{"uniprot":"Q9BQI7","gene":"PSD2","name":"PH and SEC7 domain-containing protein 2","organism":"Homo sapiens (Human)","status":"dark","length":771,"sequence":"MEEDKLLSAVPEEGDATRDPGPEPEEEPGVRNGMASEGLNSSLCSPGHERRGTPADTEEPTKDPDVAFHGLSLGLSLTNGLALGPDLNILEDSAESRPWRAGVLAEGDNASRSLYPDAEDPQLGLDGPGEPDVRDGFSATFEKILESELLRGTQYSSLDSLDGLSLTDESDSCVSFEAPLTPLIQQRARDSPEPGAGLGIGDMAFEGDMGAAGGDGELGSPLRRSISSSRSENVLSRLSLMAMPNGFHEDGPQGPGGDEDDDEEDTDKLLNSASDPSLKDGLSDSDSELSSSEGLEPGSADPLANGCQGVSEAAHRLARRLYHLEGFQRCDVARQLGKNNEFSRLVAGEYLSFFDFSGLTLDGALRTFLKAFPLMGETQERERVLTHFSRRYCQCNPDDSTSEDGIHTLTCALMLLNTDLHGHNIGKKMSCQQFIANLDQLNDGQDFAKDLLKTLYNSIKNEKLEWAIDEDELRKSLSELVDDKFGTGTKKVTRILDGGNPFLDVPQALSATTYKHGVLTRKTHADMDGKRTPRGRRGWKKFYAVLKGTILYLQKDEYRPDKALSEGDLKNAIRVHHALATRASDYSKKSNVLKLKTADWRVFLFQAPSKEEMLSWILRINLVAAIFSAPAFPAAVSSMKKFCRPLLPSCTTRLCQEEQLRSHENKLRQLTAELAEHRCHPVERGIKSKEAEEYRLKEHYLTFEKSRYETYIHLLAMKIKVGSDDLERIEARLATLEGDDPSLRKTHSSPALSQGHVTGSKTTKDATGPDT","function_summary":"A cytoplasmic, membrane-recruited guanine-nucleotide exchange factor that activates ARF small GTPases through a Sec7 catalytic core and a pleckstrin homology module that targets phosphoinositide-rich cortical membranes. By coupling local ARF activation to coat assembly and membrane remodeling, it drives endosomal carrier formation for retrieval pathways toward the Golgi and supports actin-dependent membrane dynamics at ruffles and the cleavage furrow.","plain_language":"PSD2 has barely been studied. The model's best guess: A cytoplasmic, membrane-recruited guanine-nucleotide exchange factor that activates ARF small GTPases through a Sec7 catalytic core and a pleckstrin homology module that targets phosphoinositide-rich cortical membranes. By coupling local ARF activation to coat assembly and membrane remodeling, it drives endosomal carrier formation for retrieval pathways toward the Golgi and supports actin-dependent membrane dynamics at ruffles and the cleavage furrow.","uniprot_summary":"May act as a guanine nucleotide exchange factor (GEF).","go_terms":{"molecular_function":[{"id":"GO:0005085","label":"guanyl-nucleotide exchange factor activity"},{"id":"GO:0005515","label":"protein binding"}],"biological_process":[{"id":"GO:0042147","label":"retrograde transport, endosome to Golgi"}],"cellular_component":[{"id":"GO:0032587","label":"ruffle membrane"},{"id":"GO:0032154","label":"cleavage furrow"}]},"interpro":[{"id":"IPR035999","name":"Sec7 domain superfamily","type":"homologous_superfamily","start":304,"end":472},{"id":"IPR023394","name":"Sec7, C-terminal domain superfamily","type":"homologous_superfamily","start":355,"end":472},{"id":"IPR011993","name":"PH-like domain superfamily","type":"homologous_superfamily","start":508,"end":632},{"id":"IPR000904","name":"Sec7 domain","type":"domain","start":275,"end":464},{"id":"IPR001849","name":"Pleckstrin homology domain","type":"domain","start":512,"end":627},{"id":"IPR041681","name":"Pleckstrin homology domain 9","type":"domain","start":514,"end":625},{"id":"IPR001605","name":"Pleckstrin homology domain, spectrin-type","type":"domain","start":515,"end":534},{"id":"IPR001605","name":"Pleckstrin homology domain, spectrin-type","type":"domain","start":580,"end":597},{"id":"IPR001605","name":"Pleckstrin homology domain, spectrin-type","type":"domain","start":600,"end":618}],"reasoning":"I begin with the domain architecture. The central catalytic core is defined by IPR000904 (Sec7 domain, residues 275–464), reinforced by IPR035999 (Sec7 domain superfamily, residues 304–472) and capped at the C-terminus by IPR023394 (Sec7, C-terminal domain superfamily, residues 355–472). This triad establishes a canonical Sec7-type guanine-nucleotide exchange module that catalyzes GDP release from ARF-class small GTPases. Immediately C-terminal to the Sec7 core lies a membrane-targeting module: IPR011993 (PH-like domain superfamily, residues 508–632) encompasses a well-formed pleckstrin homology unit captured by IPR001849 (Pleckstrin homology domain, residues 512–627) and refined by IPR041681 (Pleckstrin homology domain 9, residues 514–625). Multiple spectrin-type signatures—IPR001605 (Pleckstrin homology domain, spectrin-type, residues 515–534, 580–597, 600–618)—indicate a PH fold tuned for membrane-proximal protein interactions and phosphoinositide binding. The ordered layout—Sec7 catalytic engine followed by a PH-based membrane/addressing module—creates a two-module machine: the Sec7 domain generates ARF-GTP, while the PH domain positions and regulates the enzyme at specific membrane microdomains.\n\nThis architecture dictates molecular function. The Sec7 module causes guanyl-nucleotide exchange factor chemistry, matching GO:0005085 guanyl-nucleotide exchange factor activity. The PH domain and extended superfamily scaffold provide multivalent interfaces for assembling and tuning complexes, supporting GO:0005515 protein binding. Together, these features specify a membrane-anchored GEF that activates ARF GTPases precisely where phosphoinositide composition and adaptor proteins concentrate them.\n\nFrom function to process, ARF activation at membranes triggers coat assembly, cargo selection, and membrane remodeling that drive endosomal sorting and retrieval pathways. By coupling Sec7-mediated ARF activation to PH-guided membrane targeting, the protein promotes vesicle budding and tubulation that return cargo from endosomes to the Golgi apparatus, aligning with GO:0042147 retrograde transport, endosome to Golgi. The same membrane-proximal ARF signaling also feeds into actin–membrane crosstalk that underlies membrane ruffling and cell division structures.\n\nCellular location follows directly from the targeting logic. The PH domain suite binds acidic phosphoinositides enriched at dynamic cortical membranes, explaining accumulation at membrane ruffles and the cleavage furrow. These features justify GO:0032587 ruffle membrane and GO:0032154 cleavage furrow. The soluble catalytic Sec7 core and absence of transmembrane segments indicate a cytoplasmic enzyme that transiently associates with membranes; thus a cytoplasmic residence is expected alongside membrane-associated pools.\n\nMechanistically, the Sec7 domain catalyzes nucleotide exchange on ARF substrates concentrated by PH-mediated lipid and adaptor binding. This causes local bursts of ARF-GTP that recruit coatomer and accessory factors to sculpt endosomal carriers and cortical membranes. I hypothesize preferential action on ARF1 and ARF6: ARF1 supports Golgi–endosome trafficking, while ARF6 governs ruffle dynamics and cytokinetic remodeling. Likely interaction partners include ARF small GTPases themselves; coatomer components and retromer adaptors that execute endosome-to-Golgi retrieval; and actin-regulatory assemblies at ruffles and the cleavage furrow. This ensemble provides a coherent route from sequence-encoded catalytic architecture to spatially resolved membrane trafficking and cytoskeletal remodeling.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-Q9BQI7.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/Q9BQI7"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/Q9BQI7/entry","atlas":"/p/Q9BQI7"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}