{"id":"baa439f4-60dd-56ad-b215-c5d6c611799c","stable_key":"46d15d9e-d3b5-544d-ba01-b785aa3e4f42:b1-bckdh-thdp-orders-loop","predicate":"orders-substrate-recognition-loop-of","statement":"Apo/holo human E1b structures showed that ThDP binding orders the phosphorylation loop needed to recognize the lipoylated E2b domain.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"positive","is_public":true,"mechanism_event_id":"4d136a25-ddfc-58d7-a3fa-82054508680c","mechanism_event_label":"B1 binding changes the enzyme shape so it can receive its lipoyl partner.","subject":{"id":"187db168-8028-5ce6-9f8b-4bc61ebad1a0","slug":"thiamine-diphosphate","display_name":"Thiamine diphosphate","entity_type_key":"small_molecule"},"object":{"id":"82b74ccc-3ee5-5622-a8bd-0691de8cdc54","slug":"bckdh-e1","display_name":"Human branched-chain ketoacid dehydrogenase E1","entity_type_key":"protein_complex"},"evidence_count":1,"mechanism_event":{"id":"4d136a25-ddfc-58d7-a3fa-82054508680c","stable_key":"46d15d9e-d3b5-544d-ba01-b785aa3e4f42:b1-bckdh-thdp-orders-loop-event","event_type":"biochemical_relationship","label":"B1 binding changes the enzyme shape so it can receive its lipoyl partner.","description":"Apo/holo human E1b structures showed that ThDP binding orders the phosphorylation loop needed to recognize the lipoylated E2b domain.","status":"provisional","compartment":{"slug":"mitochondrial-matrix","display_name":"Mitochondrial matrix"},"participants":[{"entity":{"id":"99e4447f-bc64-5044-bbc8-cbba58545262","slug":"dbt","display_name":"Dihydrolipoyl branched-chain transacylase / DBT","entity_type_key":"protein"},"role":"lipoyl-domain source","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"fd2197c3-5a63-55f4-8bb1-bfc1e91a0e1e","slug":"protein-bound-lipoamide","display_name":"Protein-bound oxidized lipoyl-lysine","entity_type_key":"chemical_species"},"role":"carrier recognized by E1","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"187db168-8028-5ce6-9f8b-4bc61ebad1a0","slug":"thiamine-diphosphate","display_name":"Thiamine diphosphate","entity_type_key":"small_molecule"},"role":"subject","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""},{"entity":{"id":"82b74ccc-3ee5-5622-a8bd-0691de8cdc54","slug":"bckdh-e1","display_name":"Human branched-chain ketoacid dehydrogenase E1","entity_type_key":"protein_complex"},"role":"target","stoichiometry":null,"state_label":"","sequence_order":3,"notes":""}]},"contexts":[{"dimension":"cross_nutrient","value_text":"ThDP occupancy enables interaction with the lipoylated E2 carrier.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"evidence","value_text":"[{\"paper_key\": \"li-2004-bckdh\", \"source_bundle\": \"artifacts/thiamine_metabolism_sources.json\", \"passage_ids\": [\"abstract\"], \"locator\": \"Primary publication abstract\", \"preservation\": \"Exact text retained in the source bundle; full source document retained when openly retrievable.\"}]","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"experimental_model","value_text":"Human apo/holo E1b crystallography and lipoyl-domain binding.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"Preparation-specific structural/kinetic mechanism; not a human thiamine-dose response.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"nutrient","value_text":"Thiamine (vitamin B1)","comparator":null,"unit":null,"notes":"","entity":{"slug":"thiamine","display_name":"Thiamine (vitamin B1)","entity_type_key":"small_molecule"}},{"dimension":"nutrient_topic","value_text":"Thiamine research collection; topical membership is not evidence of a direct dietary effect.","comparator":null,"unit":null,"notes":"","entity":{"slug":"thiamine","display_name":"Thiamine (vitamin B1)","entity_type_key":"small_molecule"}},{"dimension":"organism","value_text":"Homo sapiens","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"plain_language","value_text":"B1 binding changes the enzyme shape so it can receive its lipoyl partner.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[li-2004-bckdh] Cross-talk between thiamin diphosphate binding and phosphorylation loop conformation in human branched-chain alpha-keto acid decarboxylase/dehydrogenase (2004). https://pubmed.ncbi.nlm.nih.gov/15166214/ DOI: 10.1074/jbc.m403611200","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"tissue_or_cell_type","value_text":"Purified proteins","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"126a89bb-c6a2-5689-8f75-216c34819f43","evidence_kind":"source_excerpt","locator":"Lines 787-799","start_line":787,"end_line":799,"excerpt":"### b1-bckdh-thdp-orders-loop\nApo/holo human E1b structures showed that ThDP binding orders the phosphorylation loop needed to recognize the lipoylated E2b domain.\nCondition category: normal\nnutrient_topic: Thiamine research collection; topical membership is not evidence of a direct dietary effect.\nplain_language: B1 binding changes the enzyme shape so it can receive its lipoyl partner.\norganism: Homo sapiens\ntissue_or_cell_type: Purified proteins\nexperimental_model: Human apo/holo E1b crystallography and lipoyl-domain binding.\nlimitations: Preparation-specific structural/kinetic mechanism; not a human thiamine-dose response.\nevidence: [{\"paper_key\": \"li-2004-bckdh\", \"source_bundle\": \"artifacts/thiamine_metabolism_sources.json\", \"passage_ids\": [\"abstract\"], \"locator\": \"Primary publication abstract\", \"preservation\": \"Exact text retained in the source bundle; full source document retained when openly retrievable.\"}]\ncross_nutrient: ThDP occupancy enables interaction with the lipoylated E2 carrier.\nnutrient: Thiamine (vitamin B1)\n[li-2004-bckdh] Cross-talk between thiamin diphosphate binding and phosphorylation loop conformation in human branched-chain alpha-keto acid decarboxylase/dehydrogenase (2004). https://pubmed.ncbi.nlm.nih.gov/15166214/ DOI: 10.1074/jbc.m403611200","model_system":"Human apo/holo E1b crystallography and lipoyl-domain binding.","directness":"author_interpretation","verification_status":"source_derived_draft","notes":"Exact curation-document quotation, not publisher quotation. Study references: [li-2004-bckdh] Cross-talk between thiamin diphosphate binding and phosphorylation loop conformation in human branched-chain alpha-keto acid decarboxylase/dehydrogenase (2004). https://pubmed.ncbi.nlm.nih.gov/15166214/ DOI: 10.1074/jbc.m403611200","relationship":"supports","weight":1.0,"link_notes":"","source":{"id":"158d2c03-ac8c-589f-8270-c468165ae346","stable_key":"import-46d15d9e-d3b5-544d-ba01-b785aa3e4f42","title":"Thiamine: mechanisms, deficiency and nutrient interactions (2026-09-17)","document_type":"imported_text","citation_label":"AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text.","file_path":"","sha256":"f376512fb3310141315548015b387833e3af45146e73fb73cd02cee20e4ddb9c","revision_id":"53bc5eda-dec8-58cc-a56f-a9eb4ab036ef","review_status":"unverified_draft","notes":""}}],"relations":[],"conflicts":[],"corrections":[],"research":null}