWGAPIIWDGSFDPDVAKQEARQQNLTIGLTIFAVGRYLEKYLERFLETAEQHFMAGQSVMYYVFTELPGAVPRVALGPGRRLPVERVARERRWQDVSMARMRTLHAALGGLPGREAHFMFCMDVDQHFSGTFGPEALAESVAQLHSWHYHWPSWLLPFERDAHSAAAMAWGQGDFYNHAAVFGGSVAALRGLTAHCAGGLDWDRARGLEARWHDESHLNKFFWLHKPAKVLSPEFCWSPDIGPRAEIRRPRLLWAPKGYRLLRN","function_summary":"A Golgi-resident, single-pass type II membrane glycosyltransferase that uses a luminal catalytic domain to transfer galactose from UDP-galactose in a manganese-dependent reaction onto glycosphingolipid acceptors. By installing beta-1,3-galactose linkages that define characteristic glycolipid epitopes, it drives assembly of complex glycosphingolipids that shape membrane organization and cell-surface architecture. Its Golgi localization and secretory-pathway interface explain associations with extracellular glyco-epitopes, while transient protein interactions and antigen-engaging surfaces support its role in building and organizing glycolipid displays.","plain_language":"A3GALT2 has barely been studied. The model's best guess: A Golgi-resident, single-pass type II membrane glycosyltransferase that uses a luminal catalytic domain to transfer galactose from UDP-galactose in a manganese-dependent reaction onto glycosphingolipid acceptors. By installing beta-1,3-galactose linkages that define characteristic glycolipid epitopes, it drives assembly of complex glycosphingolipids that shape membrane organization and cell-surface architecture.","uniprot_summary":"Involved in the biosynthesis of lacto- and globo-series glycolipids.","go_terms":{"molecular_function":[{"id":"GO:0003823","label":"antigen binding"},{"id":"GO:0005515","label":"protein binding"},{"id":"GO:0035250","label":"UDP-galactosyltransferase activity"},{"id":"GO:0048531","label":"beta-1,3-galactosyltransferase activity"},{"id":"GO:0030145","label":"manganese ion binding"}],"biological_process":[{"id":"GO:0006688","label":"glycosphingolipid biosynthetic process"}],"cellular_component":[{"id":"GO:0005576","label":"extracellular region"},{"id":"GO:0000139","label":"Golgi membrane"}]},"interpro":[{"id":"IPR029044","name":"Nucleotide-diphospho-sugar transferases","type":"homologous_superfamily","start":49,"end":340},{"id":"IPR005076","name":"Glycosyl transferase, family 6","type":"family","start":14,"end":340}],"reasoning":"I begin with the InterPro architecture. The N-terminal third of the luminal region is annotated as IPR005076 (Glycosyl transferase, family 6, residues 14–340), and this catalytic core sits within IPR029044 (Nucleotide-diphospho-sugar transferases homologous superfamily, residues 49–340). This arrangement—an N-terminal cytosolic tail followed by a single transmembrane anchor and a large luminal GT fold—is the canonical layout of type II membrane glycosyltransferases that operate in the Golgi. The GT6 family and the nucleotide-diphospho-sugar transferase superfamily together specify a metal-dependent inverting glycosyltransferase that uses UDP-sugar donors. The GT fold dictates UDP-sugar binding and catalysis, while GT6 chemistry typically requires Mn2+, which rationalizes manganese ion binding.\n\nFrom this domain logic, the molecular function resolves as follows. The GT6 catalytic core and UDP-sugar transferase superfamily cause UDP-galactosyltransferase activity (GO:0035250) and the more specific beta-1,3-galactosyltransferase activity (GO:0048531), consistent with transferring galactose in a beta-1,3 linkage to acceptor glycans. The luminal GT fold requires a divalent cation; manganese ion binding (GO:0030145) stabilizes the transition state and organizes the UDP-galactose donor. The single-pass type II topology positions the catalytic domain in the Golgi lumen, where it encounters glycosphingolipid acceptors. The presence of protein binding (GO:0005515) follows from the need to assemble with trafficking and scaffolding factors that localize and regulate Golgi enzymes. Antigen binding (GO:0003823) is explained by the enzyme’s role in generating glyco-epitopes that define glycolipid antigens; the luminal catalytic surface can transiently engage glycan-display platforms and antigen-presenting assemblies, conferring apparent antigen-binding capacity through glycan-mediated interactions.\n\nThese molecular activities feed directly into glycosphingolipid biosynthetic process (GO:0006688). By installing beta-1,3-galactose onto lactosylceramide-derived acceptors, the enzyme builds complex glycosphingolipids that shape membrane microdomains and cell–cell recognition. The causal chain is straightforward: GT6-catalyzed galactosylation in the Golgi lumen produces defined glycolipid headgroups; these headgroups determine membrane raft composition and downstream signaling.\n\nCellular localization follows from the architecture and chemistry. The single-pass type II membrane arrangement and luminal GT fold place the enzyme in the Golgi membrane (GO:0000139), where UDP-galactose is supplied and glycosphingolipid assembly occurs. The presence of a luminal catalytic domain that modifies secretory cargo explains why the functional footprint extends to the extracellular region (GO:0005576): the products and, in some cases, the enzyme itself traverse or interface with the secretory pathway, and the modified glycolipids populate the cell surface and extracellular milieu.\n\nMechanistically, the enzyme likely operates as a Mn2+-dependent inverting galactosyltransferase that recognizes lacto- and globo-series acceptors in the Golgi lumen. It binds UDP-galactose via its nucleotide-diphospho-sugar fold, coordinates Mn2+ to activate the donor, and transfers galactose to form beta-1,3 linkages that define globotriaosylceramide and related epitopes. I hypothesize transient assemblies with other Golgi-resident glycosyltransferases and trafficking adaptors that cluster GT6 enzymes into functional zones. Candidate partners include other glycolipid pathway enzymes and scaffolds that ensure efficient channeling of lactosylceramide-derived intermediates toward defined surface glycolipids.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-U3KPV4.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/U3KPV4"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/U3KPV4/entry","atlas":"/p/U3KPV4"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}