- START HERE — how to read acetoacetyl-CoA + acetyl-CoA + H₂O → HMG-CoA + CoA A synthase cartoon on the human HMGCS2 frame that actually exists: 2WYA (1.70 Å X-ray) chain A with crystal HMG-CoA product. Occupancy is product HMG-CoA, not acetyl-CoA, not acetoacetyl-CoA — never read HMG as acetyl-CoA. Cys166 ★ is the nucleophilic cysteine (UniProt ACT_SITE). Cys166 is CYS on this crystal, not CSO. Labels use PDB ids: residue 132 is Glu132, residue 301 is His301. UniProt P54868 is Glu132 / His301 — same as this mesh, not His132 / Glu301. Water is a reactant (becomes C3-OH of HMG), not a hydrolase leaving group. Covalent E~acetyl is compiled and disclosed — not a pure A-page. GOL is named, not substrate. HMGCS1 is another gene. Blue is nucleophile, not hydride. Measured Å are deposited 2WYA product-complex pairs only.
- Crystal / X-ray structures PDB 2WYA — human mitochondrial HMG-CoA synthase + HMG-CoA, 1.70 Å X-ray (Shafqat 2010). Coordinates are public. Occupancy is product HMG-CoA. GOL is named. Human HMGCS2 UniProt P54868.
- Mechanism ΓÇö Cys166 nucleophile; condensation + hydrolysis UniProt P54868 EC 2.3.3.10: acetoacetyl-CoA + acetyl-CoA + HΓééO = (3S)-HMG-CoA + CoA. This page teaches condensation (ketogenesis). On this mesh the nucleophilic cysteine is Cys166. Glu132 and His301 are named, not starred. Covalent acetyl-Cys166 is compiled, not this occupancy. HMGCS1 is another gene. Source: UniProt P54868 ┬╖ Shafqat 2010
- 0 — Setup: empty synthase pocket 2WYA occupancy is product HMG-CoA, not acetyl-CoA, not acetoacetyl-CoA. The pocket is shown empty so binding can start. Opaque, run:null (no autoplay). Cys166 ★ is the nucleophile. Cys166 is CYS, not CSO. Glu132 / His301 are named. UniProt P54868 is Glu132 / His301 — same as this mesh, not His132 / Glu301. GOL is named, not substrate. Transit 1–37 is not this mesh (Cα 49–508). HMGCS1 is another gene.Source: PDB 2WYA (1.70 Å X-ray)
- ① — Acetyl-CoA binds [schematic] Acetyl-CoA docks on the 2WYA HMG pose — not a deposited acetyl-CoA. HMG on 2WYA is product HMG-CoA, not acetyl-CoA. Overlay Å are not geomClaims.Source: 2WYA HMG pose stripped to CoA + acetyl carbons
- ② — Cys166 attacks carbonyl → acetyl-enzyme + CoA (hypothetical, lit.-based) Blue nucleophile rides from Cys166 SG onto schematic acetyl C1. Acetyl-CoA cross-fades to schematic CoA and a compiled acetyl-Cys166 stub. Covalent E~acetyl is disclosed — not a pure A-page. Occupancy is product HMG-CoA, not this acetyl-enzyme. Slow-motion on purpose. Blue = nucleophile, not hydride.Source: compiled HMGCS ping-pong · UniProt P54868 Cys166
- Γæó ΓÇö First CoA leaves Schematic CoA (from acetyl-CoA) departs. Compiled acetyl-Cys166 stays. HMG on 2WYA is product HMG-CoA, not acetyl-CoA.Source: HMGCS ping-pong bookkeeping
- ④ — Acetoacetyl-CoA and water bind [schematic] Acetoacetyl-CoA docks on the 2WYA HMG pose. Schematic water docks as a reactant (becomes C3-OH of HMG), not a hydrolase leaving group. Cys166 SG ⋯ His301 NE2 = 3.72 Å is deposited 2WYA.Source: PDB 2WYA HMG
- ⑤ — Acetyl-Cys C2 attacks → HMG-CoA (hypothetical, lit.-based) Blue nucleophile rides from compiled acetyl-Cys C2 onto the acetoacetyl ketone. Acetoacetyl-CoA + acetyl stub + water cross-fade to crystal HMG-CoA. Water is consumed into C3-OH. Glu132 / His301 are named, not starred. UniProt P54868 is Glu132 / His301 — same as this mesh, not His132 / Glu301. Cys166 SG ⋯ Glu132 OE2 = 3.37 Å is deposited 2WYA. Slow-motion on purpose. Blue = nucleophile, not hydride.Source: compiled Claisen + hydrolysis · 2WYA Cys166 / Glu132
- ⑥ — HMG-CoA leaves — HMGCL next Crystal HMG-CoA (product occupancy) departs. This page does not run HMGCS1. HMG is product HMG-CoA, not acetyl-CoA. Overlay Å are not geomClaims. Cys166 SG ⋯ HMG O7 = 3.05 Å is deposited 2WYA.Source: ketogenesis bookkeeping · EC 2.3.3.10
- How to read this page — a first-pass primer First pass: Setup (empty pocket, Cys166 ★, product HMG not acetyl, Glu132/His301 named) → ① schematic acetyl-CoA docks on HMG pose → ② blue Cys166-S → carbonyl, fade to CoA + acetyl-Cys → ③ CoA leaves → ④ schematic acetoacetyl-CoA + water dock → ⑤ acetyl-Cys C2 → ketone, fade to HMG-CoA (water consumed) → ⑥ leave; HMGCL next. Second pass: 3.72 / 3.37 / 3.05 Å are crystal facts on 2WYA product complex; acetyl-CoA, acetoacetyl-CoA, water and acetyl-Cys are [schematic]; HMG is product, not substrate. Third pass: open “Disagreements” for UniProt P54868 Glu132/His301, not His132/Glu301, product vs substrate, and HMGCS1 vs this gene.
- Chemistry primer ΓÇö ping-pong HMG-CoA synthase HMGCS2 Cys166 attacks acetyl-CoA carbonyl, releasing CoA and leaving an acetyl-enzyme. Acetoacetyl-CoA then condenses with that acetyl-Cys; water is a reactant that becomes the C3-OH of HMG-CoA. Blue is nucleophile, not hydride. This is not HMGCS1 (cytosolic / mevalonate).
- Words used on screen ΓÇö product HMG ┬╖ Cys166 Γÿà ┬╖ compiled acetyl-Cys ┬╖ water reactant Product HMG ΓÇö 2WYA occupancy, not acetyl-CoA, not acetoacetyl-CoA. Cys166 Γÿà ΓÇö nucleophile on this PDB = UniProt. Compiled acetyl-Cys ΓÇö covalent intermediate, not this occupancy. Water reactant ΓÇö becomes C3-OH, not a hydrolase leaving group.
Legend & Fidelity
- Mechanism fidelity — measured vs. inferred The measured layer: 2WYA (1.70 Å X-ray) human HMGCS2 + product HMG-CoA; Cys166 SG ⋯ His301 NE2 = 3.72 Å; Cys166 SG ⋯ Glu132 OE2 = 3.37 Å; Cys166 SG ⋯ HMG O7 = 3.05 Å. The inferred layer ([schematic]): acetyl-CoA / CoA / acetoacetyl-CoA on the HMG pose, transferring nucleophile spheres, acetyl-Cys stub, water reactant. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Product-complex Å are not acetyl-CoA geomClaims.
- Disagreements on record (a) Occupancy vs substrate. 2WYA holds product HMG-CoA, not acetyl-CoA, not acetoacetyl-CoA. (b) UniProt vs mesh numbering. UniProt P54868 is Glu132 / His301 ΓÇö same as this mesh, not His132 / Glu301 ΓÇö labels use PDB ids. (c) Covalent acetyl-Cys166 is compiled identity, not this occupancy. (d) Glu132 / His301 are named, not starred. (e) Water is a reactant (C3-OH), not a hydrolase leaving-group story. (f) Concerted vs split nucleophile/condensation ΓÇö this page splits Γæí then Γæñ for 1-event/1-step. (g) HMGCS1 is cytosolic / mevalonate, another gene. (h) GOL is named, not substrate. (i) Transit 1ΓÇô37 is not this mesh (C╬▒ 49ΓÇô508). (j) Homodimer assembly is not this cartoon.
- Regulation ΓÇö isoforms ┬╖ dimer ┬╖ matrix This condensation is monofunctional HMGCS2 only. Cytosolic HMGCS1 is another gene ΓÇö not this mesh (mevalonate / cholesterol). Homodimer assembly is not this cartoon. Matrix localization is assumed, not a catalytic event on this page.Source: UniProt P54868 ┬╖ PDB 2WYA ┬╖ Shafqat 2010
- Kinetics scope (no measured timecourse on this page) One acetoacetyl-CoA + acetyl-CoA + H₂O → HMG-CoA + CoA event is drawn, not a steady-state run. Compiled BRENDA values for EC 2.3.3.10 are not re-asserted here — no measured kcat/Km on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 2.3.3.10 — no kcat/Km re-asserted
- Sequence Human HMGCS2 UniProt P54868 ┬╖ NCBI Gene 3158. This screen uses 2WYA numbering (Cys166 = UniProt Cys166; residue 132 = Glu, 301 = His). Chain A. C╬▒ 49ΓÇô508. Transit 1ΓÇô37 is not this mesh.
- Simulation map — what you see is what is written Setup = 2WYA pocket empty (opaque, no autoplay). ① schematic acetyl-CoA moves in. ② slow-mo: blue Cys166-S → carbonyl; fade to CoA + acetyl-Cys. ③ CoA leaves. ④ schematic acetoacetyl-CoA + water move in. ⑤ slow-mo: acetyl-Cys C2 → ketone; fade to HMG-CoA; water consumed. ⑥ HMG-CoA leaves. Only these events move.
- Sources — bibliography of this page S1 — PDB 2WYA: human HMGCS2 + HMG-CoA, 1.70 Å X-ray — public coordinates; measured Cys166 SG⋯His301 NE2 = 3.72 Å · Cys166 SG⋯Glu132 OE2 = 3.37 Å · Cys166 SG⋯HMG O7 = 3.05 Å S2 — Shafqat et al., 2010, PMID:20346956 — human HMG-CoA synthase isoforms S3 — Sequence: UniProt P54868 · NCBI Gene 3158 S4 — Kinetics: BRENDA EC 2.3.3.10 — no kcat/Km re-asserted on this page
› Backbones and HMG poses are taken directly from the listed PDB entries, superposed into one common frame. Where no crystalline state exists for a step (e.g., acetyl-CoA on 2WYA, acetyl-Cys166, water reactant, nucleophile flight, product leave), the pose is drawn schematically and labeled as such in the narration. Occupancy is product HMG-CoA, not acetyl-CoA. Product-complex Å are not acetyl-CoA geomClaims.