- START HERE — how to read acetoacetate + succinyl-CoA → acetoacetyl-CoA + succinate A ping-pong CoA-transfer cartoon on the human OXCT1 / SCOT frame that actually exists: 3DLX (2.20 Å) chain A with crystal glycerol only. Occupancy is glycerol, not succinyl-CoA, not acetoacetate, not acetoacetyl-CoA, not succinate — never label GOL as substrate. TITLE = crystal structure of human 3-oxoacid CoA-transferase 1. JRNL is To be Published — no PMID; cite RCSB 3DLX. Glu344 ★ is this PDB = UniProt ACT_SITE (5-glutamyl-CoA thioester). GOL is named occupancy, not extracted, not a reactant, and not near Glu344. Succinyl-CoA / succinate / glutamyl-CoA / acetoacetate / acetoacetyl-CoA are [schematic] near Glu344. 3OXO pig covalent CoA is a named overlay, not this mesh, not geomClaims. 1O9L is rejected. Missing 1–39 transit, 287–296, and 520 are not this mesh (Cα 40–519). C-tag 521–527 SEQADV spoken. Homodimer named; teaching is chain A. Only one subunit is competent for the second transfer (UniProt). OXCT1 is extrahepatic. Liver ketogenesis does not run this enzyme. OXCT2 is another gene. Blue is Glu344 / acetoacetate carboxylate lone pair, not hydride. No white phosphoryl. No gold proton. ACAT1x next. Measured distances are deposited 3DLX-A protein pairs only — not succinyl-CoA claims.
- Crystal structures PDB 3DLX — human OXCT1 / SCOT-S, 2.20 Å, GOL only (Kavanagh et al., To be Published). Coordinates are public. Occupancy is glycerol. PDB 3OXO is pig SCOT + covalent CoA — named overlay, not this mesh. 1O9L pig + ethyl mercury is rejected. Human OXCT1 UniProt P55809.
- Mechanism ΓÇö Glu344 ACT_SITE; GOL occupancy; extrahepatic UniProt P55809 EC 2.8.3.5: acetoacetate + succinyl-CoA = acetoacetyl-CoA + succinate. This page teaches ketone utilization (extrahepatic mito). On this mesh the ACT_SITE glutamate is Glu344. GOL is not substrate. OXCT2 is another gene. ACAT1x is next. Source: UniProt P55809 ┬╖ RCSB 3DLX ┬╖ Fukao 2000
- 0 — Setup: empty SCOT pocket 3DLX occupancy is glycerol only, not succinyl-CoA. The pocket is shown empty of substrate so binding can start. Opaque, run:null (no autoplay). Glu344 ★ is ACT_SITE. GOL named, not extracted. Missing 1–39 transit / 287–296 / 520 are not this mesh (Cα 40–519). C-tag 521–527 SEQADV spoken. Homodimer named; teaching is chain A. Extrahepatic. OXCT2 other gene. 3OXO pig CoA is a named overlay. 1O9L rejected. JRNL To be Published — no PMID.Source: PDB 3DLX (2.20 Å)
- ① — Succinyl-CoA binds [schematic] Succinyl-CoA docks with the thioester toward Glu344 — not deposited. Occupancy is glycerol; never label GOL as substrate. Glu344 OE2 ⋯ Gln138 NE2 = 2.95 Å is a deposited 3DLX protein pair, not a succinyl-CoA claim. 3OXO pig CoA distances are not geomClaims.Source: PDB 3DLX empty fold + schematic succinyl-CoA
- ② — Glu344 ★ → E~CoA + succinate (hypothetical, lit.-based) Blue ball + blue arrow: Glu344 ★ (nucleophile, not hydride) attacks schematic succinyl carbonyl. Succinyl-CoA cross-fades to schematic glutamyl-CoA + schematic succinate. Occupancy is glycerol. Anhydride vs direct glutamyl-CoA is compiled (by similarity). Slow-motion on purpose. No white phosphoryl. No gold proton.Source: compiled ping-pong · UniProt P55809 Glu344 · pig overlay 3OXO named
- Γæó ΓÇö Succinate leaves Schematic succinate departs. Schematic glutamyl-CoA stays on Glu344 ΓÇö ping-pong first half-reaction. Occupancy is glycerol; never label GOL as substrate. Extrahepatic. OXCT2 is another gene. No arrows on this step.Source: ping-pong bookkeeping ┬╖ EC 2.8.3.5
- ④ — Acetoacetate binds [schematic] Acetoacetate docks toward the glutamyl-CoA stub — not deposited. Occupancy is glycerol; never label GOL as substrate. Glu344 OE2 ⋯ Gln138 OE1 = 3.40 Å is a deposited 3DLX protein pair, not an acetoacetate claim. E~CoA stays. Extrahepatic. Liver lacks SCOT.Source: PDB 3DLX empty fold + schematic acetoacetate
- ⑤ — CoA transfer → acetoacetyl-CoA (hypothetical, lit.-based) Blue ball + blue arrow: schematic acetoacetate carboxylate (nucleophile, not hydride) attacks glutamyl-CoA carbonyl. Acetoacetate cross-fades to schematic acetoacetyl-CoA. E~CoA is consumed. Occupancy is glycerol; never label GOL as substrate. Slow-motion on purpose. No white phosphoryl. No gold proton. 3OXO pig CoA is not this mesh.Source: compiled second half-reaction · UniProt P55809
- ⑥ — Acetoacetyl-CoA leaves — ACAT1x next Schematic acetoacetyl-CoA departs toward extrahepatic thiolase ACAT1x (next). Occupancy on this mesh is glycerol, not acetoacetyl-CoA. Liver lacks SCOT — this path is extrahepatic. OXCT2 is another gene. Net EC H⁺ is not a gold sphere. No white phosphoryl. Glu344 ★ is ACT_SITE. No product ghost on the next Setup.Source: ketolysis bookkeeping · EC 2.8.3.5
- How to read this page — a first-pass primer First pass: Setup (GOL occupancy, Glu344 ★, extrahepatic, no PMID) → ① schematic succinyl-CoA docks → ② blue Glu344 OE to succinyl carbonyl, fade to E~CoA + succinate → ③ succinate leaves, E~CoA stays → ④ schematic acetoacetate docks → ⑤ blue acetoacetate O to E~CoA, fade to acetoacetyl-CoA → ⑥ leave; ACAT1x next. Second pass: 2.95 / 3.40 Å are crystal facts on 3DLX protein pairs; succinyl-CoA / succinate / E~CoA / acetoacetate / acetoacetyl-CoA are [schematic]; occupancy is glycerol. Third pass: open “Disagreements” for GOL≠substrate, 3OXO pig overlay, extrahepatic vs liver, OXCT2, compiled E~CoA.
- Chemistry primer ΓÇö OXCT1 / SCOT OXCT1 transfers CoA from succinyl-CoA onto acetoacetate via a covalent 5-glutamyl-CoA (E~CoA) on Glu344. Blue is carboxylate nucleophile, not hydride. No gold proton. No white phosphoryl. This is extrahepatic mitochondrial utilization, not hepatic ketogenesis. Not a thiolase.
- Words used on screen ΓÇö GOL occupancy ┬╖ Glu344 Γÿà ┬╖ E~CoA ┬╖ extrahepatic GOL occupancy ΓÇö 3DLX holds glycerol, not succinyl-CoA. Glu344 Γÿà ΓÇö ACT_SITE on this PDB = UniProt. E~CoA ΓÇö compiled glutamyl-CoA intermediate. Extrahepatic ΓÇö liver lacks SCOT; OXCT2 is another gene.
Legend & Fidelity
- Mechanism fidelity — measured vs. inferred The measured layer: 3DLX (2.20 Å) human OXCT1 chain A GOL only; Glu344 OE2 ⋯ Gln138 NE2 = 2.95 Å; Glu344 OE2 ⋯ Gln138 OE1 = 3.40 Å. The inferred layer ([schematic]): succinyl-CoA / succinate / glutamyl-CoA / acetoacetate / acetoacetyl-CoA near Glu344, transferring blue nucleophile spheres. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Overlay / schematic / 3OXO CoA distances are not geomClaims. Occupancy distances are not succinyl-CoA claims.
- Disagreements on record (a) Occupancy vs substrates. 3DLX is glycerol, not succinyl-CoA or acetoacetate. (b) TITLE = crystal structure of human 3-oxoacid CoA-transferase 1 ΓÇö do not copy occupancy as succinyl-CoA. (c) JRNL is To be Published ΓÇö no fake PMID; cite RCSB 3DLX. (d) Glu344 Γÿà is ACT_SITE; compiled E~CoA is not deposited. (e) Anhydride vs direct glutamyl-CoA is compiled (by similarity). (f) 3OXO is pig covalent CoA ΓÇö named overlay, not this mesh, not geomClaims. (g) 1O9L pig + mercury is rejected. (h) GOL is named, not extracted, not a reactant, and not near Glu344. (i) Missing 1ΓÇô39 transit / 287ΓÇô296 / 520 are not this mesh (C╬▒ 40ΓÇô519). (j) C-tag 521ΓÇô527 SEQADV is not catalytic. (k) Homodimer assembly is not this cartoon; only one subunit is competent for the second transfer. (l) OXCT2 is another gene. (m) Extrahepatic ΓÇö liver ketogenesis does not run this enzyme. (n) Blue is nucleophile, not hydride. (o) Overlay/schematic distances are not claims. (p) Occupancy distances are not succinyl-CoA claims. (q) This page is not ketogenesis ACAT1.
- Regulation ΓÇö extrahepatic mito ┬╖ not liver ┬╖ not OXCT2 ┬╖ next ACAT1x This CoA-transfer is extrahepatic mitochondrial OXCT1 only. Liver lacks SCOT ΓÇö hepatic ketogenesis does not run this enzyme. OXCT2 is testis SCOT ΓÇö other gene. Homodimer is named, not animated. Acetoacetyl-CoA feeds ACAT1x thiolysis ΓÇö not this mesh.Source: UniProt P55809 ┬╖ PDB 3DLX ┬╖ Fukao 2000 PMID:10964512
- Kinetics scope (no measured timecourse on this page) One acetoacetate + succinyl-CoA → acetoacetyl-CoA + succinate event is drawn, not a steady-state run. Compiled BRENDA values for EC 2.8.3.5 are not re-asserted here — no measured kcat/Km on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 2.8.3.5 — no kcat/Km re-asserted
- Sequence Human OXCT1 UniProt P55809 ┬╖ NCBI Gene 5019. This screen uses 3DLX numbering (Glu344 = UniProt Glu344). Chain A. C╬▒ 40ΓÇô519. Missing 1ΓÇô39 transit / 287ΓÇô296 / 520 are not this mesh. C-tag 521ΓÇô527 SEQADV spoken.
- Simulation map — what you see is what is written Setup = 3DLX pocket empty of substrate (opaque, no autoplay). ① schematic succinyl-CoA moves in. ② slow-mo: blue Glu344 OE → succinyl carbonyl, fade to E~CoA + succinate. ③ succinate leaves; E~CoA stays. ④ schematic acetoacetate moves in. ⑤ slow-mo: blue acetoacetate O → E~CoA, fade to acetoacetyl-CoA. ⑥ acetoacetyl-CoA leaves. Only these events move.
- Sources — bibliography of this page S1 — PDB 3DLX: human OXCT1 GOL only, 2.20 Å — public coordinates; measured Glu344 OE2⋯Gln138 NE2 = 2.95 Å · Glu344 OE2⋯Gln138 OE1 = 3.40 Å; JRNL To be Published, no PMID S2 — Sequence: UniProt P55809 · NCBI Gene 5019 S3 — Extrahepatic utilization: Fukao et al., PMID:10964512 S4 — Kinetics: BRENDA EC 2.8.3.5 — no kcat/Km re-asserted on this page S5 — PDB 3OXO pig SCOT + covalent CoA — named overlay, not this mesh (PMID:20977214)
› Backbones are taken directly from the listed PDB entries, superposed into one common frame. Where no crystalline state exists for a step (e.g., succinyl-CoA, succinate, glutamyl-CoA, acetoacetate, acetoacetyl-CoA, nucleophile flight, product leave), the pose is drawn schematically and labeled as such in the narration. Occupancy is glycerol, not succinyl-CoA. Overlay / schematic / 3OXO CoA distances are not geomClaims. Occupancy distances are not succinyl-CoA claims. GOL is named, not extracted.