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START HERE — how to read L-citrulline + L-aspartate + ATP → argininosuccinate + AMP + PPi + H⁺
An adenylation cartoon on the human ASS1 frame that actually exists: 2NZ2 (2.40 Å) chain A with crystal L-citrulline + L-aspartate. Occupancy is CIR + ASP, not ATP, not AMP, not PPi, not argininosuccinate — never label ASP as ATP. Asp124 ★ is compiled (UniProt has no ACT_SITE). This page does not draw a covalent Asp intermediate. ATP / citrullyl-AMP / AMP / PPi / argininosuccinate are [schematic]. Crystallization Na⁺ at Gln107 is named, not starred, not this cartoon. SEQADV Ser A0 is a cloning artifact. Cα gaps 156 and 377 are not this mesh (Cα 4–407). Homotetramer named; teaching is chain A. White is adenyl-P. Blue is nitrogen nucleophile, not hydride. Net EC H⁺ is not a gold sphere. ASL next. Measured Å are deposited 2NZ2 CIR/ASP pairs only.
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Crystal structures
PDB 2NZ2 — human ASS1 + L-aspartate + L-citrulline, 2.40 Å (Karlberg 2008). Coordinates are public. Occupancy is CIR + ASP. No nucleotide on this frame. Human ASS1 UniProt P00966.
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Mechanism — Asp124 compiled; no nucleotide occupancy
UniProt P00966 EC 6.3.4.5: ATP + L-citrulline + L-aspartate = AMP + diphosphate + N(omega)-(L-arginino)succinate + H⁺. This page teaches citrulline adenylation then Asp-N attack (urea cycle, cytosol). On this mesh there is no UniProt ACT_SITE; Asp124 ★ is compiled. Never label ASP as ATP. ASL is next. Source: UniProt P00966 · Karlberg 2008
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0 — Setup: empty ASS1 pocket
2NZ2 occupancy is L-citrulline + L-aspartate, not ATP. The pocket is shown empty so binding can start. Opaque, run:null (no autoplay). Asp124 ★ is compiled. SEQADV Ser A0 spoken, not starred. Cα gaps 156 and 377 are not this mesh (Cα 4–407). Crystallization Na⁺ is named. Homotetramer named; teaching is chain A.Source: PDB 2NZ2 (2.40 Å)
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① — Citrulline binds
Crystal L-citrulline docks — real 2NZ2 occupancy. Glu270 OE2 ⋯ CIR N = 2.54 Å and Tyr87 OH ⋯ CIR OXT = 2.69 Å are deposited 2NZ2. No nucleotide is on this frame.Source: PDB 2NZ2 CIR
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② — ATP binds
[schematic] ATP docks near the citrulline ureido oxygen — not deposited. Never label ASP as ATP. Arg127 NH1 ⋯ CIR OXT = 2.73 Å and Asn123 ND2 ⋯ CIR O = 2.77 Å are deposited 2NZ2 (CIR contacts, not ATP geomClaims).Source: 2NZ2 CIR pose + schematic ATP
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③ — Citrulline adenylation
(hypothetical, lit.-based) White ball + white arrow: citrulline O7 attacks schematic ATP PA. CIR + ATP cross-fade to schematic citrullyl-AMP + schematic PPi. Never label ASP as ATP. Asp124 ★ is compiled; this page does not draw a covalent Asp intermediate. Slow-motion on purpose. White = adenyl-P, not hydride. Net H⁺ is not gold.Source: compiled adenylation · Karlberg 2008 · UniProt P00966
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④ — Aspartate binds
Crystal L-aspartate docks — real 2NZ2 occupancy, not ATP. Never label ASP as ATP. Thr119 OG1 ⋯ ASP O = 2.50 Å is deposited 2NZ2. Schematic citrullyl-AMP stays seated. PPi already left with adenylation.Source: PDB 2NZ2 ASP
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⑤ — Asp-N attacks citrullyl-AMP
(hypothetical, lit.-based) Blue ball + blue arrow: aspartate N attacks schematic citrullyl-AMP C7. Citrullyl-AMP + ASP cross-fade to schematic argininosuccinate + schematic AMP. Never label ASP as ATP. Asp124 OD2 ⋯ ASP N = 2.86 Å is deposited. Asp124 ★ is compiled. Slow-motion on purpose. Blue = nitrogen nucleophile, not hydride. Net H⁺ is not gold.Source: compiled Asp-N attack · Karlberg 2008 · UniProt P00966
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⑥ — Opposite leave — ASL next
Schematic argininosuccinate departs one way; schematic AMP departs the other. Argininosuccinate is the substrate of ASL (next). This page does not lyse argininosuccinate. 2NZ2 occupancy is citrulline + aspartate, not ATP. PPi already left with adenylation. Net EC H⁺ is not a gold sphere. Asp124 ★ is compiled.Source: urea-cycle bookkeeping · EC 6.3.4.5
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How to read this page — a first-pass primer
First pass: Setup (empty pocket, Asp124 ★, occupancy is CIR+ASP not ATP) → ① crystal citrulline docks → ② schematic ATP → ③ white O7 attacks ATP PA; fade to citrullyl-AMP + PPi → ④ crystal aspartate docks → ⑤ blue Asp-N attacks C7; fade to argininosuccinate + AMP → ⑥ opposite leave; ASL next. Second pass: 2.54 / 2.69 / 2.73 / 2.77 / 2.50 / 2.86 Å are crystal facts on 2NZ2 CIR/ASP; ATP and products are [schematic]; ASP is not ATP. Third pass: open “Disagreements” for no-nucleotide occupancy, compiled Asp124, Na⁺ ion, and Ser A0.
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Chemistry primer — argininosuccinate synthase
ASS1 adenylates L-citrulline on ATP, then aspartate N attacks citrullyl-AMP, releasing argininosuccinate + AMP + PPi. UniProt has no ACT_SITE. Asp124 ★ is compiled. White is adenyl-P. Blue is nitrogen nucleophile, not hydride. Net H⁺ is not a gold sphere. This is cytosolic, not mitochondrial.
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Words used on screen — real CIR · real ASP · ASP ≠ ATP · Asp124 ★
Real CIR / ASP — 2NZ2 occupancy is the two amino acids. ASP ≠ ATP — never label aspartate as nucleotide. Asp124 ★ — compiled (no UniProt ACT_SITE).
Legend & Fidelity
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Mechanism fidelity — measured vs. inferred
The measured layer: 2NZ2 (2.40 Å) human ASS1 chain A + CIR + ASP; Glu270 OE2 ⋯ CIR N = 2.54 Å; Tyr87 OH ⋯ CIR OXT = 2.69 Å; Arg127 NH1 ⋯ CIR OXT = 2.73 Å; Asn123 ND2 ⋯ CIR O = 2.77 Å; Thr119 OG1 ⋯ ASP O = 2.50 Å; Asp124 OD2 ⋯ ASP N = 2.86 Å. The inferred layer ([schematic]): ATP / citrullyl-AMP / AMP / PPi / argininosuccinate, transferring nucleophile spheres. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Occupancy Å are not ATP/ASUC geomClaims.
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Disagreements on record
(a) Occupancy vs substrates. 2NZ2 holds citrulline + aspartate, not ATP. (b) ASP ≠ ATP. Never label aspartate as nucleotide. (c) Asp124 ★ is compiled; UniProt has no ACT_SITE; this page does not draw a covalent Asp intermediate. (d) SEQADV Ser A0 is a cloning artifact, not a star. (e) Crystallization Na⁺ at Gln107 is named, not catalytic. (f) Citrullyl-AMP is compiled, not deposited. (g) Cα gaps 156 and 377 are not this mesh (Cα 4–407). (h) Homotetramer assembly is not this cartoon. (i) Net EC H⁺ is not a gold sphere. (j) Mitochondrial ASS1 is not this page. (k) Overlay/schematic Å are not claims.
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Regulation — cytosol · homotetramer · next ASL
This condensation is cytosolic ASS1 only. Argininosuccinate is the substrate of ASL — not this mesh. Homotetramer is named, not animated. Mitochondrial isoforms are another story.Source: UniProt P00966 · PDB 2NZ2 · Karlberg 2008
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Kinetics scope (no measured timecourse on this page)
One citrulline + aspartate + ATP → argininosuccinate + AMP + PPi event is drawn, not a steady-state run. Compiled BRENDA values for EC 6.3.4.5 are not re-asserted here — no measured kcat/Km on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 6.3.4.5 — no kcat/Km re-asserted
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Sequence
Human ASS1 UniProt P00966 · NCBI Gene 445. This screen uses 2NZ2 numbering (Asp124 compiled; residue 270 = Glu). Chain A. Cα 4–407. Gaps 156 and 377 are not this mesh.
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Simulation map — what you see is what is written
Setup = 2NZ2 pocket empty (opaque, no autoplay). ① crystal CIR moves in. ② schematic ATP moves in. ③ slow-mo: white CIR-O7 → ATP PA; fade to citrullyl-AMP + PPi. ④ crystal ASP moves in. ⑤ slow-mo: blue Asp-N → CAMP C7; fade to argininosuccinate + AMP. ⑥ argininosuccinate and AMP leave opposite ways. Only these events move.
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Sources — bibliography of this page
S1 — PDB 2NZ2: human ASS1 + ASP + CIR, 2.40 Å — public coordinates; measured Glu270 OE2⋯CIR N = 2.54 Å · Tyr87 OH⋯CIR OXT = 2.69 Å · Arg127 NH1⋯CIR OXT = 2.73 Å · Asn123 ND2⋯CIR O = 2.77 Å · Thr119 OG1⋯ASP O = 2.50 Å · Asp124 OD2⋯ASP N = 2.86 Å
S2 — Karlberg et al., Acta Crystallogr. D 2008, PMID:18323623 — human ASS1 + aspartate + citrulline
S3 — Sequence: UniProt P00966 · NCBI Gene 445
S4 — Kinetics: BRENDA EC 6.3.4.5 — no kcat/Km re-asserted on this page
› Backbones and CIR / ASP 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, citrullyl-AMP, AMP, PPi, argininosuccinate, nucleophile flight, product leave), the pose is drawn
schematically and labeled as such in the narration. Occupancy is citrulline + aspartate, not ATP. Occupancy Å are not ATP/ASUC geomClaims. Crystallization Na⁺ is named, not extracted as a screen species.