Carbamoyl-phosphate synthase I - 3D Mechanism Simulator

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References & Databases

START HERE — how to read HCO₃⁻ + NH₄⁺ + 2 ATP → carbamoyl phosphate + 2 ADP + Pi + 2 H⁺ A carbamoyl-phosphate cartoon on the human CPS1 frame that actually exists: 5DOU (2.60 Å) chain A with crystal ADP×2 + PO4 + NLG (N-acetylglutamate) + Mg + Ni + K. Occupancy is ADP + NAG + Pi, not ATP, not HCO₃, not NH₄, not carbamoyl phosphate — never copy the PDB title “ligand-bound form” as ATP+CP. NLG is the allosteric on-switch, not a substrate (stays every step). Ni at His337 is a purification artifact — named, not starred, not a geomClaim. UniProt lists no ACT_SITE. His659 ★ is the compiled site-1 nucleotide/Pi contact; His1202 is named at site 2. ATP / HCO₃⁻ / NH₄⁺ / carboxyphosphate / carbamate / carbamoyl phosphate are [schematic]. Two ADP sites sit ~40 Å apart on this static mesh — not a geomClaim. CPS1 uses free NH₄⁺ (no GAT). CPS2/CAD is another gene. Net EC 2 H⁺ are not gold spheres. White is phosphoryl transfer. Blue is NH₃ N-attack, not hydride. OTC next. Measured Å are deposited 5DOU pairs only.
Crystal structures PDB 5DOU — human CPS1 ligand-bound + ADP + PO4 + NLG, 2.60 Å (de Cima 2015). Coordinates are public. Occupancy is ADP×2 + PO4 + NLG. Human CPS1 UniProt P31327.
Mechanism — three half-reactions; free NH₄⁺; no GAT UniProt P31327 EC 6.3.4.16 · Rhea 18029: HCO₃⁻ + NH₄⁺ + 2 ATP = carbamoyl phosphate + 2 ADP + phosphate + 2 H⁺. Half-reactions: (1) HCO₃⁻ + ATP → carboxyphosphate + ADP. (2) carboxyphosphate + NH₄⁺ → carbamate + Pi. (3) carbamate + ATP → carbamoyl phosphate + ADP. de Cima et al., Sci. Rep. 2015, PMID:26592762. CPS2/CAD is another gene. NAGS supplies NAG (Regulation, not a page). Source: UniProt P31327 · de Cima 2015
0 — Setup: empty CPS1 pocket 5DOU occupancy is ADP×2 + PO4 + NLG (NAG) + Mg + Ni + K, not ATP, not HCO₃, not NH₄, not carbamoyl phosphate. The PDB title says ligand-bound — that is this occupancy, not ATP+CP. NAG stays allosteric. Ni at His337 is a purification artifact — not starred. The two nucleotide pockets are shown empty so binding can start. Opaque, run:null (no autoplay). His659 ★ is compiled (UniProt has no ACT_SITE). Transit 1–38 / N-His tag are not this mesh. Cα gaps 1130–1138 / 1147–1162 / 1480–1483.Source: PDB 5DOU (2.60 Å)
① — Bicarbonate binds [schematic] HCO₃⁻ docks at nucleotide site 1 — not deposited. 5DOU holds ADP + Pi here, not bicarbonate. NAG stays allosteric. Thr1391 OG1 ⋯ NLG OE2 = 2.43 Å is deposited (allosteric, not a substrate contact). CPS1 has no GAT.Source: 5DOU site-1 pose rebuilt as HCO₃⁻
② — First ATP binds Schematic ATP docks as crystal ADP site 1 plus a teaching γ-phosphate — [schematic], never label crystal ADP as ATP. His659 NE2 ⋯ ADP1 O3B = 2.47 Å is deposited 5DOU, not an ATP geomClaim. Site 2 sits ~40 Å away on this static mesh — not a geomClaim. Mg stays. Ni is an artifact.Source: 5DOU ADP site 1 rebuilt as ATP
③ — Carboxyphosphate + ADP (hypothetical, lit.-based) Bicarbonate O (white ball + white arrow) attacks schematic ATP1 PG. HCO₃ + ATP1 fade in place to schematic carboxyphosphate and crystal ADP site 1. Never label ADP as ATP. The ~40 Å two-site gap is this static mesh — the white flight is teaching, not a geomClaim. Slow-motion on purpose. White = phosphoryl, not hydride. NAG stays.Source: compiled CPS1 half-reaction 1 · de Cima 2015
④ — Ammonium binds [schematic] NH₄⁺ docks at site 1 — not deposited. CPS1 uses free ammonium (no glutamine amidotransferase). CPS2/CAD is another gene. Carboxyphosphate is compiled. NAG stays. Ni is an artifact.Source: UniProt P31327 free NH₄⁺ · 5DOU site 1
⑤ — Carbamate + Pi (hypothetical, lit.-based) Ammonia N (blue ball + blue arrow) attacks the carboxyphosphate carbon. Carboxy-P cross-fades in place to schematic carbamate and crystal PO4. Never label PO4 as carbamoyl phosphate. Arg721 NH2 ⋯ PO4 O4 = 2.47 Å is deposited. Slow-motion on purpose. Blue = nitrogen nucleophile, not hydride. His659 ★ is compiled. ADP site 1 stays.Source: compiled CPS1 half-reaction 2 · 5DOU PO4
⑥ — Second ATP binds Schematic ATP docks as crystal ADP site 2 plus a teaching γ-phosphate — [schematic], never mix site 1 with site 2. His1202 NE2 ⋯ ADP2 O1B = 3.02 Å is deposited 5DOU, not an ATP geomClaim. His1202 is named, not starred. The two ADP sites are ~40 Å apart — not a geomClaim. Carbamate is compiled.Source: 5DOU ADP site 2 rebuilt as ATP
⑦ — Carbamoyl phosphate + ADP (hypothetical, lit.-based) Carbamate rides the site-1 → site-2 tunnel transit, docks with N 3 Å from schematic ATP2 PG, then carbamate N (white ball + white arrow) attacks PG — ATP γ-phosphoryl transfer onto carbamate, giving schematic carbamoyl phosphate and crystal ADP site 2. Never label ADP as ATP. Never label PO4 as CP. The AMP-leaving phosphoryl stays on carbamate — no detached white carbamoyl group. Slow-motion on purpose. White = phosphoryl, not hydride. NAG stays.Source: compiled CPS1 half-reaction 3 · de Cima 2015
⑧ — Carbamoyl phosphate leaves — OTC next Carbamoyl phosphate departs. Crystal ADP site 1, ADP site 2, and Pi stay. NAG stays. Mg stays. Ni stays named. Carbamoyl phosphate is the substrate of OTC (next). This page does not transfer onto ornithine. 5DOU occupancy is ADP + NAG + Pi, not ATP+CP. Net EC 2 H⁺ are not gold spheres. CPS2/CAD is another gene. His659 ★ is compiled.Source: urea-cycle bookkeeping · EC 6.3.4.16

How to read this page — a first-pass primer First pass: Setup (empty pockets, His659 ★, occupancy is ADP+NAG+Pi, NAG stays, Ni artifact) → ① schematic HCO₃ docks at site 1 → ② schematic ATP1 docks on ADP1 pose → ③ white HCO₃-O → ATP1 PG, fade to carboxy-P + ADP1 → ④ schematic NH₄ docks → ⑤ blue NH₃-N → carboxy-P carbon, fade to carbamate + PO4 → ⑥ schematic ATP2 docks on ADP2 pose → ⑦ white carbamate-N → ATP2 PG, fade to CP + ADP2 → ⑧ CP leaves; ADP×2 + Pi + NAG stay; OTC next. Second pass: 2.47 / 3.02 / 2.47 / 2.43 / 2.66 Å are crystal facts on 5DOU occupancy; ATP, HCO₃, NH₄, carboxy-P, carbamate, CP are [schematic]. The ~40 Å two-site gap is not a geomClaim. Third pass: open “Disagreements” for occupancy vs title, NLG vs substrate, Ni artifact, no ACT_SITE, CPS1 ≠ CAD.
Chemistry primer — carboxy-P then carbamate then carbamoyl-P CPS1 makes mitochondrial carbamoyl phosphate from free NH₄⁺ (no GAT). Bicarbonate attacks ATP γ-P; carboxyphosphate forms and ADP stays at site 1. Ammonia attacks that carbon; Pi stays and carbamate forms. Carbamate nitrogen then attacks a second ATP; carbamoyl phosphate and ADP site 2 form. White = phosphoryl transfer (③ and ⑦). Blue = nitrogen nucleophile (⑤), not hydride. This is not CAD/CPS2 and not OTC.
Words used on screen — ADP ≠ ATP · NLG = NAG · Ni artifact · His659 ★ compiled · two sites ADP ≠ ATP — crystal occupancy is ADP at two sites; teaching ATP is schematic on those poses. NLG = NAG — allosteric activator, not a substrate; stays. Ni artifact — His337⋯NI is purification, not catalytic, not starred, not a geomClaim. His659 ★ — compiled site-1 contact; UniProt has no ACT_SITE. His1202 is named at site 2. Two sites — ADP1 vs ADP2 ~40 Å on this static mesh, not a geomClaim.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 5DOU (2.60 Å) human CPS1 + ADP×2 + PO4 + NLG; His659 NE2 ⋯ ADP1 O3B = 2.47 Å; His1202 NE2 ⋯ ADP2 O1B = 3.02 Å; Arg721 NH2 ⋯ PO4 O4 = 2.47 Å; Thr1391 OG1 ⋯ NLG OE2 = 2.43 Å; Thr1443 OG1 ⋯ NLG O7 = 2.66 Å. The inferred layer ([schematic]): ATP γ-P, HCO₃⁻, NH₄⁺, carboxyphosphate, carbamate, carbamoyl phosphate, transferring nucleophile spheres, product leave. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Occupancy Å are not ATP/HCO₃/CP geomClaims. The ~40 Å two-site gap is not a geomClaim. Title “ligand-bound form” is not ATP+CP. His337⋯NI is not a geomClaim.
Disagreements on record (a) Occupancy vs title. 5DOU holds ADP + NAG + Pi, not ATP, not HCO₃, not NH₄, not carbamoyl phosphate. The title names a ligand-bound form — that is this occupancy. (b) NLG vs substrate. NAG is allosteric; CPS1 without NAG is off. (c) Ni vs catalytic metal. Ni at His337 is a purification artifact. (d) No UniProt ACT_SITE. His659 ★ is compiled at site 1; His1202 is named at site 2. (e) Concerted vs split ③/⑤/⑦ — this page splits three half-reactions for 1-event/1-step teaching. (f) CPS1 uses free NH₄⁺; CAD/CPS2 is another gene (has GAT). (g) Two ADP sites ~40 Å is this static mesh, not a geomClaim. (h) Transit 1–38 / N-His tag are not catalytic. (i) Net 2 H⁺ are not gold spheres. (j) NAGS / ORNT1 are not pages. (k) Cα gaps 1130–1138 / 1147–1162 / 1480–1483. (l) Homooligomer; teaching = chain A.
Regulation — NAG · NAGS · phosphorylation This synthesis is mitochondrial CPS1 only. CAD/CPS2 is another gene — not this mesh. N-acetylglutamate (NLG on 5DOU) is the essential allosteric activator — NAGS supplies it (Regulation, not a page). Phosphorylation and acetylation are named here, not animated. Domain closure between the two ATP sites is not animated.Source: UniProt P31327 · PDB 5DOU · de Cima 2015
Kinetics scope (no measured timecourse on this page) One HCO₃⁻ + NH₄⁺ + 2 ATP → carbamoyl phosphate + 2 ADP + Pi + 2 H⁺ event is drawn, not a steady-state run. Compiled BRENDA values for EC 6.3.4.16 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 6.3.4.16 — no k_cat/K_m re-asserted
Sequence Human CPS1 UniProt P31327 · NCBI Gene 1373. This screen uses 5DOU numbering (His659 / His1202). Chain A. Cα 43–1493 with gaps 1130–1138 / 1147–1162 / 1480–1483. Transit 1–38 and the N-His tag (SEQADV 12–39) are not this mesh.
Simulation map — what you see is what is written Setup = 5DOU pockets empty (opaque, no autoplay); NAG/Mg/Ni stay. ① schematic HCO₃ moves in. ② schematic ATP1 moves in. ③ slow-mo: white HCO₃-O → ATP1 PG; fade to carboxy-P + ADP1. ④ schematic NH₄ moves in. ⑤ slow-mo: blue NH₃-N → carboxy-P carbon; fade to carbamate + PO4. ⑥ schematic ATP2 moves in. ⑦ slow-mo: carbamate tunnels site-1→site-2, then white N → ATP2 PG; fade to CP + ADP2. ⑧ CP leaves; ADP×2 + Pi + NAG stay. Only these events move.
Sources — bibliography of this page S1 — PDB 5DOU: human CPS1 ligand-bound + ADP + PO4 + NLG, 2.60 Å — public coordinates; measured His659 NE2⋯ADP1 O3B = 2.47 Å · His1202 NE2⋯ADP2 O1B = 3.02 Å · Arg721 NH2⋯PO4 O4 = 2.47 Å · Thr1391 OG1⋯NLG OE2 = 2.43 Å · Thr1443 OG1⋯NLG O7 = 2.66 Å S2 — de Cima et al., Sci. Rep. 2015, PMID:26592762 — human CPS1 crystal; NAG allosteric; two ATP sites S3 — Sequence: UniProt P31327 · NCBI Gene 1373 S4 — Kinetics: BRENDA EC 6.3.4.16 — no k_cat/K_m re-asserted on this page

› Backbones and ADP / PO4 / NLG poses are taken directly from the listed PDB entries, superposed into one common frame. Where no crystalline state exists for a step (e.g., ATP, HCO₃⁻, NH₄⁺, carboxyphosphate, carbamate, carbamoyl phosphate, nucleophile flight, product leave), the pose is drawn schematically and labeled as such in the narration. Occupancy is ADP + NAG + Pi, not ATP/HCO₃/CP. Occupancy Å are not ATP/HCO₃/CP geomClaims. Ni at His337 is an artifact.

site 1site 2NAG domainONphosphoryl (white)nucleophile (blue)