Aconitase - 3D Mechanism Simulator

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References & Databases

START HERE — how to read the citrate ⇄ isocitrate picture Aconitase is a reversible isomerase: citrate loses water as cis-aconitate, then takes up a fresh solvent water on the opposite face, landing isocitrate. The whole trick is a water-on / water-off at the cluster. The enzyme cannot trap its own intermediate, so the textbook pinch is crystallographic: trans-aconitate — a planar, water-free mimic of cis-aconitate — is what 1ACO actually holds. In step ② the departing water is a real product drawn whole at the leaving oxygen (never silently dropped); in step ④ the rehydration water is a fresh solvent water arriving at the Fe4 seat. Measured numbers on this page (2.90 / 2.64 / 3.56 Å) are reproduced from the deposited 1ACO coordinates on the analog, not on citrate — the citrate/isocitrate poses themselves are [schematic]. Nothing on screen teleports: molecules fade-swap in place on the same seat.
Crystal structure PDB 1ACO — pig mitochondrial aconitase with trans-aconitate bound (the cis-aconitate analog), Lauble H, Kennedy MC, Beinert H, Stout CD, J Mol Biol 1994, PMID:8151704 (PMID:8201096, companion 1994 Proteins report). The enzyme-gate closure around the analog is the canonical "closed" catalytic state.
Mechanism — the [4Fe-4S] cluster does acid/base, not redox The unique labile Fe4 is a Lewis acid that coordinates the substrate hydroxyl (Beinert & Kennedy, FASEB J 1993, DOI 10.1096/fasebj.7.15.8262321); Ser642 is the general base that abstracts the β-carbon proton and His101 the general acid/base that protonates the leaving Fe-bound OH in dehydration and activates the Fe-bound water in rehydration (M-CSA entry 552, curated on the fluorocitrate-frame chemistry of Lauble 1996). The stepwise proton order drawn on screen (Ser first, then His) is the M-CSA/Lauble reading — see Disagreements. Source: Lauble et al. 1992, Biochemistry 31:2735–2748 (PMID:1312355) — substrate binding + Ser642/His101 assignments from the 2-methylisocitrate/analog frames · Beinert & Kennedy 1993 — cluster Lewis-acid summary · Lauble et al. 1996, PNAS (PMID:8942997) — fluorocitrate mechanism trap · M-CSA entry 552
0 — Setup: 1ACO crystal The deposited closed enzyme holds the [4Fe-4S] cluster and the planar trans-aconitate analog. This is the real crystal state — everything else (citrate/isocitrate/water) is drawn on the same seat and tagged [schematic]. The cluster is redox-innocent in this reaction: the scaffold + Lewis-acid role keeps iron oxidation states unchanged.Source: PDB 1ACO (2.0 Å), Lauble 1994
① — Citrate docks — Fe4 coordination [schematic] No aconitase A citrate·Michaelis crystal is deposited (only bacterial aconitase B holds substrate co-crystals — a different family), so citrate enters as a schematic pose whose central C3-OH and a carboxylate seat onto the unique Fe4 (Lewis-acid activation), with Arg447/Arg580 organizing the distal carboxylates. The 2.64 Å number quoted on the narration belongs to the crystal analog (Fe4…OG2 of trans-aconitate), not to this schematic contact.Source: schematic pose (no aconitase A co-structure) · Arg roles: pocket-lining, from the mechanism literature (M-CSA 552)
② — Dehydration → cis-aconitate Proposed (Lauble 1992; M-CSA 552): (1) Ser642 ★ abstracts the β-carbon proton (gold ball); (2) His101 protonates the leaving Fe-bound hydroxyl (gold ball) — a whole H₂O forms at the O3 seat and departs on its own vector. The skeleton collapses to cis-aconitate, whose planar geometry the crystal's trans-aconitate analog then captures (fade-swap in place). Slow-motion on purpose, so the two proton throws read in order.Source: Lauble 1992 · M-CSA 552 — stepwise order = proposal (Disagreements card)
③ — Intermediate: trans-aconitate = cis-aconitate TS analog The planar cis-aconitate intermediate is exactly what trans-aconitate mimics, which is why the crystal chose it. Three contacts reproduce from the deposited coordinates (Rule 34): Ser642 OG…βC = 2.90 Å, Fe4…coordinating O = 2.64 Å, His101 NE2…alkene C = 3.56 Å — the same triad that makes dehydration/rehydration reversible on either side of the planar alkene.Source: measured, reproduced from PDB 1ACO coordinates (see tools/manifests/aco.json geomClaims)
④ — Rehydration → isocitrate Proposed (M-CSA 552): His101 splits the Fe-bound water — its proton goes to His (gray H ball water to His, kept as resting His-H+ for the next dehydration) and the remaining hydroxide OH- adds trans across the alkene (blue lone-pair arrow, hydroxide body flies) — while Ser642 ★ pays back the β-proton it borrowed in step ②. Watch the two balls: the lone gray ball that flies away to His101 is the proton (H⁺); the red-O + gray-H pair that stays at the Fe seat is the hydroxide (OH⁻) itself, and it attacks the alkene carbon that sits right beside His101 (His101 NE2⋯alkene C = 3.56 Å — the same screen spot, measured in step ③), so the H⁺-to-His hop and the OH⁻ stay-in-place look can be mistaken for each other. Kept plus returned protons net to zero, so no proton is created or lost on screen. The OH lands on the face opposite the one it left, which is exactly why isocitrate (not citrate) forms. The analog swaps out; isocitrate fades in place. Slow-motion on purpose.Source: M-CSA 552 · trans (anti) addition per the classic labeling work (see Words card)
⑤ — Isocitrate released — cluster stays home [schematic] Isocitrate exits toward isocitrate dehydrogenase; the [4Fe-4S] cluster stays home, redox-innocent. Net: citrate ⇄ isocitrate (TCA step 2; the reverse direction is gluconeogenic and the reaction is freely reversible).Source: Rule 4 display convention — separate product exit; no external geometry claimed

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: the 1ACO pig aconitase frame (2.0 Å) with its [4Fe-4S] cluster and trans-aconitate analog as deposited heavy atoms, and the three contacts reproduced from those coordinates into the manifest geomClaims — Ser642 OG…analog βC 2.90 Å, Fe4…coordinating O 2.64 Å, His101 NE2…alkene C 3.56 Å. These are measured on the analog, never on citrate. The inferred layer (all [schematic]): the citrate/isocitrate substrate poses, because no aconitase A citrate/isocitrate Michaelis complex is deposited (only bacterial aconitase B substrate co-crystals exist, a different family); the fresh-solvent water arrival and the hydroxide trans-attack trajectory; and the stepwise proton order (Ser first, then His), which is the Lauble/M-CSA reading — the actual order is not directly measurable and could be concerted or Fe-assisted-ordered (Disagreements card). Where a step has no crystalline state, the drawerNote supplies the schematic framing.
Why is the citrate/isocitrate "[schematic]"? The enzyme cannot trap its own intermediate, and no aconitase A (the mitochondrial/cytosolic [4Fe-4S] enzyme of this page) citrate- or isocitrate-bound Michaelis complex is deposited — 1ACO holds only trans-aconitate, the planar, water-free mimic of cis-aconitate. (Bacterial aconitase B co-crystals with citrate/isocitrate exist — e.g. AcnB, Williams 2002 — but belong to a different fold/mechanism family and are not this page's frame.) All three substrate states (citrate entering, isocitrate leaving) are therefore schematic poses rebuilt on that one measured analog frame; only the analog's own contacts are drawn as measured distances, and nothing is teleported — every substrate state fades in on the same seat.
Catalytic residues — Ser642 · His101 · Fe4 Ser642 = general base (abstracts βC–H in dehydration; reprotonates in rehydration). His101 = general acid/base (protonates the leaving Fe-bound OH in dehydration; activates the Fe-bound water in rehydration). Fe4 (unique labile iron) = Lewis acid holding the substrate hydroxyl — a structural/electrostatic role, not an electron sink. Asp165/His167/Arg447/Arg452/Arg580/Arg644 line the pocket and organize the carboxylates, but are not assigned catalytic steps on this page (M-CSA 552; Beinert & Kennedy 1993).
Disagreements on record (a) Stepwise order. The drawn sequence — Ser642 abstracts first, His101 protonates second — follows Lauble 1992 / M-CSA 552; the order of the two proton throws in the actual enzyme is not directly measurable and could be concerted or Fe-assisted-ordered. (b) No aconitase A enzyme–substrate Michaelis complex is deposited for either direction (bacterial aconitase B complexes exist but are a different family); the cartoon interconverts schematic citrate/isocitrate through the one measured analog frame. (c) The classic mocconate/fluorocitrate experiments (Lauble 1996, PMID:8942997) support the Fe4 Lewis-acid + acid/base assignment; a dissenting view routes both proton transfers through histidines only.
Words used on screen — trans-aconitate · trans addition · Lewis acid trans-aconitate — the 1,2,3-tricarboxylic acid isomer whose central double bond is trans; because cis-aconitate is the actual intermediate, trans-aconitate is "good enough" an analog for crystallization. Trans (anti) addition — the rehydrating OH and the returning β-proton land on opposite faces of the planar alkene, the classical labeling result (the deuterium experiments behind the "two-lobed" mechanism). Lewis acid Fe4 — the iron accepts electron density from the substrate O, weakening the C–OH bond for departure, without changing oxidation state. β-carbon — on this page citrate C2 (the alkene carbon next to the central acid), the one Ser642 grabs.
Kinetics scope (no measured timecourse on this page) One citrate → isocitrate event is drawn, not a steady-state run. Aconitase is a reversible, near-equilibrium step of the TCA cycle. The classical equilibrium lies toward citrate — the equilibrated mixture is roughly citrate ≈ 90% · isocitrate ≈ 7% · cis-aconitate ≈ 3–4% (Keq[isocitrate]/[citrate] ≈ 0.08), so the net forward drive in the TCA comes from downstream isocitrate dehydrogenase's removal of product, not from aconitase itself. Compiled BRENDA values for animal aconitase Km/kcat are not re-asserted here pending re-verification — the page draws no rate claim.Source: equilibrium composition is a classical textbook value (≈90:7:3–4 citrate:isocitrate:cis-aconitate at 25–37 °C, pH 7; e.g. Garrett & Grisham, Biochemistry; Lee et al. thermodynamic compilations — the exact ratio is pH/temperature-dependent, direction does not change)
Regulation — the IRP-1 switch In the cytosol the apo (cluster-less) form of this same enzyme is IRP-1 (iron regulatory protein 1): without the [4Fe-4S] cluster it binds iron-responsive elements on mRNAs and controls ferritin/transferrin-receptor translation. Fe–S cluster biogenesis (ISC machinery, frataxin) adds the cluster back and re-activates aconitase — iron sensing in one molecule. In mitochondria ACO2 is the TCA enzyme shown here.Source: UniProt P21399 (cytosolic ACO1/IRP-1) · Q99798 (mitochondrial ACO2)
Simulation map — what you see is what is written Setup = the 1ACO crystal (cluster + analog, opaque, run:null). ① citrate moves in (schematic) onto Fe4; cluster label stays. ② STAR slow-mo: Ser642 gold arrow grabs the βC-H (gold ball flies C2→Ser), His101 gold arrow hits the leaving OH (gold ball NE2→O3); a whole H₂O materializes at the O3 seat, then departs on its own vector; citrate fades as the planar analog fades in over the same seat. ③ three measured distance labels appear in turn (2.90 / 2.64 / 3.56 Å) and clear. ④ STAR slow-mo: the Fe-bound water re-enters at the Fe4 seat, His101 takes its proton (gray H ball water to His, kept as resting His-H+ for the next turn), the hydroxide body flies to the alkene carbon and attacks trans (blue), Ser642 returns the borrowed proton (gold ball Ser→βC); water consumed, analog fades out as isocitrate fades in. ⑤ isocitrate releases; cluster stays. Only these events move; everything else is a static frame of 1ACO.
Sequence Human mitochondrial aconitase ACO2 UniProt Q99798 · NCBI Gene 50 (ACO2) · cytosolic ACO1/IRP1 UniProt P21399 · NCBI Gene 48 (ACO1). Screen shows 1ACO pig numbering (Ser642/His101 — PDB-author, displayed as deposited).
Sources — bibliography of this page S1 — PDB 1ACO (2.0 Å): pig mitochondrial aconitase + trans-aconitate; Lauble et al. 1994, J Mol Biol PMID:8151704; companion report PMID:8201096, Proteins 19:98–109 S2 — Lauble, Kennedy, Beinert, Stout 1992, Biochemistry 31:2735–2748, PMID:1312355 (substrate binding; Ser642/His101 assignments) S3 — Beinert & Kennedy 1993, FASEB J 7:1442–1449, DOI 10.1096/fasebj.7.15.8262321 (unique-Fe Lewis acid; cluster role) S4 — Lauble et al. 1996, PNAS 93:13699–13703, PMID:8942997 (fluorocitrate mechanism trap) S5 — M-CSA entry 552 (curated aconitase mechanism; stepwise order used on screen) S6 — UniProt Q99798 (ACO2) · P21399 (ACO1/IRP-1) · NCBI Gene 50 / Gene 48 S7 — Repo display conventions: Rule 4 (separate product exits) · Rule 34 geometry (3 geomClaims reproduced in tools/manifests/aco.json) · [schematic] = rebuilt pose on the measured frame, no deposition claimed

› Backbones and ligand poses are taken directly from the listed PDB entries, superposed into one common frame. Where no crystalline state exists for a step (e.g., citrate/isocitrate approach, water attack), the pose is drawn schematically and labeled as such in the narration.

N-domainsC-domainsONSFe