Adenylyl cyclase - 3D Mechanism Simulator

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References & Databases

START HERE — how to read ATP → 3′,5′-cAMP + PPi on adenylyl cyclase One cyclization cartoon on the crystalline mammalian adenylyl cyclase catalytic core: 1CJK (3.00 Å) = the Gsα·VC1·IIC2 complex with the ATP analog TAT = adenosine-5′-(Rp-α-thio)-triphosphate. This is a CHIMERA: dog ADCY5 C1A (chain A, P30803) + rat ADCY2 C2A (chain B, P26769) + bovine Gsα (chain C, P04896, context). The deposited occupancy is the slowly hydrolyzable Rp-ATPαS analog plus the dual metal site Mg²⁺ (A581) / Mn²⁺ (A582); 1CJK models no cAMP and no PPi, so the cyclic product and the pyrophosphate are [schematic] — but the cAMP ring carries real cyclic-phosphodiester geometry transplanted from the 1.95 Å human soluble adenylyl cyclase product complex 4CLT (cAMP + PPi + Mg); only its pose stays [schematic]. The catalytic 3′-OH sits ~4.5 Å from the α-phosphate at an O3′-PA-O3A angle of ~125° (not in-line) — the cyclization is (proposal, lit.-based), and the general base is not assigned on this frame. Human full-length cyclase nucleotide complexes are not the first mesh; human ADCY9 (9U3P) is a companion with GTP on Gs, not ATP at the cyclase. Measured Å are deposited 1CJK pairs only. Gsα GTPase is not this page.
Crystal structures PDB 1CJK — complex of Gsα with the catalytic domains of mammalian adenylyl cyclase + adenosine-5′-(Rp-α-thio)-triphosphate, 3.00 Å; coordinates are public (the crystal also contains a bound forskolin activator and MES; they are not drawn/used on this page). Chain A = dog ADCY5 C1A (UniProt P30803, observed 377–565); chain B = rat ADCY2 C2A (UniProt P26769, observed 877–1077); chain C = bovine Gsα (UniProt P04896, 39–388, context). EC 4.6.1.1 (adenylate cyclase / ATP pyrophosphate-lyase, cyclizing). The cAMP ring geometry is taken from PDB 4CLT — the 1.95 Å human soluble adenylyl cyclase (ADCY10) product complex (cAMP + PPi + Mg) — superposed onto the 1CJK TAT pose by a ligand-based Kabsch overlay of the common adenine/ribose/O5′ atoms; that pose stays [schematic] because 4CLT is a different enzyme/isoform.
Mechanism — 3′-OH attack on the α-phosphate, cAMP + PPi Adenylyl cyclase converts ATP to the second messenger 3′,5′-cyclic AMP plus PPi. The ribose 3′-OH is the nucleophile that attacks the α-phosphate; the β,γ-diphosphate leaves as PPi. On 1CJK the deposited ligand is the slowly hydrolyzable Rp-ATPαS analog (α-phosphate sulfur), so the ring closure is [schematic] / (proposal, lit.-based) — the drawn cAMP ring itself uses real cyclic-phosphodiester geometry transplanted from 4CLT, so only its pose is schematic. The two metals (Mg²⁺ / Mn²⁺, ligated by Asp396 / Asp440) are the deposited Lewis acids; Arg1029 bidentately contacts the α-phosphate O2A (2.68 Å) and Asn1025 anchors the ribose. Source: PDB 1CJK · UniProt P30803 · BRENDA EC 4.6.1.1
0 — Setup: empty cyclase cleft + dual metals 1CJK holds the ATP analog site with Mg²⁺ (A581) and Mn²⁺ (A582) (Asp396 / Asp440 ligands) and bovine Gsα as named context. The pocket is shown empty so binding can start; 1CJK models no cAMP and no PPi. Opaque, no autoplay. The chemistry below is schematic. Source: PDB 1CJK
① — Rp-ATPαS (ATP analog) binds The crystal nucleotide TAT = Rp-α-thio-ATP docks into the C1/C2 cleft — a slowly hydrolyzable ATP analog (alpha-phosphorothioate), not ATP itself. Measured register: O3′ ⋯ PA = 4.50 Å, Ser1028 OG ⋯ O3′ = 3.27 Å, Arg1029 NH1 ⋯ O2A = 2.68 Å, Mg ⋯ S1G = 2.72 Å.Source: measured 1CJK pairs · PDB 1CJK
② — 3′-OH is deprotonated (general base unassigned) (hypothetical, lit.-based) Gold H⁺ leaves the ribose 3′-OH; the base is not assigned on this frame (the metals and the Arg1029/Ser1028 network position and stabilise, they are not shown as the base). The remaining 3′-O⁻ is the alkoxide nucleophile. Slow-motion on purpose.Source: compiled cyclase chemistry · PDB 1CJK geometry
③ — 3′-O⁻ attacks Pα → 3′,5′-cAMP + PPi (hypothetical, lit.-based) Blue 3′-O⁻ attacks the α-phosphate PA; the intact analog cross-fades in place to schematic 3′,5′-cAMP + PPi. The deposited analog is slowly hydrolyzable and the O3′-PA-O3A angle is ~125° (not in-line), so this is [schematic]. Both metals stay. Slow-motion on purpose.Source: compiled cyclase mechanism · EC 4.6.1.1
④ — PPi leaves [schematic] PPi (β,γ-diphosphate) departs; the new 3′,5′-cAMP stays. Both metals stay. 1CJK holds only the intact analog, so PPi is schematic.Source: EC 4.6.1.1 net accounting
⑤ — cAMP leaves — cyclase idle, Gsα named [schematic] 3′,5′-cAMP — the second messenger — departs; the two metals and the cleft are restored. Gsα (bovine, chain C) is named context on this chimera mesh; its GTPase is not this page. Net: ATP → 3′,5′-cAMP + PPi. Products are [schematic].Source: EC 4.6.1.1 net accounting

How to read this page — a first-pass primer First pass: Setup (empty cleft + Mg/Mn + Gsα named) → ① the ATP analog docks → ② gold H⁺ leaves the 3′-OH → ③ blue 3′-O⁻ attacks Pα, analog → cAMP + PPi → ④ PPi leaves → ⑤ cAMP leaves. Second pass: 2.54 / 1.98 / 2.14 / 2.25 / 2.72 / 2.16 / 2.68 / 3.27 / 4.50 Å are crystal facts on 1CJK atoms; cAMP, PPi and the deprotonation are [schematic]. Third pass: open “Disagreements” for the chimera, the slowly hydrolyzable analog, the unassigned base, and Gsα ≠ cyclase.
Chemistry primer — cyclizing (ATP pyrophosphate-lyase) Adenylyl cyclase is a cyclase, not a hydrolase: the ribose 3′-OH closes a cyclic phosphate onto the α-phosphorus and ejects PPi. Two metal ions (Mg²⁺ / Mn²⁺) hold the phosphates; a conserved Arg (Arg1029) stabilises the α-phosphate. Gold = H⁺ on the 3′-OH; blue = the 3′-O⁻ oxygen nucleophile. Teaching substrate = the ATP analog Rp-ATPαS. This is not a phosphodiesterase (that is PDE4, the reverse direction) and not Gsα's own GTPase.
Words used on screen — occupancy · Rp-ATPαS · chimeric · PPi Occupancy — 1CJK holds the slowly hydrolyzable Rp-ATPαS analog at the cyclase site; it is never relabeled as ATP or as a transition state. Rp-ATPαS — adenosine-5′-(Rp-α-thio)-triphosphate: the α-phosphate carries a sulfur, which blocks hydrolysis. Chimeric — the mesh joins dog C1 with rat C2 and bovine Gsα. PPi — the pyrophosphate leaving group.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 1CJK (3.00 Å) — Mg(A581) ⋯ Asp396 OD1 = 2.54 Å; Mn(A582) ⋯ Asp396 OD2 = 1.98 Å; Mg ⋯ Asp440 OD1 = 2.14 Å; Mn ⋯ Asp440 OD2 = 2.25 Å; Mg ⋯ TAT S1G = 2.72 Å; Mn ⋯ TAT O2B = 2.16 Å; Arg1029 NH1 ⋯ TAT O2A = 2.68 Å; Ser1028 OG ⋯ TAT O3′ = 3.27 Å; TAT O3′ ⋯ PA = 4.50 Å. The inferred layer ([schematic]): the cAMP pose (its 3′,5′-ring geometry is real, transplanted from 4CLT), PPi, the 3′-OH deprotonation, and product release. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. The chimera is disclosed, not hidden.
Disagreements on record (a) Chimera. 1CJK is dog ADCY5 C1 + rat ADCY2 C2 + bovine Gsα — not one human cyclase; human full-length nucleotide complexes are not the first mesh (human ADCY9 / 9U3P has GTP on Gs). (b) slowly hydrolyzable analog. TAT = Rp-ATPαS; the α-phosphate sulfur blocks turnover, so the cyclization is schematic. (c) Geometry is not in-line. O3′ ⋯ PA = 4.50 Å and O3′-PA-O3A ≈ 125° — an attack register, not a transition state. (d) General base unassigned. No residue is drawn as the base; the metals/Arg stabilise only. (e) No cAMP / no PPi modeled in 1CJK — both products are schematic; the cAMP ring geometry is transplanted from 4CLT (a different enzyme/isoform), so only its pose is [schematic]. (f) Gsα is context. Its GTPase is not this reaction; Gsα–GTP is the companion story. (g) No protein-domain swing. (h) Gaps. Chain B has a gap (953–963) and chain C a gap (66–85); only modeled Cα are drawn.
Regulation — Gsα stimulation, G-protein control Adenylyl cyclase is the effector of the G_s pathway: Gsα–GTP binds the C1/C2 interface and stimulates cAMP synthesis (the 1CJK context), while G_i inhibits and other AC isoforms are modulated by Ca²⁺/calmodulin and by PKA feedback. This page shows the catalytic chemistry only — the GTPase cycle that turns Gs off is not drawn.Source: UniProt O60503 (human ADCY9 companion) · PDB 1CJK
Kinetics scope (no measured timecourse on this page) One cyclization event is drawn, not a steady-state run. Compiled BRENDA values for EC 4.6.1.1 are not re-asserted here — no measured k_cat/K_m on this page [schematic] (qualitative only). Pair with a kinetics chapter.Source: BRENDA EC 4.6.1.1 — no k_cat/K_m re-asserted
Sequence Chimera: dog ADCY5 C1A UniProt P30803 · rat ADCY2 C2A UniProt P26769 · bovine Gsα UniProt P04896. Screen uses 1CJK author numbering (chain A 377–565, chain B 877–1077, chain C 39–388). Human ADCY9 companion O60503.
Simulation map — what you see is what is written Setup = empty 1CJK cyclase cleft + Mg/Mn + Gsα named (opaque, no autoplay). ① Rp-ATPαS analog moves in. ② slow-mo: gold H⁺ leaves the 3′-OH. ③ slow-mo: blue 3′-O⁻ attacks Pα; analog fades to cAMP + PPi. ④ PPi leaves. ⑤ cAMP leaves; metals restored. Only these events move.
Sources — bibliography of this page S1 — PDB 1CJK: Gsα·VC1·IIC2 + adenosine-5′-(Rp-α-thio)-triphosphate, 3.00 Å — public coordinates; measured Mg⋯Asp396 OD1 = 2.54 Å · Mn⋯Asp396 OD2 = 1.98 Å · Mg⋯Asp440 OD1 = 2.14 Å · Mn⋯Asp440 OD2 = 2.25 Å · Mg⋯TAT S1G = 2.72 Å · Mn⋯TAT O2B = 2.16 Å · Arg1029 NH1⋯TAT O2A = 2.68 Å · Ser1028 OG⋯TAT O3′ = 3.27 Å · TAT O3′⋯PA = 4.50 Å S2 — Sequence/annotation: UniProt P30803 (dog ADCY5) · P26769 (rat ADCY2) · P04896 (bovine Gsα) · companion O60503 (human ADCY9) S3 — Kinetics: BRENDA EC 4.6.1.1 — no k_cat/K_m re-asserted on this page (qualitative) S4 — PDB 4CLT: human soluble adenylyl cyclase (ADCY10) product complex, cAMP + PPi + Mg, 1.95 Å — the real 3′,5′-cAMP ring transplanted onto the 1CJK pose by a ligand-based Kabsch overlay (RMSD 0.69 Å); the pose stays [schematic] (different enzyme/isoform)

› 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., 3′,5′-cAMP, PPi, the 3′-OH deprotonation, product release), the pose is drawn schematically and labeled as such in the narration.

ADCY5 C1 (dog)ADCY2 C2 (rat)Gsα (bovine)Mg²⁺Mn²⁺PH⁺ (gold)nucleophile (blue)