Short-chain enoyl-CoA hydratase - 3D Mechanism Simulator

Loading structural data… (8ZRU)

References & Databases

START HERE — how to read (2E)-butenoyl-CoA + H₂O → (3S)-3-hydroxybutanoyl-CoA A crotonase cartoon on the human ECHS1 frame that actually exists: 8ZRU (2.18 Å EM) chain A apo. Occupancy is empty of substrate — never read a seated fatty acyl. Crotonyl-CoA is rebuilt from an 8ZRX CAA overlay [schematic]. CAA is acetoacetyl-CoA (oxo), not crotonyl-CoA (enoyl). Overlay Å are not geomClaims. Glu164 ★ is the general acid/base: it deprotonates the catalytic water and hands that proton back to C2. Glu144 positions and activates the catalytic water by hydrogen bonding; it is not a proton donor. Transit 1–27 is not this mesh (Cα 31–290). Gold is H⁺ from water. Blue is OH⁻ nucleophile onto C3, not hydride. Water is consumed. 2HW5 is rejected. Δ³-Δ² isomerase EC 5.3.3.8 is not this page. ECH1 is peroxisomal, another gene. HADHA/B are other genes. Measured Å are deposited 8ZRU Glu144/Glu164 pairs only.
Crystal / EM structures PDB 8ZRU — human WT ECHS1 apo, 2.18 Å EM (Su 2025). Coordinates are public. Occupancy is apo. PDB 8ZRX — human ECHS1 + acetoacetyl-CoA, overlay CoA-anchor only (not the hydratase substrate). 2HW5 (crotonyl-CoA, To-be-Published) is rejected as the teaching mesh. Human ECHS1 UniProt P30084.
Mechanism — Glu164 activates water; OH⁻ adds to C3 UniProt P30084 EC 4.2.1.17: a trans-2-enoyl-CoA is hydrated to the (3S)-3-hydroxyacyl-CoA. On this mesh the general acid/base is Glu164. Glu144 positions and activates the catalytic water by hydrogen bonding; it is not a proton donor. Also-EC 5.3.3.8 (Δ³-Δ² isomerase) is not shown. ECH1 is peroxisomal — other gene. Source: UniProt P30084 · Su 2025
0 — Setup: empty hydratase pocket 8ZRU occupancy is apo. The pocket is shown empty so binding can start. Opaque, run:null (no autoplay). Glu164 ★ is the compiled water-activating glutamate. Transit 1–27 is not this mesh. 8ZRX CAA is oxo, not this substrate. 2HW5 is not this motion.Source: PDB 8ZRU (2.18 Å EM)
① — Crotonyl-CoA binds [schematic] Crotonyl-CoA docks from an 8ZRX CAA overlay rebuilt as enoyl onto this 8ZRU apo mesh — not a deposited ternary. CAA on 8ZRX is acetoacetyl-CoA (oxo), not crotonyl-CoA (enoyl). Overlay C2/C3 distances are not geomClaims. Teaching chain is C4.Source: 8ZRU apo; overlay 8ZRX CAA rebuilt
② — Catalytic water binds [schematic] A catalytic water slides in between Glu164 ★ and the enoyl C3 face. Glu164 OE2 ⋯ Glu144 OE2 = 4.30 Å is deposited 8ZRU (the Glu144/Glu164 pair). Overlay water distances are not geomClaims. This water is consumed.Source: 8ZRU Glu164/Glu144; water schematic
③ — Glu164 takes the water proton (hypothetical, lit.-based) Gold H⁺ rides from water H2 to Glu164 OE2. Removing H2 leaves O–H1 = OH⁻. Glu144 is named as the water-activating H-bond acceptor, not a proton donor. Gold = H⁺. Overlay water distances are not geomClaims.Source: compiled crotonase Glu · UniProt P30084 · 8ZRU Glu164
④ — OH⁻ attacks C3 → 3-hydroxybutyryl-CoA (hypothetical, lit.-based) OH⁻ remnant itself flies the blue-arrow path from water O onto enoyl C3 (nucleophile, not hydride). Crotonyl-CoA cross-fades in place to schematic (3S)-3-hydroxybutanoyl-CoA (water adds syn across C2=C3, which is why the product is 3S). The water is consumed. Slow-motion on purpose. Parked gold H⁺ stays on Glu164 for this beat; Glu164 returns that same proton to C2, and that hand-back is not drawn (C2 sits on a [schematic] substrate rebuilt on an apo mesh). Overlay C3 distances are not geomClaims. Beats ③ then ④ stage a stepwise (E1cb) reading; the experiment does not separate concerted from stepwise — contested. 2HW5 is not this mesh.Source: compiled crotonase hydration · 8ZRU apo
⑤ — 3-Hydroxyacyl-CoA leaves — HADH next [schematic] (3S)-3-Hydroxybutanoyl-CoA departs toward HADH. Teaching product is C4 — HADH is taught on this same chain. The pocket returns empty. This page does not dehydrogenate and does not run HADHA/B or peroxisomal ECH1. Overlay Å are not geomClaims. Δ³-Δ² isomerase is not shown.Source: β-oxidation bookkeeping · EC 4.2.1.17

How to read this page — a first-pass primer First pass: Setup (empty pocket, Glu164 ★) → ① schematic crotonyl-CoA docks → ② schematic water docks → ③ gold H⁺ water → Glu164 → ④ OH⁻ remnant flies the arrow path onto C3, fade to 3-hydroxy → ⑤ hydroxy leaves; HADH next (C4, same chain). Second pass: 4.30 / 4.05 / 5.17 Å are crystal facts on 8ZRU empty of substrate; crotonyl / water / 3-hydroxy are [schematic]. Teaching product is C4. Third pass: open “Disagreements” for apo vs substrate, 8ZRX oxo vs enoyl, 2HW5 rejected, and ECH1 / HADHA vs this gene.
Chemistry primer — crotonase hydration ECHS1 adds water across the trans-2-enoyl C2=C3 bond. This cartoon shows Glu164 taking a water proton (gold) and OH⁻ adding to C3 (blue nucleophile, not hydride). Glu164 hands that same proton back to C2; that hand-back is not drawn (C2 sits on a [schematic] substrate rebuilt on an apo mesh). Teaching product is C4 (3S)-3-hydroxybutanoyl-CoA — HADH (next) is taught on this same chain. Water is consumed. This is not ECH1, not HADHA/B, and not the Δ³-Δ² isomerase also listed on the UniProt entry.
Words used on screen — apo · overlay · Glu164 ★ · oxo vs enoyl Apo — 8ZRU holds no fatty acyl. Overlay — crotonyl pose is 8ZRX CAA Kabsch-fitted and rebuilt as enoyl, not deposited. Glu164 ★ — PDB / UniProt SITE on this frame. Oxo vs enoyl — 8ZRX CAA is acetoacetyl-CoA (C3 carbonyl), not crotonyl-CoA (C2=C3).

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 8ZRU (2.18 Å EM) human ECHS1 apo; Glu164 OE2 ⋯ Glu144 OE2 = 4.30 Å; Glu164 OE2 ⋯ Glu144 OE1 = 4.05 Å; Glu164 CD ⋯ Glu144 CD = 5.17 Å. The inferred layer ([schematic]): crotonyl-CoA overlay rebuilt from 8ZRX CAA, water, 3-hydroxybutanoyl-CoA, transferring H⁺ / OH⁻ spheres, product leave. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Overlay Å are not geomClaims. 8ZRX CAA is oxo, not enoyl.
Disagreements on record (a) Occupancy vs substrate. 8ZRU is apo, not crotonyl-CoA. (b) 8ZRX CAA is oxo. Acetoacetyl-CoA is not the hydratase substrate; overlay C2/C3 distances are not geomClaims. (c) 2HW5 (crotonyl-CoA, To-be-Published) is rejected as the teaching mesh. (d) Transit 1–27 is not this mesh (Cα 31–290). (e) Concerted vs split water activation / OH addition — this page splits ③ then ④ for 1-event/1-step teaching. (f) ECH1 is peroxisomal, another gene. (g) HADHA / HADHB (trifunctional protein) are other genes. (h) Also-EC 5.3.3.8 Δ³-Δ² isomerase is not shown. (i) Hexamer assembly is not this cartoon. (j) C2 protonation is by Glu164 itself, not by Glu144; the hand-back is not drawn (C2 is [schematic] on this apo mesh).
Regulation — isoforms · ECHS1 deficiency This spiral is monofunctional ECHS1 only. Mitochondrial trifunctional protein (HADHA / HADHB) and peroxisomal ECH1 are other genes — not this mesh. Human ECHS1 deficiency alleles are named, not simulated. Also-EC 5.3.3.8 is named, not drawn. Matrix localization is assumed, not a catalytic event on this page.Source: UniProt P30084 · PDB 8ZRU · Su 2025
Kinetics scope (no measured timecourse on this page) One (2E)-butenoyl-CoA + H₂O → (3S)-3-hydroxybutanoyl-CoA event is drawn, not a steady-state run. Compiled BRENDA values for EC 4.2.1.17 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 4.2.1.17 — no k_cat/K_m re-asserted
Sequence Human ECHS1 UniProt P30084 · NCBI Gene 1892. This screen uses 8ZRU numbering (Glu164). Chain A. Cα 31–290. Transit 1–27 not this mesh.
Simulation map — what you see is what is written Setup = 8ZRU apo, pocket empty (opaque, no autoplay). ① schematic crotonyl-CoA moves in. ② schematic water moves in. ③ gold H⁺ water → Glu164; water becomes OH⁻. ④ slow-mo: OH⁻ remnant flies the arrow path onto C3; crotonyl fades to 3-hydroxy; water consumed. ⑤ 3-hydroxy leaves. Only these events move.
Sources — bibliography of this page S1 — PDB 8ZRU: human ECHS1 apo, 2.18 Å EM — public coordinates; measured Glu164 OE2⋯Glu144 OE2 = 4.30 Å · Glu164 OE2⋯Glu144 OE1 = 4.05 Å · Glu164 CD⋯Glu144 CD = 5.17 Å S2 — Su et al., 2025, PMID:40240482 — human ECHS1 substrate recognition; companion 8ZRX CAA overlay only S3 — Sequence: UniProt P30084 · NCBI Gene 1892 · 2HW5 rejected as teaching mesh S4 — Kinetics: BRENDA EC 4.2.1.17 — no k_cat/K_m re-asserted on this page

› Backbones are taken directly from the listed PDB entries, superposed into one common frame. Where no crystalline state exists for a step (e.g., crotonyl-CoA on 8ZRU, water, 3-hydroxyacyl-CoA, proton/OH flight, product release), the pose is drawn schematically and labeled as such in the narration. Occupancy is apo. 8ZRX CAA is oxo, not enoyl. Overlay Å are not geomClaims.

N-domainC-domainONH⁺ (gold)OH⁻ (blue)