Ornithine transcarbamylase - 3D Mechanism Simulator

Loading structural data… (1C9Y)

References & Databases

START HERE — how to read carbamoyl phosphate + L-ornithine → L-citrulline + Pi + H⁺ A carbamoyl-transfer cartoon on the human OTC frame that actually exists: 1C9Y (1.90 Å) chain A with crystal carbamoyl phosphate + norvaline. Occupancy is CP + NVA, not ornithine, not citrulline — never label NVA as ornithine. Cys303 ★ is this PDB = UniProt ACT_SITE. This page does not draw a covalent Cys-carbamoyl intermediate. SEQADV Arg270 vs UniProt Gln270 is a genuine conflict, not a catalytic star. Phe101 equals the current UniProt canonical (the 1999 SEQADV Leu101 reference is stale). Ornithine / citrulline / Pi are [schematic] on this CP+NVA pose. 1OTH PAO is a named TS-analog overlay, not this mesh. Transit 1–32 is not this mesh (Cα 34–354). Homotrimer named; teaching is chain A. Blue is nitrogen nucleophile, not hydride. Net EC H⁺ is not a gold sphere. ASS1 next. Measured Å are deposited 1C9Y CP pairs only.
Crystal structures PDB 1C9Y — human OTC + carbamoyl phosphate + L-norvaline, 1.90 Å (Shi 2000). Coordinates are public. Occupancy is CP + NVA. PDB 1OTH is the PAO TS analog — named overlay, not this mesh. Human OTC UniProt P00480.
Mechanism — Cys303 ACT_SITE; NVA ≠ ornithine UniProt P00480 EC 2.1.3.3: carbamoyl phosphate + L-ornithine = L-citrulline + phosphate + H⁺. This page teaches carbamoyl transfer (urea cycle, mitochondrion). On this mesh the ACT_SITE cysteine is Cys303. This page does not draw a covalent Cys intermediate. Norvaline is the ornithine analog. ASS1 is next (cytosol). Source: UniProt P00480 · Shi 2000
0 — Setup: empty OTC pocket 1C9Y occupancy is carbamoyl phosphate + norvaline, not ornithine, not citrulline. The pocket is shown empty so binding can start. Opaque, run:null (no autoplay). Cys303 ★ is ACT_SITE. SEQADV Arg270 vs UniProt Gln270 is spoken, not starred (Phe101 = canonical). Transit 1–32 is not this mesh (Cα 34–354). 1OTH PAO is a named overlay. Homotrimer named; teaching is chain A.Source: PDB 1C9Y (1.90 Å)
① — Carbamoyl phosphate binds Crystal carbamoyl phosphate docks — real 1C9Y occupancy, unlike 5DOU (CPS1 held ADP+Pi, not CP). Gln171 OE1 ⋯ CP N = 2.69 Å and Ser90 OG ⋯ CP O2P = 2.69 Å are deposited 1C9Y. NVA is not this ligand.Source: PDB 1C9Y CP
② — Ornithine binds [schematic] L-ornithine docks as crystal norvaline plus a teaching δ-NH₃ — never label NVA as ornithine. Norvaline has no δ-amino group. Arg92 NE ⋯ CP O4P = 2.79 Å is deposited 1C9Y (CP contact, not an ornithine geomClaim). SEQADV Arg270 is a conflict, not a star (Phe101 = current canonical).Source: 1C9Y NVA pose rebuilt as ornithine
③ — Carbamoyl transfer (hypothetical, lit.-based) Blue ball + blue arrow: ornithine N attacks crystal CP carbonyl C. CP + ornithine cross-fade to schematic citrulline + schematic Pi. Never label NVA as ornithine. Never label CP as citrulline. Arg141 NH1 ⋯ CP O3P = 2.77 Å and His168 NE2 ⋯ CP O = 2.90 Å are deposited. Cys303 ★ is ACT_SITE; this page does not draw a covalent Cys-carbamoyl. Slow-motion on purpose. Blue = nitrogen nucleophile, not hydride. Net H⁺ is not gold.Source: compiled carbamoyl transfer · Shi 2000 · UniProt P00480 Cys303
④ — Opposite leave — ASS1 next Schematic citrulline departs one way; schematic Pi departs the other — Pi caption shows ~1 s, then clears so it never covers the scene. Citrulline is the substrate of ASS1 (next, cytosol). This page does not adenylate citrulline. 1C9Y occupancy is CP + norvaline, not ornithine, not citrulline. Net EC H⁺ is not a gold sphere. Cys303 ★ is ACT_SITE.Source: urea-cycle bookkeeping · EC 2.1.3.3

How to read this page — a first-pass primer First pass: Setup (empty pocket, Cys303 ★, NVA ≠ ornithine, SEQADV) → ① crystal CP docks → ② schematic ornithine on NVA pose → ③ blue N attacks CP carbonyl; fade to citrulline + Pi → ④ opposite leave; ASS1 next. Second pass: 2.69 / 2.77 / 2.79 / 2.90 / 2.69 Å are crystal facts on 1C9Y CP; ornithine and citrulline are [schematic]; NVA is not ornithine. Third pass: open “Disagreements” for NVA vs ornithine, 1OTH overlay, Arg270 SEQADV (Phe101 = canonical), and no covalent Cys-carbamoyl.
Chemistry primer — ornithine transcarbamylase OTC transfers the carbamoyl group of carbamoyl phosphate onto L-ornithine, releasing citrulline + Pi. Cys303 is the UniProt ACT_SITE. This page does not draw a covalent Cys intermediate. Blue is nitrogen nucleophile, not hydride. Net H⁺ is not a gold sphere. This is not a cytosolic isoform.
Words used on screen — real CP · NVA ≠ ornithine · Cys303 ★ Real CP — 1C9Y occupancy is carbamoyl phosphate, unlike 5DOU. NVA ≠ ornithine — norvaline analog; teaching ornithine is schematic. Cys303 ★ — ACT_SITE on this PDB = UniProt.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 1C9Y (1.90 Å) human OTC chain A + CP + NVA; Gln171 OE1 ⋯ CP N = 2.69 Å; Arg141 NH1 ⋯ CP O3P = 2.77 Å; Arg92 NE ⋯ CP O4P = 2.79 Å; His168 NE2 ⋯ CP O = 2.90 Å; Ser90 OG ⋯ CP O2P = 2.69 Å. The inferred layer ([schematic]): ornithine / citrulline / Pi on the CP+NVA pose, transferring nucleophile spheres. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Occupancy Å are not ornithine/citrulline geomClaims.
Disagreements on record (a) Occupancy vs substrates. 1C9Y holds CP + norvaline, not ornithine, not citrulline. (b) NVA ≠ ornithine. Norvaline has no δ-NH₃. (c) Cys303 ★ is ACT_SITE; this page does not draw a covalent Cys-carbamoyl. (d) SEQADV Arg270 vs UniProt Gln270 is a genuine conflict, not a star; Phe101 equals the current UniProt canonical (the 1999 SEQADV Leu101 reference is stale — Leu101 is only a dbSNP variant). (e) 1OTH PAO is a named overlay, not this mesh. (f) Concerted vs split transfer — this page is 1-event/1-step. (g) Transit 1–32 is not this mesh (Cα 34–354). (h) Homotrimer assembly is not this cartoon. (i) Net EC H⁺ is not a gold sphere. (j) Cytosolic OTC isoforms are not this page. (k) Overlay/schematic Å are not claims.
Regulation — mitochondrion · homotrimer · next ASS1 This transfer is mitochondrial OTC only. Citrulline exits to cytosol for ASS1 — not this mesh. Homotrimer is named, not animated. Cytosolic isoforms are another story.Source: UniProt P00480 · PDB 1C9Y · Shi 2000
Kinetics scope (no measured timecourse on this page) One carbamoyl phosphate + ornithine → citrulline + Pi event is drawn, not a steady-state run. Compiled BRENDA values for EC 2.1.3.3 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 2.1.3.3 — no k_cat/K_m re-asserted
Sequence Human OTC UniProt P00480 · NCBI Gene 5009. This screen uses 1C9Y numbering (Cys303 = UniProt Cys303; residue 101 = Phe; residue 270 = Arg). Chain A. Cα 34–354. Transit 1–32 is not this mesh.
Simulation map — what you see is what is written Setup = 1C9Y pocket empty (opaque, no autoplay). ① crystal CP moves in. ② schematic ornithine moves in. ③ slow-mo: blue ornithine-N → CP C; fade to citrulline + Pi. ④ citrulline and Pi leave opposite ways. Only these events move.
Sources — bibliography of this page S1 — PDB 1C9Y: human OTC + CP + NVA, 1.90 Å — public coordinates; measured Gln171 OE1⋯CP N = 2.69 Å · Arg141 NH1⋯CP O3P = 2.77 Å · Arg92 NE⋯CP O4P = 2.79 Å · His168 NE2⋯CP O = 2.90 Å · Ser90 OG⋯CP O2P = 2.69 Å S2 — Shi et al., Proteins 2000, PMID:10813810 — human OTC + CP + norvaline S3 — Sequence: UniProt P00480 · NCBI Gene 5009 S4 — Kinetics: BRENDA EC 2.1.3.3 — no k_cat/K_m re-asserted on this page

› Backbones and CP / NVA poses are taken directly from the listed PDB entries, superposed into one common frame. Where no crystalline state exists for a step (e.g., ornithine, citrulline, Pi as product, nucleophile flight, product leave), the pose is drawn schematically and labeled as such in the narration. Occupancy is CP + norvaline, not ornithine. Occupancy Å are not ornithine/citrulline geomClaims. 1OTH PAO is named, not extracted.

N-domainC-domainONnucleophile (blue)